Starting phenix.real_space_refine on Wed Jul 1 23:23:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sro_40736/07_2026/8sro_40736.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sro_40736/07_2026/8sro_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 { model { file = "/net/cci-nas-00/data/ceres_data/8sro_40736/07_2026/8sro_40736.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sro_40736/07_2026/8sro_40736.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sro_40736/07_2026/8sro_40736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sro_40736/07_2026/8sro_40736.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.070 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 'ASP:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 1} 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: {'ASP:plan': 2, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 1} 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: {'HIS:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1} 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: {'ASN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'GLN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1} 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: 1.32, per 1000 atoms: 0.32 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: 0.40 Conformation dependent library (CDL) restraints added in 108.9 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: 0.53 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: 0.55 Time building geometry restraints manager: 0.51 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=" C3' DG E 31 " pdb=" C2' DG E 31 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DG I 31 " pdb=" C2' DG I 31 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DA J 19 " pdb=" C2' DA J 19 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.79e+00 bond pdb=" C3' DC J 20 " pdb=" C2' DC J 20 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.65e+00 bond pdb=" C3' DA F 15 " pdb=" C2' DA F 15 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.68e+00 ... (remaining 4398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 5671 1.05 - 2.10: 420 2.10 - 3.16: 194 3.16 - 4.21: 10 4.21 - 5.26: 13 Bond angle restraints: 6308 Sorted by residual: angle pdb=" O4' DC F 20 " pdb=" C1' DC F 20 " pdb=" N1 DC F 20 " ideal model delta sigma weight residual 108.00 111.67 -3.67 7.00e-01 2.04e+00 2.74e+01 angle pdb=" N3 DT E 37 " pdb=" C4 DT E 37 " pdb=" O4 DT E 37 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT E 40 " pdb=" C4 DT E 40 " pdb=" O4 DT E 40 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT I 37 " pdb=" C4 DT I 37 " pdb=" O4 DT I 37 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT E 38 " pdb=" C4 DT E 38 " pdb=" O4 DT E 38 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 ... (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: 0.001 - 0.042: 484 0.042 - 0.083: 170 0.083 - 0.125: 36 0.125 - 0.166: 0 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 2.43 2.31 0.12 2.00e-01 2.50e+01 3.75e-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: 6.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.220 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 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 : 0.005 0.046 4403 Z= 0.417 Angle : 0.701 5.262 6308 Z= 0.612 Chirality : 0.042 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.006 0.000 ARG C 358 TYR 0.014 0.002 TYR D 364 PHE 0.011 0.001 PHE A 340 TRP 0.012 0.001 TRP C 366 HIS 0.001 0.000 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.42 ( 4403) covalent geometry : angle 0.70119 / 0.61 ( 6308) hydrogen bonds : bond 0.20959 / 14.38 ( 181) hydrogen bonds : angle 7.75662 / 5.48 ( 468) *********************** 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 : 0.122 Fit side-chains REVERT: A 336 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.6574 (tmm) outliers start: 2 outliers final: 0 residues processed: 57 average time/residue: 0.0661 time to fit residues: 4.8300 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 : 0.120 ------------------------------------------------------------------------------- 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 24 optimal weight: 10.0000 chunk 26 optimal weight: 0.0470 chunk 2 optimal weight: 0.0570 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.0670 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.143126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.122884 restraints weight = 8497.874| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.51 r_work: 0.3593 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4403 Z= 0.151 Angle : 0.579 6.329 6308 Z= 0.350 Chirality : 0.038 0.206 691 Planarity : 0.005 0.092 551 Dihedral : 28.153 62.853 1204 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.24 % Allowed : 20.18 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.44), residues: 337 helix: -0.56 (0.38), residues: 185 sheet: -0.33 (0.71), residues: 46 loop : -1.61 (0.53), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 358 TYR 0.015 0.002 TYR D 364 PHE 0.009 0.001 PHE A 340 TRP 0.008 0.001 TRP C 366 HIS 0.003 0.001 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 ( 4403) covalent geometry : angle 0.57870 / 0.35 ( 6308) hydrogen bonds : bond 0.05125 / 3.43 ( 181) hydrogen bonds : angle 5.65942 / 3.99 ( 468) *********************** 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 64 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.120 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 61 average time/residue: 0.0844 time to fit residues: 6.2945 Evaluate side-chains 58 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 341 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 27 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.142776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.122560 restraints weight = 8460.393| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.50 r_work: 0.3590 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1183 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= 0.142 Angle : 0.547 5.326 6308 Z= 0.334 Chirality : 0.037 0.202 691 Planarity : 0.004 0.046 551 Dihedral : 28.214 62.134 1201 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.14 % Allowed : 18.