Starting phenix.real_space_refine on Fri Aug 22 18:19:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8teo_41193/08_2025/8teo_41193.cif Found real_map, /net/cci-nas-00/data/ceres_data/8teo_41193/08_2025/8teo_41193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8teo_41193/08_2025/8teo_41193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8teo_41193/08_2025/8teo_41193.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8teo_41193/08_2025/8teo_41193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8teo_41193/08_2025/8teo_41193.map" } resolution = 2.39 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= -0.000 sd= 0.001 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 K 2 8.98 5 S 28 5.16 5 C 4488 2.51 5 N 960 2.21 5 O 1029 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6507 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1536 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1536 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1536 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1536 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 90 Unusual residues: {' K': 2, 'POV': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 6, 'POV:plan-3': 6} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 6, 'POV:plan-3': 6} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 6, 'POV:plan-3': 6} Unresolved non-hydrogen planarities: 67 Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 6, 'POV:plan-3': 6} Unresolved non-hydrogen planarities: 67 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.75, per 1000 atoms: 0.27 Number of scatterers: 6507 At special positions: 0 Unit cell: (105.41, 105.41, 64.74, 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) K 2 19.00 S 28 16.00 O 1029 8.00 N 960 7.00 C 4488 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: 0.64 Conformation dependent library (CDL) restraints added in 422.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1480 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 86.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 226 through 248 Processing helix chain 'A' and resid 279 through 298 Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 320 through 326 Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 369 through 377 Processing helix chain 'A' and resid 380 through 392 Processing helix chain 'A' and resid 392 through 419 Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 441 Processing helix chain 'A' and resid 452 through 472 Processing helix chain 'A' and resid 473 through 489 removed outlier: 4.123A pdb=" N ILE A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 248 Processing helix chain 'B' and resid 279 through 298 Processing helix chain 'B' and resid 311 through 319 Processing helix chain 'B' and resid 320 through 326 Processing helix chain 'B' and resid 358 through 368 Processing helix chain 'B' and resid 369 through 377 Processing helix chain 'B' and resid 380 through 392 Processing helix chain 'B' and resid 392 through 419 Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 441 Processing helix chain 'B' and resid 452 through 472 Processing helix chain 'B' and resid 473 through 489 removed outlier: 4.123A pdb=" N ILE B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 248 Processing helix chain 'C' and resid 279 through 298 Processing helix chain 'C' and resid 311 through 319 Processing helix chain 'C' and resid 320 through 326 Processing helix chain 'C' and resid 358 through 368 Processing helix chain 'C' and resid 369 through 377 Processing helix chain 'C' and resid 380 through 392 Processing helix chain 'C' and resid 392 through 419 Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 441 Processing helix chain 'C' and resid 452 through 472 Processing helix chain 'C' and resid 473 through 489 removed outlier: 4.123A pdb=" N ILE C 477 " --> pdb=" O PRO C 473 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER C 479 " --> pdb=" O PRO C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 248 Processing helix chain 'D' and resid 279 through 298 Processing helix chain 'D' and resid 311 through 319 Processing helix chain 'D' and resid 320 through 326 Processing helix chain 'D' and resid 358 through 368 Processing helix chain 'D' and resid 369 through 377 Processing helix chain 'D' and resid 380 through 392 Processing helix chain 'D' and resid 392 through 419 Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 441 Processing helix chain 'D' and resid 452 through 472 Processing helix chain 'D' and resid 473 through 489 removed outlier: 4.124A pdb=" N ILE