Starting phenix.real_space_refine on Mon May 12 21:11:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srp_40737/05_2025/8srp_40737.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srp_40737/05_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_40737/05_2025/8srp_40737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srp_40737/05_2025/8srp_40737.map" model { file = "/net/cci-nas-00/data/ceres_data/8srp_40737/05_2025/8srp_40737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srp_40737/05_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-5687/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: 6.62, per 1000 atoms: 0.70 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: 2.28 Conformation dependent library (CDL) restraints added in 757.5 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: 3.74 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: 2.95 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: 4.160 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.060 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.980 ------------------------------------------------------------------------------- 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= 0.179 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 Details of bonding type rmsd hydrogen bonds : bond 0.19369 ( 496) hydrogen bonds : angle 7.28705 ( 1248) covalent geometry : bond 0.00403 (10135) covalent geometry : angle 0.65823 (14797) *********************** 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 : 0.657 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 73 average time/residue: 0.1613 time to fit residues: 17.9119 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 : 0.664 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.095080 restraints weight = 35672.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.095115 restraints weight = 33896.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.095687 restraints weight = 27569.180| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 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= 0.471 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 Details of bonding type rmsd hydrogen bonds : bond 0.09118 ( 496) hydrogen bonds : angle 5.75485 ( 1248) covalent geometry : bond 0.01040 (10135) covalent geometry : angle 0.82874 (14797) *********************** 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 : 0.664 Fit side-chains revert: symmetry clash REVERT: D 397 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7693 (ttt-90) outliers start: 16 outliers final: 14 residues processed: 73 average time/residue: 0.1645 time to fit residues: 18.2480 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 : 0.666 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.120557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.095995 restraints weight = 35947.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.096122 restraints weight = 30553.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.097064 restraints weight = 23352.058| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 10135 Z= 0.312 Angle : 0.700 10.427 14797 Z= 0.414 Chirality : 0.041 0.163 1755 Planarity : 0.005 0.113 1186 Dihedral : 29.666 139.844 3328 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % 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 : 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: -1.35 (0.29), residues: 829 helix: -0.46 (0.25), residues: 426 sheet: -0.84 (0.42), residues: 122 loop : -1.35 (0.39), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 348 HIS 0.009 0.001 HIS B 387 PHE 0.014 0.002 PHE A 340 TYR 0.019 0.002 TYR A 373 ARG 0.006 0.001 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.06247 ( 496) hydrogen bonds : angle 4.98542 ( 1248) covalent geometry : bond 0.00689 (10135) covalent geometry : angle 0.69988 (14797) *********************** 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 80 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.691 Fit side-chains REVERT: D 397 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7798 (ttt-90) outliers start: 17 outliers final: 14 residues processed: 74 average time/residue: 0.1788 time to fit residues: 19.9120 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 : 0.664 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 53 optimal weight: 6.9990 chunk 41 optimal weight: 0.0040 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 0.0270 chunk 15 optimal weight: 20.0000 chunk 82 optimal weight: 0.5980 chunk 54 optimal weight: 20.0000 chunk 51 optimal weight: 30.0000 chunk 16 optimal weight: 10.0000 overall best weight: 0.7254 ------------------------------------------------------------------------------- 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 = 0.4226 r_free = 0.4226 target = 0.123208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.099793 restraints weight = 33521.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.100263 restraints weight = 22521.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.101724 restraints weight = 17782.660| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10135 Z= 0.170 Angle : 0.612 7.835 14797 Z= 0.368 Chirality : 0.036 0.143 1755 Planarity : 0.004 0.083 1186 Dihedral : 29.545 141.001 3328 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 5.61 % Allowed : 29.44 % 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: -0.76 (0.30), residues: 829 helix: 0.05 (0.26), residues: 433 sheet: -0.80 (0.40), residues: 122 loop : -1.03 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 348 HIS 0.006 0.001 HIS A 387 PHE 0.019 0.001 PHE B 340 TYR 0.022 0.002 TYR B 364 ARG 0.005 0.001 ARG B 356 Details of bonding type rmsd hydrogen bonds : bond 0.04705 ( 496) hydrogen bonds : angle 4.24492 ( 1248) covalent geometry : bond 0.00367 (10135) covalent geometry : angle 0.61219 (14797) *********************** 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 82 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 383 ASN cc_start: 0.8383 (t0) cc_final: 0.8124 (t0) REVERT: D 397 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7237 (ttt-90) outliers start: 12 outliers final: 7 residues processed: 76 average time/residue: 0.1737 time to fit residues: 19.6826 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 : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 340 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 53 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 30.0000 chunk 70 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** D 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.119553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.095287 restraints weight = 34512.