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.44), residues: 337 helix: -0.47 (0.38), residues: 185 sheet: -0.21 (0.71), residues: 46 loop : -1.76 (0.53), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 356 TYR 0.013 0.002 TYR D 364 PHE 0.009 0.001 PHE A 340 TRP 0.011 0.001 TRP C 366 HIS 0.002 0.000 HIS C 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 ( 4403) covalent geometry : angle 0.54749 / 0.33 ( 6308) hydrogen bonds : bond 0.04594 / 3.06 ( 181) hydrogen bonds : angle 5.09023 / 3.62 ( 468) *********************** 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 to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.120 Fit side-chains REVERT: B 366 TRP cc_start: 0.8015 (t-100) cc_final: 0.7687 (t60) outliers start: 7 outliers final: 5 residues processed: 63 average time/residue: 0.0818 time to fit residues: 6.3013 Evaluate side-chains 63 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.125 ------------------------------------------------------------------------------- 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 6 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 0.0000 chunk 21 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 28 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 9 optimal weight: 0.2980 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.144241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.124263 restraints weight = 8452.324| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.46 r_work: 0.3617 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4403 Z= 0.129 Angle : 0.537 5.047 6308 Z= 0.324 Chirality : 0.037 0.212 691 Planarity : 0.004 0.029 551 Dihedral : 28.214 62.712 1201 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.35 % Allowed : 22.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.44), residues: 337 helix: -0.28 (0.39), residues: 185 sheet: -0.17 (0.73), residues: 46 loop : -1.78 (0.52), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 375 TYR 0.012 0.002 TYR B 364 PHE 0.020 0.001 PHE A 340 TRP 0.015 0.001 TRP C 366 HIS 0.002 0.000 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 4403) covalent geometry : angle 0.53721 / 0.32 ( 6308) hydrogen bonds : bond 0.03962 / 2.67 ( 181) hydrogen bonds : angle 4.72093 / 3.41 ( 468) *********************** 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 65 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.116 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 63 average time/residue: 0.0687 time to fit residues: 5.4864 Evaluate side-chains 58 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain C residue 390 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 33 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.143967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.123870 restraints weight = 8545.439| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.48 r_work: 0.3614 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4403 Z= 0.133 Angle : 0.540 5.121 6308 Z= 0.323 Chirality : 0.037 0.213 691 Planarity : 0.004 0.027 551 Dihedral : 28.251 63.639 1201 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.69 % Allowed : 21.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.45), residues: 337 helix: -0.25 (0.39), residues: 185 sheet: -0.26 (0.73), residues: 46 loop : -1.81 (0.53), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 358 TYR 0.013 0.002 TYR A 373 PHE 0.012 0.001 PHE A 340 TRP 0.013 0.001 TRP C 366 HIS 0.002 0.000 HIS C 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 4403) covalent geometry : angle 0.53959 / 0.32 ( 6308) hydrogen bonds : bond 0.03948 / 2.63 ( 181) hydrogen bonds : angle 4.54358 / 3.30 ( 468) *********************** 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 64 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.120 Fit side-chains REVERT: D 371 PHE cc_start: 0.7665 (m-80) cc_final: 0.7412 (m-80) outliers start: 6 outliers final: 6 residues processed: 60 average time/residue: 0.0774 time to fit residues: 5.8369 Evaluate side-chains 62 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 0.3980 chunk 19 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 9 optimal weight: 0.0670 chunk 35 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.143331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.122920 restraints weight = 8692.619| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.52 r_work: 0.3594 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4403 Z= 0.146 Angle : 0.548 5.108 6308 Z= 0.327 Chirality : 0.037 0.207 691 Planarity : 0.004 0.028 551 Dihedral : 28.260 63.414 1201 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.45), residues: 337 helix: -0.23 (0.39), residues: 186 sheet: -0.41 (0.73), residues: 46 loop : -1.80 (0.53), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 358 TYR 0.020 0.002 TYR A 373 PHE 0.012 0.001 PHE A 340 TRP 0.012 0.001 TRP D 366 HIS 0.010 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 ( 4403) covalent geometry : angle 0.54812 / 0.33 ( 6308) hydrogen bonds : bond 0.03940 / 2.58 ( 181) hydrogen bonds : angle 4.44759 / 3.25 ( 468) *********************** 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 66 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.188 Fit side-chains REVERT: D 366 TRP cc_start: 0.8034 (t60) cc_final: 0.7831 (t60) REVERT: D 371 PHE cc_start: 0.7799 (m-80) cc_final: 0.7566 (m-80) outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 0.0671 time to fit residues: 5.3081 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 : 0.124 ------------------------------------------------------------------------------- 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 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 24 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 0.0010 chunk 32 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.143639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.123430 restraints weight = 8743.924| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.51 r_work: 0.3605 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4403 Z= 0.138 Angle : 0.545 5.296 6308 Z= 0.325 Chirality : 0.037 0.228 691 Planarity : 0.004 0.022 551 Dihedral : 28.243 63.390 1201 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.45), residues: 337 helix: -0.15 (0.40), residues: 186 sheet: -0.44 (0.74), residues: 46 loop : -1.74 (0.54), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 356 TYR 0.016 0.002 TYR A 373 PHE 0.012 0.001 PHE A 340 TRP 0.007 0.001 TRP D 366 HIS 0.011 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 ( 4403) covalent geometry : angle 0.54538 / 0.32 ( 6308) hydrogen bonds : bond 0.03797 / 2.50 ( 181) hydrogen bonds : angle 4.37467 / 3.20 ( 468) *********************** 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 63 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.124 Fit side-chains REVERT: D 371 PHE cc_start: 0.7786 (m-80) cc_final: 0.7558 (m-80) outliers start: 7 outliers final: 6 residues processed: 58 average time/residue: 0.0637 time to fit residues: 4.8145 Evaluate side-chains 60 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.143355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.123141 restraints weight = 8545.407| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.48 r_work: 0.3602 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4403 Z= 0.141 Angle : 0.545 5.099 6308 Z= 0.325 Chirality : 0.037 0.247 691 Planarity : 0.004 0.041 551 Dihedral : 28.265 63.668 1201 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.59 % Allowed : 21.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.46), residues: 337 helix: -0.07 (0.40), residues: 186 sheet: -0.40 (0.74), residues: 50 loop : -1.73 (0.56), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 358 TYR 0.017 0.002 TYR A 373 PHE 0.014 0.001 PHE A 340 TRP 0.007 0.001 TRP D 366 HIS 0.010 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 4403) covalent geometry : angle 0.54520 / 0.32 ( 6308) hydrogen bonds : bond 0.03836 / 2.51 ( 181) hydrogen bonds : angle 4.33025 / 3.18 ( 468) *********************** 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 64 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.137 Fit side-chains REVERT: D 371 PHE cc_start: 0.7796 (m-80) cc_final: 0.7570 (m-80) outliers start: 8 outliers final: 8 residues processed: 58 average time/residue: 0.0705 time to fit residues: 5.1693 Evaluate side-chains 63 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 0.1980 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.0670 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.144309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.124101 restraints weight = 8641.558| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.49 r_work: 0.3619 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4403 Z= 0.129 Angle : 0.540 5.175 6308 Z= 0.321 Chirality : 0.036 0.261 691 Planarity : 0.004 0.033 551 Dihedral : 28.269 63.645 1201 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.46), residues: 337 helix: 0.01 (0.40), residues: 186 sheet: -0.42 (0.74), residues: 50 loop : -1.66 (0.57), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 375 TYR 0.011 0.002 TYR A 373 PHE 0.013 0.001 PHE A 340 TRP 0.014 0.001 TRP B 366 HIS 0.009 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 4403) covalent geometry : angle 0.53963 / 0.32 ( 6308) hydrogen bonds : bond 0.03628 / 2.38 ( 181) hydrogen bonds : angle 4.27829 / 3.15 ( 468) *********************** 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 64 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.122 Fit side-chains REVERT: D 371 PHE cc_start: 0.7852 (m-80) cc_final: 0.7643 (m-80) REVERT: C 373 TYR cc_start: 0.7837 (t80) cc_final: 0.7542 (t80) outliers start: 6 outliers final: 6 residues processed: 60 average time/residue: 0.0897 time to fit residues: 6.5373 Evaluate side-chains 61 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.119 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.143953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.123758 restraints weight = 8524.344| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.47 r_work: 0.3612 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4403 Z= 0.140 Angle : 0.554 5.824 6308 Z= 0.326 Chirality : 0.037 0.258 691 Planarity : 0.004 0.041 551 Dihedral : 28.295 63.905 1201 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.69 % Allowed : 22.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.46), residues: 337 helix: 0.05 (0.40), residues: 186 sheet: -0.45 (0.74), residues: 50 loop : -1.69 (0.57), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 375 TYR 0.014 0.002 TYR A 373 PHE 0.014 0.001 PHE A 340 TRP 0.007 0.001 TRP D 366 HIS 0.008 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 4403) covalent geometry : angle 0.55416 / 0.33 ( 6308) hydrogen bonds : bond 0.03778 / 2.47 ( 181) hydrogen bonds : angle 4.27108 / 3.14 ( 468) ********************** 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 60 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.072 Fit side-chains REVERT: C 373 TYR cc_start: 0.7846 (t80) cc_final: 0.7564 (t80) outliers start: 6 outliers final: 6 residues processed: 56 average time/residue: 0.0665 time to fit residues: 4.6665 Evaluate side-chains 60 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.130 ------------------------------------------------------------------------------- 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 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 16 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.143463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.123306 restraints weight = 8518.394| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.46 r_work: 0.3609 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2014 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= 0.145 Angle : 0.558 5.386 6308 Z= 0.329 Chirality : 0.037 0.294 691 Planarity : 0.004 0.034 551 Dihedral : 28.290 63.320 1201 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.69 % Allowed : 23.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.46), residues: 337 helix: 0.02 (0.40), residues: 186 sheet: -0.53 (0.74), residues: 50 loop : -1.67 (0.58), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 358 TYR 0.015 0.002 TYR A 373 PHE 0.016 0.001 PHE A 340 TRP 0.007 0.001 TRP B 366 HIS 0.008 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 4403) covalent geometry : angle 0.55833 / 0.33 ( 6308) hydrogen bonds : bond 0.03818 / 2.49 ( 181) hydrogen bonds : angle 4.28708 / 3.16 ( 468) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1113.33 seconds wall clock time: 19 minutes 49.63 seconds (1189.63 seconds total)