D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER D 479 " --> pdb=" O PRO D 475 " (cutoff:3.500A) 489 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 888 1.31 - 1.43: 1808 1.43 - 1.56: 3788 1.56 - 1.68: 84 1.68 - 1.81: 44 Bond restraints: 6612 Sorted by residual: bond pdb=" C31 POV A 701 " pdb=" O31 POV A 701 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C31 POV D 704 " pdb=" O31 POV D 704 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C31 POV B 703 " pdb=" O31 POV B 703 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C31 POV C 702 " pdb=" O31 POV C 702 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C31 POV C 701 " pdb=" O31 POV C 701 " ideal model delta sigma weight residual 1.327 1.440 -0.113 2.00e-02 2.50e+03 3.17e+01 ... (remaining 6607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 8504 1.93 - 3.86: 182 3.86 - 5.78: 153 5.78 - 7.71: 13 7.71 - 9.64: 16 Bond angle restraints: 8868 Sorted by residual: angle pdb=" C32 POV B 708 " pdb=" C31 POV B 708 " pdb=" O31 POV B 708 " ideal model delta sigma weight residual 110.66 120.30 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C32 POV D 703 " pdb=" C31 POV D 703 " pdb=" O31 POV D 703 " ideal model delta sigma weight residual 110.66 120.30 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C32 POV C 701 " pdb=" C31 POV C 701 " pdb=" O31 POV C 701 " ideal model delta sigma weight residual 110.66 120.26 -9.60 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C32 POV B 703 " pdb=" C31 POV B 703 " pdb=" O31 POV B 703 " ideal model delta sigma weight residual 110.66 120.26 -9.60 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C32 POV D 704 " pdb=" C31 POV D 704 " pdb=" O31 POV D 704 " ideal model delta sigma weight residual 110.66 120.26 -9.60 3.00e+00 1.11e-01 1.02e+01 ... (remaining 8863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.01: 3524 23.01 - 46.02: 256 46.02 - 69.03: 60 69.03 - 92.04: 0 92.04 - 115.05: 4 Dihedral angle restraints: 3844 sinusoidal: 1576 harmonic: 2268 Sorted by residual: dihedral pdb=" C3 POV C 702 " pdb=" C31 POV C 702 " pdb=" O31 POV C 702 " pdb=" C32 POV C 702 " ideal model delta sinusoidal sigma weight residual 172.61 57.56 115.05 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" C3 POV B 703 " pdb=" C31 POV B 703 " pdb=" O31 POV B 703 " pdb=" C32 POV B 703 " ideal model delta sinusoidal sigma weight residual 172.61 57.58 115.03 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" C3 POV D 704 " pdb=" C31 POV D 704 " pdb=" O31 POV D 704 " pdb=" C32 POV D 704 " ideal model delta sinusoidal sigma weight residual 172.61 57.58 115.03 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 3841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 776 0.038 - 0.075: 226 0.075 - 0.113: 52 0.113 - 0.151: 13 0.151 - 0.188: 5 Chirality restraints: 1072 Sorted by residual: chirality pdb=" CA LEU B 472 " pdb=" N LEU B 472 " pdb=" C LEU B 472 " pdb=" CB LEU B 472 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CA LEU C 472 " pdb=" N LEU C 472 " pdb=" C LEU C 472 " pdb=" CB LEU C 472 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CA LEU D 472 " pdb=" N LEU D 472 " pdb=" C LEU D 472 " pdb=" CB LEU D 472 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.74e-01 ... (remaining 1069 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 472 " -0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO D 473 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO D 473 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 473 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 472 " 0.055 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO A 473 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 472 " -0.055 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO B 473 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 473 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 473 " -0.046 5.00e-02 4.00e+02 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.84: 2061 2.84 - 3.41: 7234 3.41 - 3.99: 12345 3.99 - 4.56: 17852 4.56 - 5.14: 25567 Nonbonded interactions: 65059 Sorted by model distance: nonbonded pdb=" OE2 GLU A 283 " pdb=" NH2 ARG A 371 " model vdw 2.259 3.120 nonbonded pdb=" OE2 GLU B 283 " pdb=" NH2 ARG B 371 " model vdw 2.260 3.120 nonbonded pdb=" OE2 GLU D 283 " pdb=" NH2 ARG D 371 " model vdw 2.260 3.120 nonbonded pdb=" OE2 GLU C 283 " pdb=" NH2 ARG C 371 " model vdw 2.260 3.120 nonbonded pdb=" OE2 GLU C 283 " pdb=" NH1 ARG C 368 " model vdw 2.272 3.120 ... (remaining 65054 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 226 through 489 or (resid 702 and (name C31 or name C32 or \ name