Starting phenix.real_space_refine on Wed Feb 14 14:41:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8srp_40737/02_2024/8srp_40737.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8srp_40737/02_2024/8srp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8srp_40737/02_2024/8srp_40737.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8srp_40737/02_2024/8srp_40737.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8srp_40737/02_2024/8srp_40737.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8srp_40737/02_2024/8srp_40737.pdb" } 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 Residue "A GLU 362": "OE1" <-> "OE2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "B GLU 399": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.54, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.31 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 4.56 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: 3.05 Time building geometry restraints manager: 5.60 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: 95.83 - 103.46: 469 103.46 - 111.09: 5160 111.09 - 118.72: 3253 118.72 - 126.35: 5131 126.35 - 133.98: 784 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 2.520 nonbonded pdb=" NH2 ARG A 397 " pdb=" OP1 DT K 18 " model vdw 2.421 2.520 nonbonded pdb=" N GLU B 399 " pdb=" OE1 GLU B 399 " model vdw 2.422 2.520 nonbonded pdb=" O5' DG M 27 " pdb=" NH2 ARG B 397 " model vdw 2.448 2.520 nonbonded pdb=" O THR A 368 " pdb=" NE ARG A 375 " model vdw 2.466 2.520 ... (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 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: 4.530 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: 13.680 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 32.730 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 10135 Z= 0.229 Angle : 0.658 16.173 14797 Z= 0.395 Chirality : 0.035 0.129 1755 Planarity : 0.007 0.201 1186 Dihedral : 28.750 137.356 3799 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.47 % Allowed : 29.91 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.29), residues: 829 helix: -1.02 (0.24), residues: 444 sheet: -0.32 (0.44), residues: 122 loop : -0.83 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 348 HIS 0.006 0.001 HIS A 387 PHE 0.014 0.001 PHE A 340 TYR 0.031 0.002 TYR B 330 ARG 0.007 0.001 ARG C 358 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.742 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 73 average time/residue: 0.1728 time to fit residues: 19.1490 Evaluate side-chains 70 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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: 8.9990 chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 51 optimal weight: 30.0000 chunk 40 optimal weight: 50.0000 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: 0.3980 overall best weight: 4.2586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1597 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= 0.583 Angle : 0.808 13.293 14797 Z= 0.474 Chirality : 0.048 0.198 1755 Planarity : 0.006 0.136 1186 Dihedral : 29.708 136.764 3330 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.25 % Favored : 89.63 % Rotamer: Outliers : 7.94 % Allowed : 25.70 % Favored : 66.36 % 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: -1.80 (0.28), residues: 829 helix: -1.01 (0.24), residues: 426 sheet: -0.52 (0.43), residues: 122 loop : -1.51 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 366 HIS 0.013 0.002 HIS B 387 PHE 0.021 0.002 PHE B 367 TYR 0.023 0.003 TYR D 364 ARG 0.006 0.001 ARG B 356 *********************** 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 77 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 60 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: D 397 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7708 (ttt-90) outliers start: 17 outliers final: 15 residues processed: 71 average time/residue: 0.1655 time to fit residues: 18.2407 Evaluate side-chains 73 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 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 50 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 61 optimal weight: 0.0770 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10135 Z= 0.216 Angle : 0.625 8.178 14797 Z= 0.374 Chirality : 0.036 0.134 1755 Planarity : 0.005 0.107 1186 Dihedral : 29.570 139.855 3328 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 5.14 % Allowed : 29.44 % 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 (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: -0.83 (0.30), residues: 829 helix: -0.08 (0.26), residues: 426 sheet: -0.46 (0.42), residues: 122 loop : -1.11 (0.40), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 348 HIS 0.006 0.001 HIS A 387 PHE 0.016 0.001 PHE B 340 TYR 0.020 0.002 TYR B 364 ARG 0.007 0.001 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.729 Fit side-chains REVERT: D 397 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7579 (ttt-90) outliers start: 11 outliers final: 7 residues processed: 73 average time/residue: 0.1778 time to fit residues: 19.3717 Evaluate side-chains 72 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 