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.095833 restraints weight = 27418.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.097486 restraints weight = 18784.645| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 10135 Z= 0.355 Angle : 0.722 11.203 14797 Z= 0.426 Chirality : 0.042 0.156 1755 Planarity : 0.005 0.077 1186 Dihedral : 29.583 140.908 3328 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 8.41 % Allowed : 25.70 % 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: -1.18 (0.29), residues: 829 helix: -0.29 (0.25), residues: 439 sheet: -1.06 (0.40), residues: 122 loop : -1.21 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 366 HIS 0.011 0.002 HIS B 387 PHE 0.016 0.002 PHE D 395 TYR 0.026 0.003 TYR A 364 ARG 0.008 0.001 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.06974 ( 496) hydrogen bonds : angle 4.66518 ( 1248) covalent geometry : bond 0.00790 (10135) covalent geometry : angle 0.72238 (14797) *********************** 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 : 0.747 Fit side-chains REVERT: D 397 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7744 (ttt-90) outliers start: 18 outliers final: 15 residues processed: 71 average time/residue: 0.1470 time to fit residues: 16.4816 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 : 0.643 ------------------------------------------------------------------------------- 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 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 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 352 GLU Chi-restraints excluded: chain B residue 377 HIS 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: 1.9990 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 47 optimal weight: 30.0000 chunk 92 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 40.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.4199 r_free = 0.4199 target = 0.121545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.097549 restraints weight = 33704.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.098076 restraints weight = 23393.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.098879 restraints weight = 17681.826| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10135 Z= 0.216 Angle : 0.640 9.486 14797 Z= 0.381 Chirality : 0.037 0.140 1755 Planarity : 0.004 0.071 1186 Dihedral : 29.543 142.055 3328 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 7.01 % Allowed : 26.64 % Favored : 66.36 % 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: -0.85 (0.30), residues: 829 helix: 0.02 (0.26), residues: 439 sheet: -1.14 (0.40), residues: 122 loop : -1.00 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 348 HIS 0.008 0.001 HIS B 387 PHE 0.014 0.001 PHE B 340 TYR 0.017 0.002 TYR A 364 ARG 0.004 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.05240 ( 496) hydrogen bonds : angle 4.27761 ( 1248) covalent geometry : bond 0.00477 (10135) covalent geometry : angle 0.63981 (14797) *********************** 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 80 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.721 Fit side-chains REVERT: D 397 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7416 (ttt-90) outliers start: 15 outliers final: 13 residues processed: 73 average time/residue: 0.1657 time to fit residues: 18.4434 Evaluate side-chains 77 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 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 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 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: 0.0770 chunk 67 optimal weight: 10.0000 chunk 90 optimal weight: 0.0980 chunk 93 optimal weight: 0.6980 chunk 39 optimal weight: 40.0000 chunk 31 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 chunk 46 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- 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 = 0.4228 r_free = 0.4228 target = 0.123567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.099999 restraints weight = 33510.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.100935 restraints weight = 22525.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.102168 restraints weight = 15310.003| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10135 Z= 0.154 Angle : 0.607 7.822 14797 Z= 0.362 Chirality : 0.035 0.162 1755 Planarity : 0.004 0.066 1186 Dihedral : 29.473 143.144 3328 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.67 % Allowed : 28.97 % Favored : 66.36 % 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: -0.60 (0.30), residues: 829 helix: 0.26 (0.26), residues: 439 sheet: -1.13 (0.40), residues: 122 loop : -0.93 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 348 HIS 0.007 0.001 HIS A 387 PHE 0.027 0.002 PHE A 367 TYR 0.018 0.001 TYR B 364 ARG 0.006 0.001 ARG A 386 Details of bonding type rmsd hydrogen bonds : bond 0.04446 ( 496) hydrogen bonds : angle 3.95991 ( 1248) covalent geometry : bond 0.00333 (10135) covalent geometry : angle 0.60658 (14797) *********************** 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 79 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: D 397 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7321 (ttt-90) outliers start: 10 outliers final: 8 residues processed: 74 average time/residue: 0.1645 time to fit residues: 18.5246 Evaluate side-chains 76 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 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 340 PHE Chi-restraints excluded: chain C residue 390 SER 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: 0.7980 chunk 91 optimal weight: 0.0770 chunk 44 optimal weight: 30.0000 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 0.0170 chunk 98 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 14 optimal weight: 0.0020 chunk 1 optimal weight: 0.0030 overall best weight: 0.1794 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.124862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.102707 restraints weight = 34502.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.102805 restraints weight = 28684.