Starting phenix.real_space_refine on Sun Mar 10 18:55:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sro_40736/03_2024/8sro_40736.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sro_40736/03_2024/8sro_40736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sro_40736/03_2024/8sro_40736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sro_40736/03_2024/8sro_40736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sro_40736/03_2024/8sro_40736.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sro_40736/03_2024/8sro_40736.pdb" } resolution = 3.3 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= 0.070 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 72 5.49 5 S 9 5.16 5 C 2447 2.51 5 N 748 2.21 5 O 856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "B TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B GLU 399": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4132 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 682 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 82} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "D" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 626 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 80} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 86 Chain: "B" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 695 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 82} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 653 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 74 Chain: "J" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "I" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 368 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "F" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "E" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 368 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Time building chain proxies: 2.81, per 1000 atoms: 0.68 Number of scatterers: 4132 At special positions: 0 Unit cell: (59.08, 88.62, 81.868, 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 9 16.00 P 72 15.00 O 856 8.00 N 748 7.00 C 2447 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: 2.06 Conformation dependent library (CDL) restraints added in 512.6 milliseconds 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 682 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 4 sheets defined 50.7% alpha, 9.0% beta 29 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 327 through 333 removed outlier: 3.876A pdb=" N PHE A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 351 Processing helix chain 'A' and resid 359 through 371 Processing helix chain 'A' and resid 379 through 392 removed outlier: 3.616A pdb=" N ALA A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE A 385 " --> pdb=" O TRP A 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 341 through 351 Processing helix chain 'D' and resid 359 through 371 removed outlier: 3.599A pdb=" N HIS D 365 " --> pdb=" O ASN D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 392 removed outlier: 3.650A pdb=" N ALA D 384 " --> pdb=" O THR D 380 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ILE D 385 " --> pdb=" O TRP D 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 333 removed outlier: 3.996A pdb=" N LYS B 332 " --> pdb=" O MET B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 351 Processing helix chain 'B' and resid 360 through 371 removed outlier: 3.793A pdb=" N HIS B 365 " --> pdb=" O ASN B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 392 removed outlier: 4.151A pdb=" N ALA B 384 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 333 removed outlier: 3.538A pdb=" N LYS C 332 " --> pdb=" O ASP C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 351 Processing helix chain 'C' and resid 359 through 371 removed outlier: 3.874A pdb=" N HIS C 365 " --> pdb=" O ASN C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 392 removed outlier: 3.549A pdb=" N ALA C 384 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE C 385 " --> pdb=" O TRP C 381 " (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 'D' and resid 395 through 399 Processing sheet with id=AA3, first strand: chain 'B' and resid 358 through 359 removed outlier: 3.538A pdb=" N THR B 407 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 395 through 399 115 hydrogen bonds defined for protein. 