Starting phenix.real_space_refine on Tue Feb 11 22:59:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8teo_41193/02_2025/8teo_41193.cif Found real_map, /net/cci-nas-00/data/ceres_data/8teo_41193/02_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_41193/02_2025/8teo_41193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8teo_41193/02_2025/8teo_41193.map" model { file = "/net/cci-nas-00/data/ceres_data/8teo_41193/02_2025/8teo_41193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8teo_41193/02_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-5592/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: 4.61, per 1000 atoms: 0.71 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: 1.58 Conformation dependent library (CDL) restraints added in 814.3 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: 0.59 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: 1.73 Time building geometry restraints manager: 1.83 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: 1.130 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.080 Find NCS groups from input model: 0.330 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:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.650 ------------------------------------------------------------------------------- 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= 0.614 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 *********************** 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 : 0.695 Fit side-chains outliers start: 4 outliers final: 8 residues processed: 114 average time/residue: 1.4760 time to fit residues: 175.1283 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 : 0.662 ------------------------------------------------------------------------------- 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: 0.2936 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- 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= 0.200 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 *********************** 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 : 0.765 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: 0.7868 (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: 0.7361 (ttp-170) outliers start: 5 outliers final: 4 residues processed: 125 average time/residue: 1.6898 time to fit residues: 219.1589 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 : 0.701 ------------------------------------------------------------------------------- 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: 0.6980 chunk 46 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.124241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.094903 restraints weight = 7215.909| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.67 r_work: 0.2891 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1618 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= 0.176 Angle : 0.503 4.935 8868 Z= 0.261 Chirality : 0.040 0.137 1072 Planarity : 0.004 0.042 1020 Dihedral : 10.904 63.511 1068 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.75 % Allowed : 8.89 % Favored : 90.36 % 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: 3.49 (0.32), residues: 752 helix: 2.74 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 0.40 (0.60), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 289 HIS 0.001 0.001 HIS A 378 PHE 0.018 0.001 PHE D 244 TYR 0.008 0.001 TYR B 323 ARG 0.006 0.001 ARG D 362 *********************** 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 : 0.685 Fit side-chains REVERT: A 487 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7361 (ttp-170) REVERT: B 247 GLU cc_start: 0.8155 (pt0) cc_final: 0.7871 (pt0) REVERT: B 316 ASP cc_start: 0.7968 (m-30) cc_final: 0.7748 (m-30) REVERT: B 487 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7362 (ttp-170) REVERT: C 487 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7375 (ttp-170) REVERT: D 487 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7367 (ttp-170) outliers start: 5 outliers final: 4 residues processed: 118 average time/residue: 1.3956 time to fit residues: 171.8508 Evaluate side-chains 115 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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: 4.9990 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.122469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.093190 restraints weight = 7273.204| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.67 r_work: 0.2873 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1911 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= 0.178 Angle : 0.491 5.328 8868 Z= 0.256 Chirality : 0.040 0.137 1072 Planarity : 0.004 0.037 1020 Dihedral : 9.523 57.907 1068 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.20 % Allowed : 10.84 % Favored : 87.95 % 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 (0.32), residues: 752 helix: 2.72 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.33 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 289 HIS 0.002 0.001 HIS B 378 PHE 0.019 0.001 PHE C 244 TYR 0.008 0.001 TYR A 323 ARG 0.004 0.000 ARG B 362 *********************** 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 : 0.729 Fit side-chains REVERT: A 487 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7338 (ttp-170) REVERT: B 487 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7359 (ttp-170) REVERT: C 487 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7375 (ttp-170) REVERT: D 487 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7365 (ttp-170) outliers start: 8 outliers final: 3 residues processed: 125 average time/residue: 1.2808 time to fit residues: 167.8680 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 : 0.709 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 26 optimal weight: 0.0170 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 0.0970 overall best weight: 0.5016 ------------------------------------------------------------------------------- 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 = 0.123354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.094720 restraints weight = 7247.033| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.77 r_work: 0.2897 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2000 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= 0.143 Angle : 0.460 4.942 8868 Z= 0.238 Chirality : 0.038 0.134 1072 Planarity : 0.004 0.033 1020 Dihedral : 8.308 56.939 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 : 1.66 % Allowed : 13.55 % Favored : 84.79 % 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 : 0.30 (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 0.005 0.001 TYR A 323 ARG 0.003 0.000 ARG B 362 *********************** 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 123 