C33 or name C34 or name C35)) or (resid 703 through 704 and (name C32 or n \ ame C33 or name C34 or name C35)))) selection = (chain 'B' and (resid 226 through 489 or (resid 702 and (name C31 or name C32 or \ name C33 or name C34 or name C35)) or (resid 703 through 704 and (name C32 or n \ ame C33 or name C34 or name C35)))) selection = (chain 'C' and (resid 226 through 489 or (resid 702 and (name C31 or name C32 or \ name C33 or name C34 or name C35)) or (resid 703 through 704 and (name C32 or n \ ame C33 or name C34 or name C35)))) selection = (chain 'D' and (resid 226 through 489 or (resid 702 and (name C31 or name C32 or \ name C33 or name C34 or name C35)) or (resid 703 through 704 and (name C32 or n \ ame C33 or name C34 or name C35)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.000 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 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:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 0.009 0.115 6612 Z= 0.449 Angle : 0.967 9.640 8868 Z= 0.399 Chirality : 0.041 0.188 1072 Planarity : 0.008 0.083 1020 Dihedral : 16.683 115.049 2364 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.60 % Allowed : 5.42 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.31), residues: 752 helix: 1.79 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -0.48 (0.65), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 487 TYR 0.008 0.001 TYR B 415 PHE 0.033 0.002 PHE A 433 TRP 0.007 0.001 TRP B 289 HIS 0.002 0.001 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00911 ( 6612) covalent geometry : angle 0.96746 ( 8868) hydrogen bonds : bond 0.12783 ( 489) hydrogen bonds : angle 3.69670 ( 1395) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.262 Fit side-chains outliers start: 4 outliers final: 8 residues processed: 114 average time/residue: 0.7356 time to fit residues: 87.2046 Evaluate side-chains 112 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.2980 chunk 74 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.127282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.098959 restraints weight = 7249.159| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.70 r_work: 0.2965 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6612 Z= 0.126 Angle : 0.517 5.117 8868 Z= 0.271 Chirality : 0.040 0.138 1072 Planarity : 0.006 0.062 1020 Dihedral : 13.229 74.040 1072 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.75 % Allowed : 8.13 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.44 (0.31), residues: 752 helix: 2.74 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 0.21 (0.61), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 362 TYR 0.011 0.001 TYR D 323 PHE 0.025 0.002 PHE D 433 TRP 0.006 0.001 TRP C 289 HIS 0.001 0.001 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6612) covalent geometry : angle 0.51679 ( 8868) hydrogen bonds : bond 0.04679 ( 489) hydrogen bonds : angle 3.12034 ( 1395) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 0.294 Fit side-chains REVERT: A 487 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7391 (ttp-170) REVERT: B 247 GLU cc_start: 0.8078 (pt0) cc_final: 0.7848 (pt0) REVERT: B 487 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7348 (ttp-170) REVERT: C 487 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7370 (ttp-170) REVERT: D 487 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7380 (ttp-170) outliers start: 5 outliers final: 3 residues processed: 125 average time/residue: 0.8121 time to fit residues: 105.1147 Evaluate side-chains 118 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 12 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.123365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.094414 restraints weight = 7235.354| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.67 r_work: 0.2882 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6612 Z= 0.132 Angle : 0.516 5.247 8868 Z= 0.267 Chirality : 0.040 0.141 1072 Planarity : 0.004 0.042 1020 Dihedral : 10.970 63.977 1066 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.75 % Allowed : 10.09 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.45 (0.32), residues: 752 helix: 2.70 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 0.40 (0.61), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 362 TYR 0.009 0.001 TYR B 323 PHE 0.019 0.002 PHE C 244 TRP 0.008 0.001 TRP D 289 HIS 0.002 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6612) covalent geometry : angle 0.51630 ( 8868) hydrogen bonds : bond 0.04719 ( 489) hydrogen bonds : angle 3.09406 ( 1395) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 