Starting phenix.real_space_refine on Mon Apr 28 01:24:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8teo_41193/04_2025/8teo_41193.cif Found real_map, /net/cci-nas-00/data/ceres_data/8teo_41193/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8teo_41193/04_2025/8teo_41193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8teo_41193/04_2025/8teo_41193.map" model { file = "/net/cci-nas-00/data/ceres_data/8teo_41193/04_2025/8teo_41193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8teo_41193/04_2025/8teo_41193.cif" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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, 'GLU:plan': 2, 'ARG:plan': 1, '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, 'GLU:plan': 2, 'ARG:plan': 1, '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, 'GLU:plan': 2, 'ARG:plan': 1, '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, 'GLU:plan': 2, 'ARG:plan': 1, '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-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 7} 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-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 7} 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-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 7} 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-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 7} 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: 4.85, per 1000 atoms: 0.75 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: 1.73 Conformation dependent library (CDL) restraints added in 905.7 milliseconds 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: 0.63 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: 1.67 Time building geometry restraints manager: 2.01 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.330 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.340 ------------------------------------------------------------------------------- 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 : 8.59 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.007 0.001 TRP B 289 HIS 0.002 0.001 HIS B 486 PHE 0.033 0.002 PHE A 433 TYR 0.008 0.001 TYR B 415 ARG 0.008 0.001 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.12783 ( 489) hydrogen bonds : angle 3.69670 ( 1395) covalent geometry : bond 0.00911 ( 6612) covalent geometry : angle 0.96746 ( 8868) *********************** 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 : 0.690 Fit side-chains outliers start: 4 outliers final: 8 residues processed: 114 average time/residue: 1.3555 time to fit residues: 161.2694 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 : 0.666 ------------------------------------------------------------------------------- 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 64 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 0.0980 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 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 = 0.3516 r_free = 0.3516 target = 0.126126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.097135 restraints weight = 7135.474| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.63 r_work: 0.2934 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6612 Z= 0.141 Angle : 0.541 5.579 8868 Z= 0.285 Chirality : 0.041 0.146 1072 Planarity : 0.006 0.060 1020 Dihedral : 13.320 75.922 1072 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.75 % Allowed : 7.98 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.31), residues: 752 helix: 2.74 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 0.57 (0.61), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 289 HIS 0.002 0.001 HIS D 378 PHE 0.026 0.002 PHE C 433 TYR 0.011 0.001 TYR D 323 ARG 0.004 0.001 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.04900 ( 489) hydrogen bonds : angle 3.18252 ( 1395) covalent geometry : bond 0.00311 ( 6612) covalent geometry : angle 0.54088 ( 8868) *********************** 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 : 0.752 Fit side-chains REVERT: A 487 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7365 (ttp-170) REVERT: B 247 GLU cc_start: 0.8117 (pt0) cc_final: 0.7869 (pt0) REVERT: B 487 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7334 (ttp-170) REVERT: C 487 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7342 (ttp-170) REVERT: D 487 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7360 (ttp-170) outliers start: 5 outliers final: 4 residues processed: 125 average time/residue: 1.5949 time to fit residues: 206.9840 Evaluate side-chains 118 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE 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 16 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 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 = 0.3481 r_free = 0.3481 target = 0.123602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.094222 restraints weight = 7213.905| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.67 r_work: 0.2884 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1650 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= 0.131 Angle : 0.510 5.096 8868 Z= 0.265 Chirality : 0.040 0.135 1072 Planarity : 0.004 0.042 1020 Dihedral : 10.947 63.707 1068 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.75 % Allowed : 9.19 