LEU 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 68 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 30.0000 chunk 43 optimal weight: 5.9990 chunk 61 optimal weight: 0.1980 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10135 Z= 0.210 Angle : 0.604 8.102 14797 Z= 0.363 Chirality : 0.036 0.173 1755 Planarity : 0.004 0.084 1186 Dihedral : 29.422 140.748 3328 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 6.07 % Allowed : 27.57 % 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: -0.54 (0.30), residues: 829 helix: 0.22 (0.26), residues: 434 sheet: -0.60 (0.41), residues: 122 loop : -0.96 (0.41), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 348 HIS 0.007 0.001 HIS A 387 PHE 0.017 0.001 PHE A 340 TYR 0.025 0.002 TYR A 364 ARG 0.008 0.001 ARG A 337 *********************** 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 81 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.778 Fit side-chains REVERT: D 397 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7257 (ttt-90) outliers start: 13 outliers final: 10 residues processed: 73 average time/residue: 0.2047 time to fit residues: 21.9166 Evaluate side-chains 76 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 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 B residue 336 MET 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 1 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 40.0000 chunk 82 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 86 optimal weight: 0.0470 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.1756 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= 0.254 Angle : 0.621 9.256 14797 Z= 0.371 Chirality : 0.036 0.198 1755 Planarity : 0.004 0.075 1186 Dihedral : 29.417 141.191 3328 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % 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 : 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: -0.54 (0.30), residues: 829 helix: 0.26 (0.26), residues: 436 sheet: -0.71 (0.40), residues: 122 loop : -0.98 (0.41), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 366 HIS 0.007 0.001 HIS B 387 PHE 0.016 0.001 PHE A 340 TYR 0.018 0.002 TYR A 364 ARG 0.008 0.001 ARG A 337 *********************** 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 76 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.663 Fit side-chains REVERT: D 397 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7448 (ttt-90) outliers start: 13 outliers final: 11 residues processed: 70 average time/residue: 0.1480 time to fit residues: 16.2636 Evaluate side-chains 75 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 335 ASN Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 366 TRP Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 20.0000 chunk 8 optimal weight: 40.0000 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 93 optimal weight: 0.7980 chunk 10 optimal weight: 0.0030 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 388 ASN ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.1960 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= 0.243 Angle : 0.609 8.483 14797 Z= 0.365 Chirality : 0.036 0.215 1755 Planarity : 0.004 0.069 1186 Dihedral : 29.390 142.084 3328 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 7.94 % Allowed : 24.77 % Favored : 67.29 % 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: -0.49 (0.30), residues: 829 helix: 0.33 (0.27), residues: 434 sheet: -0.78 (0.41), residues: 122 loop : -0.97 (0.41), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 366 HIS 0.007 0.001 HIS B 387 PHE 0.021 0.001 PHE A 367 TYR 0.020 0.002 TYR A 364 ARG 0.005 0.000 ARG A 386 *********************** 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 81 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 64 time to evaluate : 0.819 Fit side-chains REVERT: D 397 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7216 (ttt-90) outliers start: 17 outliers final: 13 residues processed: 73 average time/residue: 0.1644 time to fit residues: 18.3470 Evaluate side-chains 77 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 366 TRP Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 44 optimal weight: 30.0000 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 10135 Z= 0.445 Angle : 0.711 10.926 14797 Z= 0.421 Chirality : 0.042 0.219 1755 Planarity : 0.005 0.067 1186 Dihedral : 29.515 142.455 3328 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 6.54 % Allowed : 24.77 % Favored : 68.69 % 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: -0.95 (0.30), residues: 829 helix: -0.06 (0.25), residues: 439 sheet: -1.02 (0.41), residues: 122 loop : -1.17 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 366 HIS 0.010 0.001 HIS B 387 PHE 0.018 0.002 PHE A 367 TYR 0.021 0.003 TYR A 364 ARG 0.008 0.001 ARG B 356 *********************** 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 74 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.816 Fit side-chains REVERT: D 397 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7757 (ttt-90) outliers start: 14 outliers final: 12 residues processed: 68 average time/residue: 0.1587 time to fit residues: 17.0133 Evaluate