0.250 Fit side-chains REVERT: A 316 ASP cc_start: 0.8005 (m-30) cc_final: 0.7743 (m-30) REVERT: A 487 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7375 (ttp-170) REVERT: B 247 GLU cc_start: 0.8177 (pt0) cc_final: 0.7909 (pt0) REVERT: B 487 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7379 (ttp-170) REVERT: C 487 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7396 (ttp-170) REVERT: D 487 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7392 (ttp-170) outliers start: 5 outliers final: 3 residues processed: 117 average time/residue: 0.7212 time to fit residues: 88.0189 Evaluate side-chains 113 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 64 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.120676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.091325 restraints weight = 7244.393| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.66 r_work: 0.2840 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6612 Z= 0.156 Angle : 0.529 6.137 8868 Z= 0.278 Chirality : 0.041 0.144 1072 Planarity : 0.004 0.039 1020 Dihedral : 9.970 57.506 1066 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.36 % Allowed : 10.99 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.47 (0.32), residues: 752 helix: 2.68 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 0.58 (0.60), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 362 TYR 0.008 0.001 TYR C 323 PHE 0.018 0.002 PHE D 244 TRP 0.006 0.001 TRP C 289 HIS 0.002 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 6612) covalent geometry : angle 0.52927 ( 8868) hydrogen bonds : bond 0.05164 ( 489) hydrogen bonds : angle 3.16855 ( 1395) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.273 Fit side-chains REVERT: A 380 LYS cc_start: 0.8628 (tppp) cc_final: 0.8135 (tptp) REVERT: A 485 TYR cc_start: 0.9091 (t80) cc_final: 0.8828 (t80) REVERT: A 487 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7361 (ttp-170) REVERT: B 487 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7350 (ttp-170) REVERT: C 395 GLU cc_start: 0.8651 (mp0) cc_final: 0.8418 (mp0) REVERT: C 485 TYR cc_start: 0.9099 (t80) cc_final: 0.8841 (t80) REVERT: C 487 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7357 (ttp-170) REVERT: D 380 LYS cc_start: 0.8647 (tppp) cc_final: 0.8189 (tptp) REVERT: D 395 GLU cc_start: 0.8653 (mp0) cc_final: 0.8418 (mp0) REVERT: D 487 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7369 (ttp-170) outliers start: 9 outliers final: 4 residues processed: 125 average time/residue: 0.6563 time to fit residues: 85.7186 Evaluate side-chains 119 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 59 optimal weight: 0.2980 chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.121479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.092646 restraints weight = 7278.072| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.67 r_work: 0.2860 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6612 Z= 0.124 Angle : 0.481 5.571 8868 Z= 0.251 Chirality : 0.039 0.140 1072 Planarity : 0.004 0.033 1020 Dihedral : 8.798 57.623 1066 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.51 % Allowed : 12.35 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.50 (0.32), residues: 752 helix: 2.72 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.24 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 362 TYR 0.005 0.001 TYR A 323 PHE 0.022 0.001 PHE B 244 TRP 0.005 0.001 TRP D 454 HIS 0.002 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6612) covalent geometry : angle 0.48118 ( 8868) hydrogen bonds : bond 0.04566 ( 489) hydrogen bonds : angle 3.05130 ( 1395) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.218 Fit side-chains REVERT: A 487 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7379 (ttp-170) REVERT: B 247 GLU cc_start: 0.8256 (pt0) cc_final: 0.7973 (pt0) REVERT: B 487 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7353 (ttp-170) REVERT: C 487 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7388 (ttp-170) REVERT: D 487 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7391 (ttp-170) outliers start: 10 outliers final: 2 residues processed: 119 average time/residue: 0.5139 time to fit residues: 63.8044 Evaluate side-chains 112 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 10 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.120797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.091466 restraints weight = 7297.464| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.67 r_work: 0.2845 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6612 Z= 0.140 Angle : 0.497 6.040 8868 