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.32), residues: 752 helix: 2.72 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 0.42 (0.60), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 289 HIS 0.001 0.001 HIS B 378 PHE 0.019 0.002 PHE D 244 TYR 0.008 0.001 TYR B 323 ARG 0.005 0.001 ARG D 362 Details of bonding type rmsd hydrogen bonds : bond 0.04699 ( 489) hydrogen bonds : angle 3.11437 ( 1395) covalent geometry : bond 0.00284 ( 6612) covalent geometry : angle 0.50978 ( 8868) *********************** 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 123 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.749 Fit side-chains REVERT: A 487 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7350 (ttp-170) REVERT: B 247 GLU cc_start: 0.8170 (pt0) cc_final: 0.7888 (pt0) REVERT: B 487 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7358 (ttp-170) REVERT: C 487 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7377 (ttp-170) REVERT: D 487 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7368 (ttp-170) outliers start: 5 outliers final: 4 residues processed: 118 average time/residue: 1.3130 time to fit residues: 161.9466 Evaluate side-chains 114 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE 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 73 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.123038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.093621 restraints weight = 7271.562| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.71 r_work: 0.2878 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1859 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= 0.123 Angle : 0.482 5.186 8868 Z= 0.251 Chirality : 0.039 0.136 1072 Planarity : 0.004 0.038 1020 Dihedral : 9.662 58.064 1068 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.20 % Allowed : 10.99 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.32), residues: 752 helix: 2.73 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.26 (0.62), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 289 HIS 0.002 0.001 HIS C 378 PHE 0.018 0.001 PHE C 244 TYR 0.007 0.001 TYR C 323 ARG 0.005 0.000 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.04512 ( 489) hydrogen bonds : angle 3.04741 ( 1395) covalent geometry : bond 0.00261 ( 6612) covalent geometry : angle 0.48206 ( 8868) *********************** 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: 8 poor density : 121 time to evaluate : 0.678 Fit side-chains REVERT: A 487 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7340 (ttp-170) REVERT: B 487 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7358 (ttp-170) REVERT: C 487 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7373 (ttp-170) REVERT: D 487 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7373 (ttp-170) outliers start: 8 outliers final: 4 residues processed: 125 average time/residue: 1.1732 time to fit residues: 153.9265 Evaluate side-chains 121 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE 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 69 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 31 optimal weight: 0.0040 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.123524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.094472 restraints weight = 7240.219| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.77 r_work: 0.2890 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1994 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= 0.113 Angle : 0.465 5.165 8868 Z= 0.242 Chirality : 0.039 0.135 1072 Planarity : 0.004 0.033 1020 Dihedral : 8.413 56.708 1068 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.66 % Allowed : 13.70 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.32), residues: 752 helix: 2.84 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.31 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 289 HIS 0.001 0.001 HIS A 378 PHE 0.018 0.001 PHE B 244 TYR 0.006 0.001 TYR A 323 ARG 0.004 0.000 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 489) hydrogen bonds : angle 2.99497 ( 1395) covalent geometry : bond 0.00235 ( 6612) covalent geometry : angle 0.46543 ( 8868) *********************** 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 124 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.791 Fit side-chains REVERT: A 487 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7351 (ttp-170) REVERT: B 247 GLU cc_start: 0.8207 (pt0) cc_final: 0.7924 (pt0) REVERT: B 487 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7349 (ttp-170) REVERT: C 487 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7366 (ttp-170) REVERT: D 487 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7358 (ttp-170) outliers start: 11 outliers final: 2 residues processed: 117 average time/residue: 1.3693 time to fit residues: 167.4685 Evaluate side-chains 114 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 17 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 0.0980 chunk 46 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.122648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.093297 restraints weight = 7156.259| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.70 r_work: 0.2875 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2078 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= 0.119 Angle : 0.473 5.131 8868 