336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 891 1.33 - 1.45: 1384 1.45 - 1.57: 1974 1.57 - 1.69: 140 1.69 - 1.81: 14 Bond restraints: 4403 Sorted by residual: bond pdb=" N ARG B 356 " pdb=" CA ARG B 356 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.49e-02 4.50e+03 4.48e+00 bond pdb=" N PHE A 411 " pdb=" CA PHE A 411 " ideal model delta sigma weight residual 1.456 1.476 -0.020 1.28e-02 6.10e+03 2.39e+00 bond pdb=" N GLU A 412 " pdb=" CA GLU A 412 " ideal model delta sigma weight residual 1.458 1.479 -0.021 1.90e-02 2.77e+03 1.19e+00 bond pdb=" C GLU B 355 " pdb=" N ARG B 356 " ideal model delta sigma weight residual 1.333 1.346 -0.013 1.39e-02 5.18e+03 8.87e-01 bond pdb=" CA ASP D 409 " pdb=" C ASP D 409 " ideal model delta sigma weight residual 1.529 1.519 0.010 1.04e-02 9.25e+03 8.63e-01 ... (remaining 4398 not shown) Histogram of bond angle deviations from ideal: 97.80 - 105.04: 314 105.04 - 112.29: 2366 112.29 - 119.53: 1339 119.53 - 126.77: 1983 126.77 - 134.02: 306 Bond angle restraints: 6308 Sorted by residual: angle pdb=" N ASP A 409 " pdb=" CA ASP A 409 " pdb=" C ASP A 409 " ideal model delta sigma weight residual 114.56 111.16 3.40 1.27e+00 6.20e-01 7.18e+00 angle pdb=" C3' DC F 20 " pdb=" C2' DC F 20 " pdb=" C1' DC F 20 " ideal model delta sigma weight residual 101.60 97.80 3.80 1.50e+00 4.44e-01 6.43e+00 angle pdb=" N VAL D 408 " pdb=" CA VAL D 408 " pdb=" C VAL D 408 " ideal model delta sigma weight residual 106.53 110.02 -3.49 1.41e+00 5.03e-01 6.13e+00 angle pdb=" N ALA C 353 " pdb=" CA ALA C 353 " pdb=" C ALA C 353 " ideal model delta sigma weight residual 109.81 115.07 -5.26 2.21e+00 2.05e-01 5.67e+00 angle pdb=" N ALA D 353 " pdb=" CA ALA D 353 " pdb=" C ALA D 353 " ideal model delta sigma weight residual 109.81 115.02 -5.21 2.21e+00 2.05e-01 5.55e+00 ... (remaining 6303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 1600 17.58 - 35.16: 425 35.16 - 52.73: 268 52.73 - 70.31: 84 70.31 - 87.89: 3 Dihedral angle restraints: 2380 sinusoidal: 1341 harmonic: 1039 Sorted by residual: dihedral pdb=" CD ARG B 356 " pdb=" NE ARG B 356 " pdb=" CZ ARG B 356 " pdb=" NH1 ARG B 356 " ideal model delta sinusoidal sigma weight residual 0.00 -85.30 85.30 1 1.00e+01 1.00e-02 8.81e+01 dihedral pdb=" CG ARG B 356 " pdb=" CD ARG B 356 " pdb=" NE ARG B 356 " pdb=" CZ ARG B 356 " ideal model delta sinusoidal sigma weight residual -90.00 -2.11 -87.89 2 1.50e+01 4.44e-03 2.13e+01 dihedral pdb=" CA PRO B 354 " pdb=" C PRO B 354 " pdb=" N GLU B 355 " pdb=" CA GLU B 355 " ideal model delta harmonic sigma weight residual -180.00 -163.58 -16.42 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 2377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 558 0.042 - 0.083: 113 0.083 - 0.125: 18 0.125 - 0.166: 1 0.166 - 0.208: 1 Chirality restraints: 691 Sorted by residual: chirality pdb=" CA GLU A 412 " pdb=" N GLU A 412 " pdb=" C GLU A 412 " pdb=" CB GLU A 412 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C1' DC F 20 " pdb=" O4' DC F 20 " pdb=" C2' DC F 20 " pdb=" N1 DC F 20 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CA VAL A 408 " pdb=" N VAL A 408 " pdb=" C VAL A 408 " pdb=" CB VAL A 408 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 688 not shown) Planarity restraints: 551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 356 " 1.099 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG B 356 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B 356 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 356 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 356 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 410 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.60e+00 pdb=" C GLU A 410 " -0.022 2.00e-02 2.50e+03 pdb=" O GLU A 410 " 0.008 2.00e-02 2.50e+03 pdb=" N PHE A 411 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC F 20 " 0.014 2.00e-02 2.50e+03 7.79e-03 1.36e+00 pdb=" N1 DC F 20 " -0.017 2.00e-02 2.50e+03 pdb=" C2 DC F 20 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DC F 20 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DC F 20 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC F 20 " 0.002 2.00e-02 2.50e+03 pdb=" N4 DC F 20 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DC F 20 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DC F 20 " -0.001 2.00e-02 2.50e+03 ... (remaining 548 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 1530 2.91 - 3.41: 3812 3.41 - 3.90: 7566 3.90 - 4.40: 8473 4.40 - 4.90: 12239 Nonbonded interactions: 33620 Sorted by model distance: nonbonded pdb=" O ALA C 384 " pdb=" ND2 ASN C 388 " model vdw 2.409 2.520 nonbonded pdb=" OD1 ASN B 383 " pdb=" NH2 ARG B 386 " model vdw 2.415 2.520 nonbonded pdb=" O VAL B 408 " pdb=" CG1 VAL B 408 " model vdw 2.519 3.460 nonbonded pdb=" NH2 ARG B 397 " pdb=" O5' DG E 27 " model vdw 2.520 2.520 nonbonded pdb=" O TYR A 373 " pdb=" N ARG A 375 " model vdw 2.527 2.520 ... (remaining 33615 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 328 through 330 and (name N or name CA or name C or name \ O or name CB )) or resid 331 or (resid 332 through 334 and (name N or name CA or \ name C or name O or name CB )) or resid 335 or (resid 336 and (name N or name C \ A or name C or name O or name CB )) or resid 337 through 339 or (resid 340 and ( \ name N or name CA or name C or name O or name CB )) or resid 341 through 351 or \ (resid 352 through 353 and (name N or name CA or name C or name O or name CB )) \ or resid 354 through 356 or (resid 357 through 359 and (name N or name CA or nam \ e C or name O or name CB )) or resid 360 through 361 or (resid 362 and (name N o \ r name CA or name C or name O or name CB )) or resid 363 through 