Z= 0.261 Chirality : 0.040 0.141 1072 Planarity : 0.004 0.032 1020 Dihedral : 8.504 57.778 1064 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.96 % Allowed : 14.16 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.53 (0.32), residues: 752 helix: 2.73 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.29 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 362 TYR 0.006 0.001 TYR C 323 PHE 0.018 0.001 PHE B 244 TRP 0.006 0.001 TRP B 454 HIS 0.002 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6612) covalent geometry : angle 0.49728 ( 8868) hydrogen bonds : bond 0.04906 ( 489) hydrogen bonds : angle 3.11350 ( 1395) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.270 Fit side-chains REVERT: A 487 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7350 (ttp-170) REVERT: B 247 GLU cc_start: 0.8235 (pt0) cc_final: 0.7981 (pt0) REVERT: B 487 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7341 (ttp-170) REVERT: C 487 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7355 (ttp-170) REVERT: D 487 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7368 (ttp-170) outliers start: 13 outliers final: 1 residues processed: 116 average time/residue: 0.6530 time to fit residues: 79.0429 Evaluate side-chains 111 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 59 optimal weight: 0.0000 chunk 63 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.122558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.093273 restraints weight = 7265.637| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.70 r_work: 0.2874 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6612 Z= 0.112 Angle : 0.461 5.114 8868 Z= 0.241 Chirality : 0.038 0.136 1072 Planarity : 0.004 0.030 1020 Dihedral : 7.914 58.338 1062 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.20 % Allowed : 15.21 % Favored : 83.58 % 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 aren not related in a simple way. whole: 3.66 (0.32), residues: 752 helix: 2.83 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.28 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 362 TYR 0.005 0.001 TYR B 485 PHE 0.021 0.001 PHE B 244 TRP 0.005 0.001 TRP D 454 HIS 0.001 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 6612) covalent geometry : angle 0.46093 ( 8868) hydrogen bonds : bond 0.04302 ( 489) hydrogen bonds : angle 3.00069 ( 1395) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.178 Fit side-chains REVERT: A 487 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7318 (ttp-170) REVERT: B 487 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7350 (ttp-170) REVERT: C 487 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7352 (ttp-170) REVERT: D 487 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7368 (ttp-170) outliers start: 8 outliers final: 3 residues processed: 115 average time/residue: 0.6851 time to fit residues: 82.0627 Evaluate side-chains 113 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 61 optimal weight: 0.0070 chunk 44 optimal weight: 6.9990 chunk 45 optimal weight: 0.1980 chunk 38 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.123223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.093641 restraints weight = 7321.044| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.73 r_work: 0.2880 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6612 Z= 0.109 Angle : 0.457 5.347 8868 Z= 0.239 Chirality : 0.038 0.134 1072 Planarity : 0.004 0.030 1020 Dihedral : 7.599 58.662 1060 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.96 % Allowed : 14.16 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.71 (0.32), residues: 752 helix: 2.86 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.27 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 362 TYR 0.005 0.001 TYR B 485 PHE 0.019 0.001 PHE B 244 TRP 0.005 0.001 TRP D 454 HIS 0.001 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 6612) covalent geometry : angle 0.45665 ( 8868) hydrogen bonds : bond 0.04213 ( 489) hydrogen bonds : angle 2.94925 ( 1395) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.198 Fit side-chains REVERT: A 487 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7321 (ttp-170) REVERT: B 487 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7351 (ttp-170) REVERT: C 487 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7362 (ttp-170) REVERT: D 487 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7368 (ttp-170) outliers start: 13 outliers final: 5 residues processed: 115 average time/residue: 0.6440 time to fit residues: 77.1446 Evaluate side-chains 117 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 