Starting phenix.real_space_refine on Sat Aug 23 03:10:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srp_40737/08_2025/8srp_40737.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srp_40737/08_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_40737/08_2025/8srp_40737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srp_40737/08_2025/8srp_40737.map" model { file = "/net/cci-nas-00/data/ceres_data/8srp_40737/08_2025/8srp_40737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srp_40737/08_2025/8srp_40737.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 212 5.49 5 S 6 5.16 5 C 5333 2.51 5 N 1760 2.21 5 O 2205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9516 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 664 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "I" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 419 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 4, 'TRANS': 79} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 347 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 5, 'PHE:plan': 7, 'HIS:plan': 5, 'ASN:plan1': 5, 'ARG:plan': 8, 'TRP:plan': 4, 'GLU:plan': 6, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 227 Chain: "N" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1108 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "M" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1103 Classifications: {'DNA': 54} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 53} Chain: "L" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1087 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} Chain: "K" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1083 Classifications: {'DNA': 53} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 52} Chain: "J" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 419 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 4, 'TRANS': 79} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 347 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 5, 'PHE:plan': 7, 'HIS:plan': 5, 'ASN:plan1': 5, 'ARG:plan': 8, 'TRP:plan': 4, 'GLU:plan': 6, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 227 Chain: "H" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 424 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 4, 'TRANS': 80} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 317 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 5, 'PHE:plan': 7, 'HIS:plan': 5, 'ASN:plan1': 5, 'ARG:plan': 8, 'TRP:plan': 4, 'GLU:plan': 7, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 231 Chain: "G" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 419 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 4, 'TRANS': 79} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 347 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 5, 'PHE:plan': 7, 'HIS:plan': 5, 'ASN:plan1': 5, 'ARG:plan': 8, 'TRP:plan': 4, 'GLU:plan': 6, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 227 Chain: "F" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 424 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 4, 'TRANS': 80} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 317 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 5, 'PHE:plan': 7, 'HIS:plan': 5, 'ASN:plan1': 5, 'ARG:plan': 8, 'TRP:plan': 4, 'GLU:plan': 7, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 231 Chain: "E" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 419 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 4, 'TRANS': 79} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 347 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 5, 'PHE:plan': 7, 'HIS:plan': 5, 'ASN:plan1': 5, 'ARG:plan': 8, 'TRP:plan': 4, 'GLU:plan': 6, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 227 Chain: "D" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 628 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 640 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 79} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 679 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 82} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 62 Time building chain proxies: 2.55, per 1000 atoms: 0.27 Number of scatterers: 9516 At special positions: 0 Unit cell: (79.336, 86.932, 181.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 P 212 15.00 O 2205 8.00 N 1760 7.00 C 5333 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 282.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 327 through 334 removed outlier: 3.950A pdb=" N PHE A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 332 " --> pdb=" O MET A 328 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS A 334 " --> pdb=" O TYR A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 327 through 334' Processing helix chain 'A' and resid 341 through 351 Processing helix chain 'A' and resid 359 through 371 removed outlier: 3.568A pdb=" N PHE A 371 " --> pdb=" O PHE A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 392 removed outlier: 4.982A pdb=" N ILE A 385 " --> pdb=" O TRP A 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 329 through 334 Processing helix chain 'I' and resid 341 through 351 Processing helix chain 'I' and resid 359 through 371 Processing helix chain 'I' and resid 379 through 392 removed outlier: 3.696A pdb=" N ALA I 384 " --> pdb=" O THR I 380 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE I 385 " --> pdb=" O TRP I 381 " (cutoff:3.500A) Processing helix chain 'J' and resid 329 through 334 Processing helix chain 'J' and resid 341 through 351 Processing helix chain 'J' and resid 359 through 371 removed outlier: 3.719A pdb=" N HIS J 365 " --> pdb=" O ASN J 361 " (cutoff:3.500A) Processing helix chain 'J' and resid 379 through 392 removed outlier: 3.812A pdb=" N ALA J 384 " --> pdb=" O THR J 380 " (cutoff:3.500A) Processing helix chain 'H' and resid 329 through 334 Processing helix chain 'H' and resid 341 through 350 Processing