Starting phenix.real_space_refine on Thu Nov 14 05:09:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sro_40736/11_2024/8sro_40736.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sro_40736/11_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_40736/11_2024/8sro_40736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sro_40736/11_2024/8sro_40736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sro_40736/11_2024/8sro_40736.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sro_40736/11_2024/8sro_40736.cif" } 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. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 4.10, per 1000 atoms: 0.99 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 356.2 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: 1.73 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: 1.18 Time building geometry restraints manager: 1.27 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: 0.00 - 1.05: 5964 1.05 - 2.10: 224 2.10 - 3.16: 97 3.16 - 4.21: 11 4.21 - 5.26: 12 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 3.120 nonbonded pdb=" OD1 ASN B 383 " pdb=" NH2 ARG B 386 " model vdw 2.415 3.120 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 3.120 nonbonded pdb=" O TYR A 373 " pdb=" N ARG A 375 " model vdw 2.527 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 4.500 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.280 Find NCS groups from input model: 0.190 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.060 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.348 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: 0.1592 time to fit residues: 11.4971 Evaluate side-chains 56 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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: 0.4980 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7707 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4403 Z= 0.211 Angle : 0.560 5.177 6308 Z= 0.331 Chirality : 0.035 0.169 691 Planarity : 0.004 0.054 551 Dihedral : 27.822 63.578 1204 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.24 % Allowed : 20.63 % Favored : 77.13 % 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: -1.23 (0.45), residues: 337 helix: -0.43 (0.40), residues: 185 sheet: -0.17 (0.74), residues: 46 loop : -1.57 (0.54), 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 0.018 0.002 TYR D 364 ARG 0.005 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 65 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.334 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.2039 time to fit residues: 15.1724 Evaluate side-chains 62 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 VAL 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: 0.6980 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7723 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4403 Z= 0.221 Angle : 0.551 5.292 6308 Z= 0.326 Chirality : 0.035 0.186 691 Planarity : 0.004 0.035 551 Dihedral : 27.735 63.704 1201 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.59 % Allowed : 18.39 % 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: -1.28 (0.45), residues: 337 helix: -0.42 (0.39), residues: 185 sheet: -0.09 (0.73), residues: 46 loop : -1.76 (0.55), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 366 HIS 0.003 0.001 HIS B 387 PHE 0.011 0.001 PHE A 340 TYR 0.015 0.002 TYR D 364 ARG 0.008 0.001 ARG B 356 *********************** 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 71 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.326 Fit side-chains REVERT: D 371 PHE cc_start: 0.7639 (m-80) cc_final: 0.7426 (m-80) outliers start: 8 outliers final: 6 residues processed: 66 average time/residue: 0.2087 time to fit residues: 16.6551 Evaluate side-chains 65 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 3 optimal weight: 0.0370 chunk 15 optimal weight: 4.9990 chunk 21 optimal weight: 0.0870 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.0170 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 0.3474 ------------------------------------------------------------------------------- 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: 0.7677 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4403 Z= 0.186 Angle : 0.541 5.140 6308 Z= 0.318 Chirality : 0.034 0.227 691 Planarity : 0.004 0.030 551 Dihedral : 27.640 64.470 1201 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.24 % Allowed : 21.08 % 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: -1.17 (0.45), residues: 337 helix: -0.29 (0.39), residues: 186 sheet: -0.22 (0.72), residues: 46 loop : -1.70 (0.54), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 366 HIS 0.002 0.000 HIS B 387 PHE 0.016 0.001 PHE A 340 TYR 0.012 0.002 TYR D 364 ARG 0.007 0.001 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 to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.302 Fit side-chains REVERT: D 371 PHE cc_start: 0.7733 (m-80) cc_final: 0.7527 (m-80) outliers start: 5 outliers final: 5 residues processed: 66 average time/residue: 0.1763 time to fit residues: 14.2016 Evaluate side-chains 66 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 VAL 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 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: 0.0070 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1582 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= 0.202 Angle : 0.546 5.259 6308 Z= 0.321 Chirality : 0.034 0.207 691 Planarity : 0.004 0.027 551 Dihedral : 27.619 64.809 1201 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.14 % Allowed : 20.18 % 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: -1.15 (0.45), residues: 337 helix: -0.24 (0.40), residues: 186 sheet: -0.32 (0.73), residues: 46 loop : -1.71 (0.55), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 366 HIS 0.013 0.001 HIS B 334 PHE 0.012 0.001 PHE A 340 TYR 0.018 0.002 TYR C 373 ARG 0.007 0.000 ARG C 358 *********************** 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 to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.373 Fit side-chains REVERT: D 366 TRP cc_start: 0.7976 (t60) cc_final: 0.7753 (t60) outliers start: 7 outliers final: 6 residues processed: 64 average time/residue: 0.1974 time to fit residues: 15.3393 Evaluate side-chains 66 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 398 VAL Chi-restraints excluded: chain C residue 380 THR 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: 3.