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.103754 restraints weight = 20926.923| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.2409 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= 0.148 Angle : 0.592 9.035 14797 Z= 0.353 Chirality : 0.034 0.146 1755 Planarity : 0.004 0.060 1186 Dihedral : 29.350 144.397 3328 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.21 % Allowed : 30.37 % 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 (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: -0.40 (0.30), residues: 829 helix: 0.45 (0.26), residues: 439 sheet: -1.05 (0.41), residues: 122 loop : -0.88 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 348 HIS 0.005 0.001 HIS A 387 PHE 0.015 0.001 PHE A 367 TYR 0.020 0.001 TYR A 364 ARG 0.006 0.001 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 496) hydrogen bonds : angle 3.65622 ( 1248) covalent geometry : bond 0.00319 (10135) covalent geometry : angle 0.59192 (14797) *********************** 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 80 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: D 397 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7284 (ttt-90) REVERT: C 373 TYR cc_start: 0.6745 (t80) cc_final: 0.6475 (t80) outliers start: 9 outliers final: 6 residues processed: 75 average time/residue: 0.1897 time to fit residues: 20.8321 Evaluate side-chains 72 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 366 TRP Chi-restraints excluded: chain C residue 391 LEU 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: 0.7980 chunk 26 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 47 optimal weight: 40.0000 chunk 38 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.119865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.096323 restraints weight = 35521.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.096072 restraints weight = 28543.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.096846 restraints weight = 22862.107| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 10135 Z= 0.340 Angle : 0.698 11.828 14797 Z= 0.412 Chirality : 0.041 0.153 1755 Planarity : 0.005 0.065 1186 Dihedral : 29.429 144.204 3328 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 6.07 % Allowed : 28.04 % 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: -0.80 (0.30), residues: 829 helix: 0.09 (0.26), residues: 435 sheet: -1.26 (0.40), residues: 122 loop : -0.94 (0.42), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 366 HIS 0.009 0.001 HIS B 387 PHE 0.021 0.002 PHE A 367 TYR 0.032 0.003 TYR B 373 ARG 0.007 0.001 ARG D 386 Details of bonding type rmsd hydrogen bonds : bond 0.06576 ( 496) hydrogen bonds : angle 4.23952 ( 1248) covalent geometry : bond 0.00753 (10135) covalent geometry : angle 0.69775 (14797) *********************** 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 74 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.682 Fit side-chains REVERT: A 383 ASN cc_start: 0.8314 (t0) cc_final: 0.7984 (t0) REVERT: D 397 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7721 (ttt-90) outliers start: 13 outliers final: 11 residues processed: 69 average time/residue: 0.1459 time to fit residues: 15.8388 Evaluate side-chains 73 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 366 TRP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain B residue 377 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 88 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 44 optimal weight: 40.0000 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.4191 r_free = 0.4191 target = 0.121172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.097780 restraints weight = 35609.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.097982 restraints weight = 26518.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.099364 restraints weight = 19141.917| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10135 Z= 0.231 Angle : 0.637 9.717 14797 Z= 0.378 Chirality : 0.037 0.143 1755 Planarity : 0.004 0.061 1186 Dihedral : 29.417 144.584 3328 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 4.21 % Allowed : 31.31 % 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: -0.67 (0.30), residues: 829 helix: 0.19 (0.26), residues: 430 sheet: -1.26 (0.40), residues: 122 loop : -0.82 (0.42), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 366 HIS 0.007 0.001 HIS B 387 PHE 0.022 0.001 PHE A 367 TYR 0.034 0.002 TYR B 373 ARG 0.002 0.000 ARG C 397 Details of bonding type rmsd hydrogen bonds : bond 0.05095 ( 496) hydrogen bonds : angle 4.02279 ( 1248) covalent geometry : bond 0.00512 (10135) covalent geometry : angle 0.63735 (14797) ********************** 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 73 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.720 Fit side-chains REVERT: A 383 ASN cc_start: 0.8341 (t0) cc_final: 0.7997 (t0) REVERT: D 397 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7289 (ttt-90) outliers start: 9 outliers final: 7 residues processed: 69 average time/residue: 0.1529 time to fit residues: 16.7010 Evaluate side-chains 72 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 340 PHE Chi-restraints excluded: chain C residue 391 LEU 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: 10.0000 chunk 87 optimal weight: 0.5980 chunk 85 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4226 r_free = 0.4226 target = 0.123360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.100230 restraints weight = 34038.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.100655 restraints weight = 23760.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.101223 restraints weight = 19171.268| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2756 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= 0.162 Angle : 0.601 8.264 14797 Z= 0.357 Chirality : 0.035 0.142 1755 Planarity : 0.004 0.063 1186 Dihedral : 29.336 145.599 3328 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.27 % Allowed : 31.78 % 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: -0.43 (0.31), residues: 829 helix: 0.39 (0.27), residues: 430 sheet: -1.18 (0.41), residues: 122 loop : -0.72 (0.42), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 366 HIS 0.006 0.001 HIS A 387 PHE 0.016 0.001 PHE A 367 TYR 0.028 0.002 TYR B 373 ARG 0.003 0.001 ARG B 356 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 496) hydrogen bonds : angle 3.72160 ( 1248) covalent geometry : bond 0.00351 (10135) covalent geometry : angle 0.60067 (14797) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2543.55 seconds wall clock time: 45 minutes 15.11 seconds (2715.11 seconds total)