Z= 0.245 Chirality : 0.039 0.136 1072 Planarity : 0.004 0.033 1020 Dihedral : 7.984 57.066 1064 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.51 % Allowed : 14.16 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.32), residues: 752 helix: 2.86 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.26 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 454 HIS 0.001 0.001 HIS A 378 PHE 0.018 0.001 PHE B 244 TYR 0.006 0.001 TYR B 323 ARG 0.003 0.000 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 489) hydrogen bonds : angle 2.99031 ( 1395) covalent geometry : bond 0.00250 ( 6612) covalent geometry : angle 0.47284 ( 8868) *********************** 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 119 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.678 Fit side-chains REVERT: A 487 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7353 (ttp-170) REVERT: B 247 GLU cc_start: 0.8259 (pt0) cc_final: 0.7959 (pt0) REVERT: B 487 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7330 (ttp-170) REVERT: C 487 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7367 (ttp-170) REVERT: D 487 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7340 (ttp-170) outliers start: 10 outliers final: 7 residues processed: 113 average time/residue: 1.2748 time to fit residues: 150.6985 Evaluate side-chains 118 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 231 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 453 VAL 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 6 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 chunk 47 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.123677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.094521 restraints weight = 7207.244| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.66 r_work: 0.2896 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2165 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= 0.108 Angle : 0.453 4.855 8868 Z= 0.235 Chirality : 0.038 0.134 1072 Planarity : 0.004 0.030 1020 Dihedral : 7.611 56.950 1064 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.36 % Allowed : 13.70 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.32), residues: 752 helix: 2.91 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.26 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 454 HIS 0.001 0.001 HIS D 378 PHE 0.018 0.001 PHE C 244 TYR 0.005 0.001 TYR B 483 ARG 0.003 0.000 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 489) hydrogen bonds : angle 2.92953 ( 1395) covalent geometry : bond 0.00222 ( 6612) covalent geometry : angle 0.45335 ( 8868) *********************** 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 125 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.739 Fit side-chains REVERT: A 487 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7327 (ttp-170) REVERT: B 247 GLU cc_start: 0.8222 (pt0) cc_final: 0.7921 (pt0) REVERT: B 487 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7354 (ttp-170) REVERT: C 487 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7370 (ttp-170) REVERT: D 487 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7363 (ttp-170) outliers start: 9 outliers final: 6 residues processed: 120 average time/residue: 1.2871 time to fit residues: 161.6822 Evaluate side-chains 120 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 231 ILE Chi-restraints excluded: chain B residue 281 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 75 optimal weight: 0.0170 chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.123224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.094409 restraints weight = 7215.796| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.68 r_work: 0.2892 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2164 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= 0.108 Angle : 0.454 4.851 8868 Z= 0.236 Chirality : 0.038 0.133 1072 Planarity : 0.004 0.030 1020 Dihedral : 7.458 57.123 1062 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.81 % Allowed : 13.10 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.79 (0.32), residues: 752 helix: 2.93 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.23 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 454 HIS 0.001 0.001 HIS A 378 PHE 0.017 0.001 PHE B 244 TYR 0.005 0.001 TYR D 483 ARG 0.003 0.000 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 489) hydrogen bonds : angle 2.91557 ( 1395) covalent geometry : bond 0.00222 ( 6612) covalent geometry : angle 0.45365 ( 8868) *********************** 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: 12 poor density : 111 time to evaluate : 0.738 Fit side-chains REVERT: A 487 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7363 (ttp-170) REVERT: B 247 GLU cc_start: 0.8192 (pt0) cc_final: 0.7957 (pt0) REVERT: B 487 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7380 (ttp-170) REVERT: C 487 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7397 (ttp-170) REVERT: D 487 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7379 (ttp-170) outliers start: 12 outliers final: 6 residues processed: 118 average time/residue: 1.3016 time to fit residues: 160.7441 Evaluate side-chains 119 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 231 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 32 