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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: 0.7796 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 4403 Z= 0.333 Angle : 0.604 5.660 6308 Z= 0.354 Chirality : 0.038 0.193 691 Planarity : 0.005 0.036 551 Dihedral : 27.795 63.973 1201 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.48 % Allowed : 18.83 % 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: -1.35 (0.45), residues: 337 helix: -0.46 (0.38), residues: 186 sheet: -0.25 (0.71), residues: 50 loop : -1.80 (0.60), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 366 HIS 0.007 0.001 HIS B 334 PHE 0.009 0.001 PHE C 395 TYR 0.021 0.003 TYR A 373 ARG 0.006 0.001 ARG A 375 *********************** 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 72 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.306 Fit side-chains REVERT: D 366 TRP cc_start: 0.8102 (t60) cc_final: 0.7847 (t60) REVERT: C 373 TYR cc_start: 0.7927 (t80) cc_final: 0.7613 (t80) outliers start: 10 outliers final: 10 residues processed: 64 average time/residue: 0.1905 time to fit residues: 14.7943 Evaluate side-chains 71 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 377 HIS 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 405 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 0.0570 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- 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: 0.7741 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4403 Z= 0.211 Angle : 0.563 5.719 6308 Z= 0.330 Chirality : 0.035 0.230 691 Planarity : 0.004 0.032 551 Dihedral : 27.699 64.768 1201 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.04 % Allowed : 19.73 % 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: -1.09 (0.46), residues: 337 helix: -0.26 (0.39), residues: 186 sheet: -0.26 (0.71), residues: 50 loop : -1.59 (0.61), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 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 A 373 ARG 0.008 0.000 ARG A 375 *********************** 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 72 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.360 Fit side-chains REVERT: D 366 TRP cc_start: 0.8036 (t60) cc_final: 0.7793 (t60) outliers start: 9 outliers final: 9 residues processed: 66 average time/residue: 0.2007 time to fit residues: 16.0365 Evaluate side-chains 70 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 377 HIS 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 341 THR 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: 0.8980 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 0.0050 chunk 9 optimal weight: 0.0010 overall best weight: 0.2600 ------------------------------------------------------------------------------- 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: 0.7648 moved from start: 0.2013 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= 0.187 Angle : 0.552 6.027 6308 Z= 0.324 Chirality : 0.034 0.247 691 Planarity : 0.004 0.028 551 Dihedral : 27.538 66.153 1201 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.24 % Allowed : 21.52 % 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: -0.78 (0.47), residues: 337 helix: 0.04 (0.41), residues: 186 sheet: -0.35 (0.73), residues: 50 loop : -1.44 (0.59), 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 0.013 0.001 PHE A 340 TYR 0.036 0.002 TYR C 373 ARG 0.007 0.001 ARG A 375 *********************** 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 69 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.372 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 66 average time/residue: 0.1926 time to fit residues: 15.5174 Evaluate side-chains 65 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.0050 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 overall best weight: 1.1198 ------------------------------------------------------------------------------- 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: 0.7735 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4403 Z= 0.271 Angle : 0.574 5.569 6308 Z= 0.336 Chirality : 0.036 0.245 691 Planarity : 0.004 0.035 551 Dihedral : 27.597 64.926 1201 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.69 % Allowed : 22.42 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.47), residues: 337 helix: -0.09 (0.40), residues: 186 sheet: -0.25 (0.76), residues: 50 loop : -1.51 (0.61), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 366 HIS 0.007 0.001 HIS B 334 PHE 0.015 0.001 PHE A 340 TYR 0.023 0.002 TYR C 373 ARG 0.009 0.001 ARG A 375 *********************** 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 65 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.397 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 61 average time/residue: 0.1674 time to fit residues: 12.9994 Evaluate side-chains 63 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain C residue 380 THR 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: 0.5980 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7715 moved from start: 0.2084 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= 0.221 Angle : 0.566 5.445 6308 Z= 0.331 Chirality : 0.036 0.278 691 Planarity : 0.004 0.030 551 Dihedral : 27.582 64.877 1201 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % 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: -0.92 (0.47), residues: 337 helix: -0.09 (0.40), residues: 186 sheet: -0.31 (0.75), residues: 50 loop : -1.49 (0.61), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 366 HIS 0.007 0.001 HIS B 334 PHE 0.013 0.001 PHE A 340 TYR 0.024 0.002 TYR C 373 ARG 0.008 0.001 ARG A 375 ********************** 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 64 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.320 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 61 average time/residue: 0.1618 time to fit residues: 12.4431 Evaluate side-chains 64 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 398 VAL 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: 3.9990 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 = 0.4013 r_free = 0.4013 target = 0.141809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.121281 restraints weight = 8426.960| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.51 r_work: 0.3572 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4403 Z= 0.248 Angle : 0.573 5.505 6308 Z= 0.335 Chirality : 0.036 0.255 691 Planarity : 0.004 0.034 551 Dihedral : 27.615 64.705 1201 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.79 % Allowed : 22.87 % 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: -0.93 (0.47), residues: 337 helix: -0.12 (0.40), residues: 186 sheet: -0.29 (0.74), residues: 50 loop : -1.50 (0.62), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 366 HIS 0.007 0.001 HIS B 334 PHE 0.016 0.001 PHE A 340 TYR 0.024 0.002 TYR C 373 ARG 0.008 0.001 ARG A 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1355.71 seconds wall clock time: 25 minutes 14.20 seconds (1514.20 seconds total)