374 or (resid 3 \ 75 through 376 and (name N or name CA or name C or name O or name CB )) or resid \ 377 through 397 or (resid 398 and (name N or name CA or name C or name O or nam \ e CB )) or resid 399 through 407 or (resid 408 through 412 and (name N or name C \ A or name C or name O or name CB )))) selection = (chain 'B' and ((resid 328 through 330 and (name N or name CA or name C or name \ O or name CB )) or resid 331 or (resid 332 through 334 and (name N or name CA or \ name C or name O or name CB )) or resid 335 or (resid 336 and (name N or name C \ A or name C or name O or name CB )) or resid 337 through 339 or (resid 340 and ( \ name N or name CA or name C or name O or name CB )) or resid 341 through 351 or \ (resid 352 through 353 and (name N or name CA or name C or name O or name CB )) \ or resid 354 through 355 or (resid 356 through 359 and (name N or name CA or nam \ e C or name O or name CB )) or resid 360 through 381 or (resid 382 and (name N o \ r name CA or name C or name O or name CB )) or resid 383 through 392 or (resid 3 \ 93 and (name N or name CA or name C or name O or name CB )) or resid 394 through \ 397 or (resid 398 and (name N or name CA or name C or name O or name CB )) or r \ esid 399 through 407 or (resid 408 through 412 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'C' and (resid 328 through 333 or (resid 334 and (name N or name CA or na \ me C or name O or name CB )) or resid 335 or (resid 336 and (name N or name CA o \ r name C or name O or name CB )) or resid 337 through 339 or (resid 340 and (nam \ e N or name CA or name C or name O or name CB )) or resid 341 through 357 or (re \ sid 358 through 359 and (name N or name CA or name C or name O or name CB )) or \ resid 360 through 392 or (resid 393 and (name N or name CA or name C or name O o \ r name CB )) or resid 394 through 397 or (resid 398 and (name N or name CA or na \ me C or name O or name CB )) or resid 399 through 407 or (resid 408 through 412 \ and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 328 through 351 or (resid 352 through 353 and (name N or n \ ame CA or name C or name O or name CB )) or resid 354 through 374 or (resid 375 \ through 376 and (name N or name CA or name C or name O or name CB )) or resid 37 \ 7 through 392 or (resid 393 and (name N or name CA or name C or name O or name C \ B )) or resid 394 through 412)) } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' } 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 individual isotropic 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: 2.640 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: 13.360 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.190 Find NCS groups from input model: 0.280 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 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 : 0.003 0.046 4403 Z= 0.181 Angle : 0.559 5.262 6308 Z= 0.332 Chirality : 0.034 0.208 691 Planarity : 0.021 0.492 551 Dihedral : 26.264 87.888 1698 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.90 % Allowed : 21.08 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.43), residues: 337 helix: -1.09 (0.37), residues: 185 sheet: -0.10 (0.78), residues: 46 loop : -1.50 (0.54), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 366 HIS 0.001 0.000 HIS B 387 PHE 0.011 0.001 PHE A 340 TYR 0.014 0.002 TYR D 364 ARG 0.006 0.000 ARG C 358 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.364 Fit side-chains REVERT: A 336 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.6574 (tmm) outliers start: 2 outliers final: 0 residues processed: 57 average time/residue: 0.1547 time to fit residues: 11.1518 Evaluate side-chains 56 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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: 0.7702 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4403 Z= 0.210 Angle : 0.558 5.202 6308 Z= 0.330 Chirality : 0.035 0.169 691 Planarity : 0.004 0.023 551 Dihedral : 27.792 63.596 1204 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.79 % Allowed : 19.73 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.46), residues: 337 helix: -0.40 (0.40), residues: 185 sheet: -0.11 (0.76), residues: 46 loop : -1.56 (0.55), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 366 HIS 0.003 0.001 HIS B 392 PHE 0.011 0.001 PHE A 340 TYR 0.019 0.002 TYR D 364 ARG 0.006 0.000 ARG C 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.366 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 60 average time/residue: 0.1902 time to fit residues: 14.0432 Evaluate side-chains 61 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 390 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 0.0670 chunk 24 optimal weight: 10.0000 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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: 0.7688 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4403 Z= 0.192 Angle : 0.540 5.238 6308 Z= 0.319 Chirality : 0.034 0.179 691 Planarity : 0.003 0.024 551 Dihedral : 27.657 