helix chain 'H' and resid 359 through 371 Processing helix chain 'H' and resid 379 through 392 removed outlier: 3.727A pdb=" N ALA H 384 " --> pdb=" O THR H 380 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE H 385 " --> pdb=" O TRP H 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 351 Processing helix chain 'G' and resid 359 through 371 removed outlier: 3.639A pdb=" N HIS G 365 " --> pdb=" O ASN G 361 " (cutoff:3.500A) Processing helix chain 'G' and resid 379 through 392 removed outlier: 3.807A pdb=" N ALA G 384 " --> pdb=" O THR G 380 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE G 385 " --> pdb=" O TRP G 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 333 Processing helix chain 'F' and resid 341 through 351 removed outlier: 3.607A pdb=" N ARG F 347 " --> pdb=" O ALA F 343 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP F 348 " --> pdb=" O THR F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 371 removed outlier: 3.621A pdb=" N HIS F 365 " --> pdb=" O ASN F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 392 removed outlier: 3.918A pdb=" N ALA F 384 " --> pdb=" O THR F 380 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE F 385 " --> pdb=" O TRP F 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 334 Processing helix chain 'E' and resid 341 through 351 Processing helix chain 'E' and resid 359 through 371 removed outlier: 3.576A pdb=" N PHE E 367 " --> pdb=" O ILE E 363 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR E 368 " --> pdb=" O TYR E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 376 removed outlier: 3.698A pdb=" N ASN E 376 " --> pdb=" O TYR E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 392 removed outlier: 3.943A pdb=" N ALA E 384 " --> pdb=" O THR E 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 334 Processing helix chain 'D' and resid 341 through 351 Processing helix chain 'D' and resid 359 through 371 Processing helix chain 'D' and resid 379 through 392 removed outlier: 3.751A pdb=" N ALA D 384 " --> pdb=" O THR D 380 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE D 385 " --> pdb=" O TRP D 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 333 Processing helix chain 'C' and resid 341 through 351 Processing helix chain 'C' and resid 359 through 371 removed outlier: 3.702A pdb=" N HIS C 365 " --> pdb=" O ASN C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 392 removed outlier: 3.798A pdb=" N ALA C 384 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ILE C 385 " --> pdb=" O TRP C 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 341 through 351 Processing helix chain 'B' and resid 359 through 371 removed outlier: 3.581A pdb=" N PHE B 371 " --> pdb=" O PHE B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 392 removed outlier: 3.964A pdb=" N ALA B 384 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS B 392 " --> pdb=" O ASN B 388 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 395 through 399 Processing sheet with id=AA2, first strand: chain 'I' and resid 396 through 399 Processing sheet with id=AA3, first strand: chain 'J' and resid 396 through 399 Processing sheet with id=AA4, first strand: chain 'H' and resid 396 through 400 removed outlier: 3.542A pdb=" N THR H 407 " --> pdb=" O VAL H 396 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 357 through 358 Processing sheet with id=AA6, first strand: chain 'F' and resid 357 through 359 Processing sheet with id=AA7, first strand: chain 'E' and resid 396 through 400 removed outlier: 3.770A pdb=" N VAL E 396 " --> pdb=" O THR E 407 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 395 through 399 Processing sheet with id=AA9, first strand: chain 'C' and resid 395 through 399 Processing sheet with id=AB1, first strand: chain 'B' and resid 396 through 399 293 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 203 hydrogen bonds 402 hydrogen bond angles 0 basepair planarities 91 basepair parallelities 176 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 1.21 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: 5.550 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.580 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.910 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.29), residues: 829 helix: -1.02 (0.24), residues: 444 sheet: -0.32 (0.44), residues: 122 loop : -0.83 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 358 TYR 0.031 0.002 TYR B 330 PHE 0.014 0.001 PHE A 340 TRP 0.012 0.001 TRP C 348 HIS 0.006 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00403 (10135) covalent geometry : angle 0.65823 (14797) hydrogen bonds : bond 0.19369 ( 496) hydrogen bonds : angle 7.28705 ( 1248) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.254 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 73 average time/residue: 0.0777 time to fit residues: 8.6235 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 : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 340 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.0470 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 30.0000 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.4684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4227 r_free = 0.4227 target = 0.123121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.099354 restraints weight = 34474.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.100329 restraints weight = 26764.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.100653 restraints weight = 20606.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.100840 restraints weight = 15282.