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.121740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.092574 restraints weight = 7300.605| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.67 r_work: 0.2865 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2266 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= 0.126 Angle : 0.479 5.468 8868 Z= 0.251 Chirality : 0.039 0.139 1072 Planarity : 0.004 0.029 1020 Dihedral : 7.756 58.921 1062 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.51 % Allowed : 13.55 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.32), residues: 752 helix: 2.85 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.34 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 454 HIS 0.002 0.001 HIS D 378 PHE 0.016 0.001 PHE B 244 TYR 0.005 0.001 TYR A 323 ARG 0.003 0.000 ARG D 368 Details of bonding type rmsd hydrogen bonds : bond 0.04587 ( 489) hydrogen bonds : angle 2.99928 ( 1395) covalent geometry : bond 0.00272 ( 6612) covalent geometry : angle 0.47941 ( 8868) *********************** 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 122 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.689 Fit side-chains REVERT: A 380 LYS cc_start: 0.8657 (tppp) cc_final: 0.8152 (tptp) REVERT: A 487 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7353 (ttp-170) REVERT: B 247 GLU cc_start: 0.8251 (pt0) cc_final: 0.7938 (pt0) REVERT: B 487 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7343 (ttp-170) REVERT: C 380 LYS cc_start: 0.8645 (tppp) cc_final: 0.8129 (tptp) REVERT: C 487 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7379 (ttp-170) REVERT: D 487 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7358 (ttp-170) outliers start: 10 outliers final: 7 residues processed: 116 average time/residue: 1.5640 time to fit residues: 189.7717 Evaluate side-chains 119 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 281 LEU 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 72 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 62 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 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 = 0.3474 r_free = 0.3474 target = 0.122884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.093733 restraints weight = 7339.380| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.68 r_work: 0.2881 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2284 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= 0.113 Angle : 0.460 4.981 8868 Z= 0.240 Chirality : 0.038 0.136 1072 Planarity : 0.004 0.030 1020 Dihedral : 7.561 58.780 1062 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.81 % Allowed : 13.70 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.32), residues: 752 helix: 2.89 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.24 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 454 HIS 0.001 0.001 HIS A 378 PHE 0.018 0.001 PHE B 244 TYR 0.005 0.001 TYR A 323 ARG 0.003 0.000 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 489) hydrogen bonds : angle 2.95459 ( 1395) covalent geometry : bond 0.00235 ( 6612) covalent geometry : angle 0.46002 ( 8868) ********************** 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 121 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.739 Fit side-chains REVERT: A 380 LYS cc_start: 0.8637 (tppp) cc_final: 0.8152 (tptp) REVERT: A 487 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7349 (ttp-170) REVERT: B 247 GLU cc_start: 0.8239 (pt0) cc_final: 0.7966 (pt0) REVERT: B 380 LYS cc_start: 0.8648 (tppp) cc_final: 0.8136 (tptp) REVERT: B 487 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7355 (ttp-170) REVERT: C 380 LYS cc_start: 0.8654 (tppp) cc_final: 0.8156 (tptp) REVERT: C 487 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7365 (ttp-170) REVERT: D 380 LYS cc_start: 0.8652 (tppp) cc_final: 0.8144 (tptp) REVERT: D 487 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7353 (ttp-170) outliers start: 12 outliers final: 8 residues processed: 113 average time/residue: 1.4698 time to fit residues: 173.5077 Evaluate side-chains 118 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 281 LEU 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 51 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.121486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.091951 restraints weight = 7365.149| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.72 r_work: 0.2853 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2361 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= 0.129 Angle : 0.478 5.566 8868 Z= 0.251 Chirality : 0.039 0.139 1072 Planarity : 0.004 0.028 1020 Dihedral : 7.690 58.770 1060 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.81 % Allowed : 13.70 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.32), residues: 752 helix: 2.84 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.34 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 454 HIS 0.002 0.001 HIS D 378 PHE 0.016 0.001 PHE B 244 TYR 0.005 0.001 TYR A 323 ARG 0.002 0.000 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 489) hydrogen bonds : angle 3.02119 ( 1395) covalent geometry : bond 0.00280 ( 6612) covalent geometry : angle 0.47836 ( 8868) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6459.96 seconds wall clock time: 111 minutes 54.89 seconds (6714.89 seconds total)