64.195 1201 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.69 % Allowed : 19.28 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.45), residues: 337 helix: -0.36 (0.40), residues: 185 sheet: -0.08 (0.76), residues: 46 loop : -1.67 (0.55), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 406 HIS 0.002 0.000 HIS C 387 PHE 0.014 0.001 PHE A 340 TYR 0.013 0.002 TYR D 364 ARG 0.005 0.000 ARG C 358 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.336 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.1778 time to fit residues: 13.8646 Evaluate side-chains 64 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 390 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.7755 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4403 Z= 0.268 Angle : 0.576 5.465 6308 Z= 0.338 Chirality : 0.036 0.187 691 Planarity : 0.004 0.023 551 Dihedral : 27.769 64.308 1201 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.04 % Allowed : 19.28 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.44), residues: 337 helix: -0.45 (0.39), residues: 185 sheet: -0.11 (0.73), residues: 46 loop : -1.83 (0.55), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 366 HIS 0.003 0.001 HIS B 387 PHE 0.011 0.001 PHE A 340 TYR 0.016 0.002 TYR C 364 ARG 0.005 0.000 ARG C 358 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.320 Fit side-chains REVERT: D 371 PHE cc_start: 0.7649 (m-80) cc_final: 0.7402 (m-80) outliers start: 9 outliers final: 8 residues processed: 64 average time/residue: 0.1942 time to fit residues: 15.1041 Evaluate side-chains 69 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 405 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 0.0980 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.0170 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.5620 ------------------------------------------------------------------------------- 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: 0.7702 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4403 Z= 0.198 Angle : 0.549 5.369 6308 Z= 0.323 Chirality : 0.035 0.208 691 Planarity : 0.003 0.023 551 Dihedral : 27.639 65.132 1201 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.79 % Allowed : 21.97 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.45), residues: 337 helix: -0.31 (0.39), residues: 185 sheet: -0.14 (0.71), residues: 50 loop : -1.72 (0.58), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 366 HIS 0.002 0.001 HIS C 387 PHE 0.017 0.001 PHE A 340 TYR 0.012 0.002 TYR B 364 ARG 0.007 0.000 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.362 Fit side-chains REVERT: D 371 PHE cc_start: 0.7613 (m-80) cc_final: 0.7346 (m-80) outliers start: 4 outliers final: 4 residues processed: 66 average time/residue: 0.1552 time to fit residues: 12.6841 Evaluate side-chains 66 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 405 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.0050 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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: 0.7680 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4403 Z= 0.189 Angle : 0.546 5.352 6308 Z= 0.321 Chirality : 0.034 0.216 691 Planarity : 0.003 0.024 551 Dihedral : 27.586 65.527 1201 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.59 % Allowed : 19.73 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.46), residues: 337 helix: -0.16 (0.40), residues: 186 sheet: -0.20 (0.72), residues: 50 loop : -1.64 (0.59), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 366 HIS 0.011 0.001 HIS B 334 PHE 0.013 0.001 PHE A 340 TYR 0.018 0.002 TYR C 373 ARG 0.004 0.000 ARG C 358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.364 Fit side-chains REVERT: D 371 PHE cc_start: 0.7648 (m-80) cc_final: 0.7410 (m-80) REVERT: B 397 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6860 (ttt180) outliers start: 8 outliers final: 6 residues processed: 64 average time/residue: 0.1695 time to fit residues: 13.4972 Evaluate side-chains 66 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain B 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 405 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 0.0270 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- 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: 0.7739 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4403 Z= 0.251 Angle : 0.568 5.401 6308 Z= 0.333 Chirality : 0.036 0.221 691 Planarity : 0.004 0.025 551 Dihedral : 27.638 65.392 1201 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.14 % Allowed : 21.08 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.46), residues: 337 helix: -0.24 (0.40), residues: 186 sheet: -0.10 (0.72), residues: 50 loop : -1.68 (0.59), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 366 HIS 0.010 0.001 HIS B 334 PHE 0.016 0.001 PHE A 340 TYR 0.013 0.002 TYR C 364 ARG 0.007 0.000 ARG C 358 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.368 Fit side-chains REVERT: D 366 TRP cc_start: 0.7983 (t60) cc_final: 0.7004 (t-100) REVERT: D 371 