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.100975 restraints weight = 14168.204| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10135 Z= 0.220 Angle : 0.631 8.222 14797 Z= 0.379 Chirality : 0.037 0.136 1755 Planarity : 0.005 0.133 1186 Dihedral : 29.508 137.717 3330 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 5.14 % Allowed : 26.17 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.29), residues: 829 helix: -0.32 (0.25), residues: 430 sheet: -0.19 (0.44), residues: 122 loop : -1.13 (0.39), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 369 TYR 0.019 0.002 TYR B 364 PHE 0.014 0.001 PHE A 340 TRP 0.011 0.001 TRP B 366 HIS 0.006 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00479 (10135) covalent geometry : angle 0.63131 (14797) hydrogen bonds : bond 0.05532 ( 496) hydrogen bonds : angle 5.01019 ( 1248) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: D 397 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7852 (ttt-90) outliers start: 11 outliers final: 7 residues processed: 75 average time/residue: 0.0966 time to fit residues: 10.4971 Evaluate side-chains 76 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 363 ILE Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain B residue 336 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 78 optimal weight: 0.0870 chunk 21 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- 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** C 387 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.121996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.099025 restraints weight = 35108.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.099127 restraints weight = 29729.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.100145 restraints weight = 22367.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.100040 restraints weight = 16128.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.100353 restraints weight = 15493.021| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10135 Z= 0.238 Angle : 0.640 9.176 14797 Z= 0.383 Chirality : 0.038 0.189 1755 Planarity : 0.005 0.106 1186 Dihedral : 29.472 139.958 3328 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 6.07 % Allowed : 26.64 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.30), residues: 829 helix: -0.05 (0.26), residues: 430 sheet: -0.41 (0.43), residues: 122 loop : -1.11 (0.40), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 397 TYR 0.025 0.002 TYR A 364 PHE 0.017 0.001 PHE A 340 TRP 0.008 0.001 TRP B 366 HIS 0.007 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00522 (10135) covalent geometry : angle 0.63990 (14797) hydrogen bonds : bond 0.05447 ( 496) hydrogen bonds : angle 4.54458 ( 1248) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: D 397 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7669 (ttt-90) outliers start: 13 outliers final: 10 residues processed: 77 average time/residue: 0.0867 time to fit residues: 9.9828 Evaluate side-chains 77 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 397 ARG Chi-restraints excluded: chain C residue 340 PHE 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 377 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 0.0170 chunk 56 optimal weight: 9.9990 chunk 8 optimal weight: 0.0570 chunk 43 optimal weight: 40.0000 chunk 15 optimal weight: 30.0000 chunk 44 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 40 optimal weight: 40.0000 chunk 53 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 overall best weight: 4.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN D 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.118269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.094125 restraints weight = 35241.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.093818 restraints weight = 32452.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.094607 restraints weight = 26109.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.094741 restraints weight = 18808.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.095251 restraints weight = 17310.311| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2386 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= 0.437 Angle : 0.809 13.437 14797 Z= 0.476 Chirality : 0.047 0.207 1755 Planarity : 0.006 0.090 1186 Dihedral : 29.719 139.613 3328 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 12.15 % Allowed : 22.43 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.28), residues: 829 helix: -0.85 (0.24), residues: 435 sheet: -1.08 (0.41), residues: 122 loop : -1.61 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 375 TYR 0.032 0.004 TYR A 364 PHE 0.019 0.003 PHE A 340 TRP 0.012 0.002 TRP B 366 HIS 0.013 0.002 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00966 (10135) covalent geometry : angle 0.80911 (14797) hydrogen bonds : bond 0.09229 ( 496) hydrogen bonds : angle 5.25047 ( 1248) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.210 Fit side-chains REVERT: A 364 TYR cc_start: 0.8417 (m-80) cc_final: 0.8184 (m-80) REVERT: D 397 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7633 (ttt-90) outliers start: 26 outliers final: 21 residues processed: 81 average time/residue: 0.0725 time to fit residues: 9.1956 Evaluate side-chains 84 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 388 ASN Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 366 TRP Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 377 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 0.0060 chunk 37 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 94 optimal weight: 0.0060 chunk 55 optimal weight: 10.0000 chunk 43 optimal weight: 50.0000 chunk 63 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.3014 ------------------------------------------------------------------------------- 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 = 0.4199 r_free = 0.4199 target = 0.121561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.097745 restraints weight = 33951.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.098358 restraints weight = 24364.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.098967 restraints weight = 19160.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.098926 restraints weight = 14395.