side-chains 73 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 366 TRP Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 30.0000 chunk 8 optimal weight: 40.0000 chunk 75 optimal weight: 7.9990 chunk 87 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10135 Z= 0.251 Angle : 0.628 8.566 14797 Z= 0.376 Chirality : 0.037 0.234 1755 Planarity : 0.004 0.064 1186 Dihedral : 29.473 143.205 3328 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 7.01 % Allowed : 25.70 % Favored : 67.29 % 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: -0.68 (0.30), residues: 829 helix: 0.18 (0.26), residues: 439 sheet: -1.05 (0.41), residues: 122 loop : -0.96 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 348 HIS 0.006 0.001 HIS B 387 PHE 0.017 0.001 PHE A 367 TYR 0.018 0.002 TYR A 364 ARG 0.005 0.000 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.743 Fit side-chains REVERT: D 397 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7322 (ttt-90) outliers start: 15 outliers final: 14 residues processed: 71 average time/residue: 0.1575 time to fit residues: 17.6372 Evaluate side-chains 76 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 341 THR Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 366 TRP Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 0.0270 chunk 39 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 overall best weight: 0.9042 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.2436 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= 0.211 Angle : 0.604 7.723 14797 Z= 0.361 Chirality : 0.036 0.249 1755 Planarity : 0.004 0.063 1186 Dihedral : 29.384 144.347 3328 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % 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 : 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: 0.40 (0.26), residues: 439 sheet: -1.05 (0.40), residues: 122 loop : -0.83 (0.43), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 348 HIS 0.005 0.001 HIS A 387 PHE 0.017 0.001 PHE C 340 TYR 0.019 0.002 TYR B 373 ARG 0.008 0.001 ARG A 337 *********************** 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 79 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.787 Fit side-chains REVERT: D 397 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7266 (ttt-90) REVERT: B 352 GLU cc_start: 0.4476 (OUTLIER) cc_final: 0.4252 (pt0) outliers start: 13 outliers final: 11 residues processed: 72 average time/residue: 0.1659 time to fit residues: 18.2768 Evaluate side-chains 76 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 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 B residue 352 GLU Chi-restraints excluded: chain B residue 398 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 0.0870 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 8 optimal weight: 40.0000 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 40.0000 chunk 63 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2555 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= 0.201 Angle : 0.595 7.522 14797 Z= 0.356 Chirality : 0.035 0.261 1755 Planarity : 0.004 0.059 1186 Dihedral : 29.314 145.113 3328 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 6.07 % Allowed : 26.17 % Favored : 67.76 % 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: -0.37 (0.31), residues: 829 helix: 0.44 (0.27), residues: 430 sheet: -1.00 (0.41), residues: 122 loop : -0.76 (0.41), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 366 HIS 0.006 0.001 HIS A 387 PHE 0.016 0.001 PHE C 340 TYR 0.024 0.002 TYR B 373 ARG 0.006 0.000 ARG A 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.811 Fit side-chains REVERT: D 397 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7290 (ttt-90) outliers start: 13 outliers final: 10 residues processed: 70 average time/residue: 0.1719 time to fit residues: 18.4405 Evaluate side-chains 75 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 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 B residue 352 GLU Chi-restraints excluded: chain B residue 398 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 69 optimal weight: 0.0980 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.121503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.097652 restraints weight = 33918.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.097975 restraints weight = 23705.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.099832 restraints weight = 16843.616| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10135 Z= 0.294 Angle : 0.627 8.730 14797 Z= 0.375 Chirality : 0.037 0.253 1755 Planarity : 0.004 0.063 1186 Dihedral : 29.340 145.204 3328 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 6.07 % Allowed : 25.23 % Favored : 68.69 % 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: -0.49 (0.30), residues: 829 helix: 0.33 (0.26), residues: 430 sheet: -1.06 (0.41), residues: 122 loop : -0.81 (0.42), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 366 HIS 0.007 0.001 HIS B 387 PHE 0.017 0.002 PHE C 340 TYR 0.032 0.003 TYR B 373 ARG 0.004 0.000 ARG A 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1604.37 seconds wall clock time: 29 minutes 53.98 seconds (1793.98 seconds total)