75 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 42 optimal weight: 0.0470 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.122728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.093764 restraints weight = 7347.956| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.72 r_work: 0.2882 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6612 Z= 0.109 Angle : 0.455 4.875 8868 Z= 0.237 Chirality : 0.038 0.133 1072 Planarity : 0.004 0.030 1020 Dihedral : 7.483 59.119 1060 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.36 % Allowed : 14.91 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.72 (0.32), residues: 752 helix: 2.87 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.25 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 368 TYR 0.005 0.001 TYR B 323 PHE 0.020 0.001 PHE B 244 TRP 0.005 0.001 TRP D 454 HIS 0.001 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 6612) covalent geometry : angle 0.45493 ( 8868) hydrogen bonds : bond 0.04169 ( 489) hydrogen bonds : angle 2.94401 ( 1395) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.210 Fit side-chains REVERT: A 380 LYS cc_start: 0.8681 (tppp) cc_final: 0.8179 (tptp) REVERT: A 487 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7354 (ttp-170) REVERT: B 487 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7368 (ttp-170) REVERT: C 380 LYS cc_start: 0.8675 (tppp) cc_final: 0.8132 (tptp) REVERT: C 487 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7373 (ttp-170) REVERT: D 487 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7380 (ttp-170) outliers start: 9 outliers final: 5 residues processed: 116 average time/residue: 0.5777 time to fit residues: 70.1772 Evaluate side-chains 118 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.118421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.089018 restraints weight = 7203.078| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.68 r_work: 0.2805 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 6612 Z= 0.197 Angle : 0.554 6.896 8868 Z= 0.293 Chirality : 0.042 0.147 1072 Planarity : 0.004 0.029 1020 Dihedral : 8.646 56.867 1060 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.36 % Allowed : 14.91 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.57 (0.32), residues: 752 helix: 2.72 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 0.81 (0.62), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 368 TYR 0.007 0.001 TYR C 415 PHE 0.018 0.002 PHE C 244 TRP 0.006 0.002 TRP B 454 HIS 0.003 0.002 HIS D 486 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 6612) covalent geometry : angle 0.55374 ( 8868) hydrogen bonds : bond 0.05651 ( 489) hydrogen bonds : angle 3.24439 ( 1395) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.227 Fit side-chains REVERT: A 380 LYS cc_start: 0.8684 (tppp) cc_final: 0.8142 (tptp) REVERT: A 487 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7396 (ttp-170) REVERT: B 380 LYS cc_start: 0.8687 (tppp) cc_final: 0.8147 (tptp) REVERT: B 487 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7385 (ttp-170) REVERT: C 380 LYS cc_start: 0.8681 (tppp) cc_final: 0.8145 (tptp) REVERT: C 487 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7404 (ttp-170) REVERT: D 380 LYS cc_start: 0.8682 (tppp) cc_final: 0.8143 (tptp) REVERT: D 487 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7401 (ttp-170) outliers start: 9 outliers final: 2 residues processed: 115 average time/residue: 0.6562 time to fit residues: 78.6073 Evaluate side-chains 116 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.120826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.091468 restraints weight = 7198.737| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.65 r_work: 0.2846 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6612 Z= 0.132 Angle : 0.488 5.669 8868 Z= 0.258 Chirality : 0.039 0.141 1072 Planarity : 0.004 0.030 1020 Dihedral : 8.137 58.334 1060 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.90 % Allowed : 15.36 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.58 (0.32), residues: 752 helix: 2.75 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 0.66 (0.61), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 362 TYR 0.005 0.001 TYR B 323 PHE 0.020 0.001 PHE B 244 TRP 0.007 0.001 TRP D 454 HIS 0.002 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6612) covalent geometry : angle 0.48832 ( 8868) hydrogen bonds : bond 0.04763 ( 489) hydrogen bonds : angle 3.13833 ( 1395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2973.98 seconds wall clock time: 51 minutes 17.25 seconds (3077.25 seconds total)