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.099114 restraints weight = 12768.443| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.2141 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= 0.206 Angle : 0.641 8.706 14797 Z= 0.384 Chirality : 0.037 0.141 1755 Planarity : 0.005 0.081 1186 Dihedral : 29.602 141.374 3328 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 6.54 % Allowed : 28.04 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.30), residues: 829 helix: -0.19 (0.26), residues: 439 sheet: -1.06 (0.40), residues: 122 loop : -1.07 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 386 TYR 0.017 0.002 TYR B 364 PHE 0.015 0.001 PHE A 340 TRP 0.010 0.001 TRP C 348 HIS 0.006 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00450 (10135) covalent geometry : angle 0.64128 (14797) hydrogen bonds : bond 0.05417 ( 496) hydrogen bonds : angle 4.47824 ( 1248) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.232 Fit side-chains REVERT: D 397 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7379 (ttt-90) outliers start: 14 outliers final: 10 residues processed: 72 average time/residue: 0.0738 time to fit residues: 8.3100 Evaluate side-chains 71 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain 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 363 ILE Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 50.0000 chunk 99 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 30.0000 chunk 67 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.121142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.096938 restraints weight = 34328.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.097517 restraints weight = 25282.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.098213 restraints weight = 19527.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.098152 restraints weight = 14939.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.098333 restraints weight = 13367.347| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2268 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= 0.221 Angle : 0.636 9.124 14797 Z= 0.381 Chirality : 0.037 0.140 1755 Planarity : 0.004 0.072 1186 Dihedral : 29.515 142.057 3328 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.76 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.30), residues: 829 helix: -0.05 (0.26), residues: 439 sheet: -1.15 (0.39), residues: 122 loop : -1.01 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 386 TYR 0.019 0.002 TYR A 364 PHE 0.027 0.001 PHE A 367 TRP 0.011 0.001 TRP B 366 HIS 0.008 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00487 (10135) covalent geometry : angle 0.63588 (14797) hydrogen bonds : bond 0.05527 ( 496) hydrogen bonds : angle 4.28568 ( 1248) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.265 Fit side-chains REVERT: D 397 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7415 (ttt-90) outliers start: 13 outliers final: 12 residues processed: 67 average time/residue: 0.0795 time to fit residues: 8.2880 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 : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 9.9990 chunk 2 optimal weight: 0.5980 chunk 54 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.4202 r_free = 0.4202 target = 0.121847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.098026 restraints weight = 33690.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.098450 restraints weight = 23838.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.099955 restraints weight = 18671.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.099633 restraints weight = 13429.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.099917 restraints weight = 12346.521| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10135 Z= 0.210 Angle : 0.625 9.178 14797 Z= 0.374 Chirality : 0.036 0.142 1755 Planarity : 0.004 0.067 1186 Dihedral : 29.461 143.178 3328 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 5.61 % Allowed : 28.97 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.30), residues: 829 helix: 0.10 (0.26), residues: 439 sheet: -1.17 (0.40), residues: 122 loop : -0.90 (0.43), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 337 TYR 0.023 0.002 TYR B 373 PHE 0.018 0.001 PHE A 367 TRP 0.010 0.001 TRP B 366 HIS 0.006 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00461 (10135) covalent geometry : angle 0.62495 (14797) hydrogen bonds : bond 0.05039 ( 496) hydrogen bonds : angle 4.10798 ( 1248) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.261 Fit side-chains REVERT: D 397 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7196 (ttt-90) outliers start: 12 outliers final: 10 residues processed: 70 average time/residue: 0.0829 time to fit residues: 8.8831 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 : 0.255 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.0270 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 30.0000 chunk 67 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- 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 = 0.4183 r_free = 0.4183 target = 0.120678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.096851 restraints weight = 35420.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.096848 restraints weight = 28961.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.097840 restraints weight = 23082.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.097766 restraints weight = 16616.