PHE cc_start: 0.7704 (m-80) cc_final: 0.7434 (m-80) REVERT: B 397 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6844 (ttt180) outliers start: 7 outliers final: 6 residues processed: 66 average time/residue: 0.1842 time to fit residues: 14.9169 Evaluate side-chains 68 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 405 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 27 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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: 0.7694 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4403 Z= 0.198 Angle : 0.555 5.333 6308 Z= 0.326 Chirality : 0.034 0.250 691 Planarity : 0.003 0.023 551 Dihedral : 27.603 65.679 1201 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.04 % Allowed : 21.52 % Favored : 74.44 % 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: -0.90 (0.46), residues: 337 helix: -0.09 (0.40), residues: 186 sheet: -0.11 (0.73), residues: 50 loop : -1.57 (0.59), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 366 HIS 0.008 0.001 HIS B 334 PHE 0.012 0.001 PHE A 340 TYR 0.010 0.002 TYR B 330 ARG 0.005 0.000 ARG C 358 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.380 Fit side-chains REVERT: D 366 TRP cc_start: 0.7972 (t60) cc_final: 0.6948 (t-100) REVERT: D 371 PHE cc_start: 0.7739 (m-80) cc_final: 0.7511 (m-80) REVERT: B 397 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6849 (ttt180) outliers start: 9 outliers final: 8 residues processed: 67 average time/residue: 0.1862 time to fit residues: 15.3530 Evaluate side-chains 71 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 394 CYS Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 405 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.0270 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.7440 ------------------------------------------------------------------------------- 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: 0.7713 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4403 Z= 0.224 Angle : 0.561 5.427 6308 Z= 0.329 Chirality : 0.035 0.242 691 Planarity : 0.003 0.023 551 Dihedral : 27.600 65.521 1201 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.14 % Allowed : 22.87 % Favored : 73.99 % 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: -0.90 (0.47), residues: 337 helix: -0.07 (0.40), residues: 186 sheet: -0.14 (0.74), residues: 50 loop : -1.62 (0.59), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 366 HIS 0.009 0.001 HIS B 334 PHE 0.016 0.001 PHE A 340 TYR 0.010 0.002 TYR C 364 ARG 0.005 0.000 ARG C 358 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.388 Fit side-chains REVERT: D 371 PHE cc_start: 0.7833 (m-80) cc_final: 0.7598 (m-80) REVERT: B 397 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6858 (ttt180) outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 0.1729 time to fit residues: 13.3343 Evaluate side-chains 66 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 405 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7720 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4403 Z= 0.224 Angle : 0.564 5.387 6308 Z= 0.331 Chirality : 0.035 0.260 691 Planarity : 0.003 0.023 551 Dihedral : 27.610 65.540 1201 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.24 % Allowed : 23.32 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.47), residues: 337 helix: -0.02 (0.40), residues: 186 sheet: -0.13 (0.74), residues: 50 loop : -1.60 (0.61), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 366 HIS 0.007 0.001 HIS B 334 PHE 0.012 0.001 PHE A 340 TYR 0.011 0.002 TYR B 330 ARG 0.005 0.000 ARG C 358 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.350 Fit side-chains REVERT: B 397 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6878 (ttt180) REVERT: C 337 ARG cc_start: 0.7189 (tpp80) cc_final: 0.6875 (tpt170) outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.1773 time to fit residues: 13.4118 Evaluate side-chains 62 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 405 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 0.0670 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.143039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.122674 restraints weight = 8355.180| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.51 r_work: 0.3588 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4403 Z= 0.213 Angle : 0.560 5.408 6308 Z= 0.328 Chirality : 0.035 0.260 691 Planarity : 0.003 0.024 551 Dihedral : 27.581 65.546 1201 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.24 % Allowed : 22.42 % Favored : 75.34 % 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: -0.84 (0.47), residues: 337 helix: 0.01 (0.41), residues: 186 sheet: -0.28 (0.73), residues: 50 loop : -1.56 (0.61), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 366 HIS 0.008 0.001 HIS B 334 PHE 0.014 0.001 PHE A 340 TYR 0.015 0.002 TYR B 373 ARG 0.005 0.000 ARG C 358 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1300.01 seconds wall clock time: 24 minutes 58.22 seconds (1498.22 seconds total)