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.098094 restraints weight = 15324.902| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 10135 Z= 0.259 Angle : 0.649 9.705 14797 Z= 0.387 Chirality : 0.038 0.141 1755 Planarity : 0.004 0.064 1186 Dihedral : 29.467 143.688 3328 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.30), residues: 829 helix: 0.06 (0.26), residues: 439 sheet: -1.30 (0.40), residues: 122 loop : -0.95 (0.43), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 337 TYR 0.019 0.002 TYR B 373 PHE 0.020 0.002 PHE A 367 TRP 0.012 0.001 TRP B 366 HIS 0.007 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00572 (10135) covalent geometry : angle 0.64922 (14797) hydrogen bonds : bond 0.05740 ( 496) hydrogen bonds : angle 4.21779 ( 1248) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.257 Fit side-chains REVERT: D 397 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7524 (ttt-90) outliers start: 15 outliers final: 13 residues processed: 71 average time/residue: 0.0750 time to fit residues: 8.4142 Evaluate side-chains 76 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 10.0000 chunk 1 optimal weight: 0.0020 chunk 0 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.122748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.100561 restraints weight = 35261.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.100727 restraints weight = 30299.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.101392 restraints weight = 23319.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.101525 restraints weight = 16248.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.101915 restraints weight = 15313.116| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.2597 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= 0.165 Angle : 0.603 8.035 14797 Z= 0.360 Chirality : 0.035 0.142 1755 Planarity : 0.004 0.062 1186 Dihedral : 29.394 144.670 3328 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 5.14 % Allowed : 28.97 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.31), residues: 829 helix: 0.33 (0.26), residues: 434 sheet: -1.22 (0.39), residues: 122 loop : -0.78 (0.43), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 337 TYR 0.017 0.002 TYR B 373 PHE 0.016 0.001 PHE A 367 TRP 0.010 0.001 TRP C 348 HIS 0.006 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00359 (10135) covalent geometry : angle 0.60318 (14797) hydrogen bonds : bond 0.04446 ( 496) hydrogen bonds : angle 3.85191 ( 1248) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.252 Fit side-chains REVERT: D 397 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7324 (ttt-90) outliers start: 11 outliers final: 9 residues processed: 70 average time/residue: 0.0777 time to fit residues: 8.5636 Evaluate side-chains 74 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 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 C residue 391 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain B residue 336 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.0070 chunk 12 optimal weight: 40.0000 chunk 95 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 10 optimal weight: 0.0030 chunk 8 optimal weight: 30.0000 chunk 35 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 overall best weight: 2.6014 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.119865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.096208 restraints weight = 35092.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.096579 restraints weight = 26474.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.098197 restraints weight = 18981.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.097861 restraints weight = 13562.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.098044 restraints weight = 12960.986| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 10135 Z= 0.306 Angle : 0.678 12.214 14797 Z= 0.403 Chirality : 0.040 0.136 1755 Planarity : 0.005 0.062 1186 Dihedral : 29.446 144.733 3328 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.30), residues: 829 helix: 0.03 (0.26), residues: 430 sheet: -1.33 (0.40), residues: 122 loop : -0.91 (0.42), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 386 TYR 0.022 0.003 TYR A 364 PHE 0.024 0.002 PHE A 367 TRP 0.022 0.001 TRP B 366 HIS 0.009 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00676 (10135) covalent geometry : angle 0.67836 (14797) hydrogen bonds : bond 0.06471 ( 496) hydrogen bonds : angle 4.25636 ( 1248) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.276 Fit side-chains REVERT: D 397 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7641 (ttt-90) REVERT: B 352 GLU cc_start: 0.4962 (OUTLIER) cc_final: 0.4608 (pp20) outliers start: 12 outliers final: 10 residues processed: 70 average time/residue: 0.0740 time to fit residues: 8.1156 Evaluate side-chains 74 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 80 optimal weight: 0.5980 chunk 52 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 44 optimal weight: 40.0000 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.120819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.097209 restraints weight = 34879.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.097620 restraints weight = 26374.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.098037 restraints weight = 21564.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.098173 restraints weight = 16041.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.098356 restraints weight = 14899.193| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10135 Z= 0.229 Angle : 0.637 9.837 14797 Z= 0.380 Chirality : 0.037 0.137 1755 Planarity : 0.004 0.062 1186 Dihedral : 29.442 145.018 3328 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 6.07 % Allowed : 28.97 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.31), residues: 829 helix: 0.14 (0.26), residues: 430 sheet: -1.31 (0.40), residues: 122 loop : -0.83 (0.43), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 337 TYR 0.022 0.002 TYR B 373 PHE 0.020 0.001 PHE A 367 TRP 0.016 0.001 TRP B 366 HIS 0.008 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00506 (10135) covalent geometry : angle 0.63746 (14797) hydrogen bonds : bond 0.05356 ( 496) hydrogen bonds : angle 4.08097 ( 1248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1513.87 seconds wall clock time: 26 minutes 49.22 seconds (1609.22 seconds total)