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.704 Fit side-chains REVERT: A 487 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7342 (ttp-170) REVERT: B 247 GLU cc_start: 0.8220 (pt0) cc_final: 0.7934 (pt0) REVERT: B 487 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7363 (ttp-170) REVERT: C 487 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7375 (ttp-170) REVERT: D 487 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7365 (ttp-170) outliers start: 11 outliers final: 2 residues processed: 116 average time/residue: 1.3690 time to fit residues: 165.9857 Evaluate side-chains 113 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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: 0.8980 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.121187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.091853 restraints weight = 7164.932| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.66 r_work: 0.2849 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2178 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= 0.202 Angle : 0.499 5.849 8868 Z= 0.260 Chirality : 0.040 0.140 1072 Planarity : 0.004 0.032 1020 Dihedral : 8.360 58.358 1064 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.20 % Allowed : 14.46 % 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: 3.61 (0.32), residues: 752 helix: 2.78 (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 0.005 0.001 TRP D 454 HIS 0.002 0.001 HIS C 378 PHE 0.017 0.001 PHE B 244 TYR 0.006 0.001 TYR B 323 ARG 0.003 0.000 ARG B 362 *********************** 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: 8 poor density : 111 time to evaluate : 0.676 Fit side-chains REVERT: A 487 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7348 (ttp-170) REVERT: B 247 GLU cc_start: 0.8290 (pt0) cc_final: 0.7990 (pt0) REVERT: B 487 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7351 (ttp-170) REVERT: C 487 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7357 (ttp-170) REVERT: D 487 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7364 (ttp-170) outliers start: 8 outliers final: 2 residues processed: 115 average time/residue: 1.4096 time to fit residues: 169.1218 Evaluate side-chains 115 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 6 optimal weight: 0.0370 chunk 25 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.122574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.093450 restraints weight = 7205.030| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.67 r_work: 0.2880 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2198 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= 0.149 Angle : 0.462 5.075 8868 Z= 0.240 Chirality : 0.038 0.138 1072 Planarity : 0.004 0.031 1020 Dihedral : 7.868 57.469 1064 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.20 % Allowed : 14.46 % 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 : 0.28 (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 A 378 PHE 0.019 0.001 PHE B 244 TYR 0.005 0.001 TYR B 323 ARG 0.003 0.000 ARG B 362 *********************** 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 123 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.700 Fit side-chains REVERT: A 487 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7332 (ttp-170) REVERT: B 247 GLU cc_start: 0.8229 (pt0) cc_final: 0.7963 (pt0) REVERT: B 487 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7338 (ttp-170) REVERT: C 487 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7351 (ttp-170) REVERT: D 487 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7347 (ttp-170) outliers start: 8 outliers final: 4 residues processed: 119 average time/residue: 1.3116 time to fit residues: 163.3206 Evaluate side-chains 116 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.121428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.092277 restraints weight = 7202.045| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.66 r_work: 0.2859 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2305 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= 0.179 Angle : 0.479 5.570 8868 Z= 0.251 Chirality : 0.039 0.138 1072 Planarity : 0.004 0.030 1020 Dihedral : 7.925 58.915 1060 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.96 % Allowed : 13.70 % 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: 3.67 (0.32), residues: 752 helix: 2.81 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.39 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 454 HIS 0.002 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 C 368 *********************** 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 122 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.695 Fit side-chains REVERT: A 487 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7346 (ttp-170) REVERT: B 247 GLU cc_start: 0.8262 (pt0) cc_final: 0.7979 (pt0) REVERT: B 487 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7327 (ttp-170) REVERT: C 487 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7366 (ttp-170) REVERT: D 487 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7357 (ttp-170) outliers start: 13 outliers final: 5 residues processed: 117 average time/residue: 1.4469 time to fit residues: 176.8100 Evaluate side-chains 115 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 32 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 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 = 0.3468 r_free = 0.3468 target = 0.122169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.093378 restraints weight = 7311.155| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.68 r_work: 0.2875 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2292 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= 0.152 Angle : 0.461 5.024 8868 Z= 0.241 Chirality : 0.038 0.136 1072 Planarity : 0.004 0.030 1020 Dihedral : 7.633 58.868 1060 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.20 % Allowed : 15.06 % 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 (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: 2.86 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.28 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 454 HIS 0.001 0.001 HIS D 378 PHE 0.019 0.001 PHE A 244 TYR 0.004 0.001 TYR A 323 ARG 0.003 0.000 ARG B 362 *********************** 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 118 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.717 Fit side-chains REVERT: A 487 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7349 (ttp-170) REVERT: B 247 GLU cc_start: 0.8250 (pt0) cc_final: 0.7978 (pt0) REVERT: B 487 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7353 (ttp-170) REVERT: C 380 LYS cc_start: 0.8677 (tppp) cc_final: 0.8184 (tptp) REVERT: C 487 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7370 (ttp-170) REVERT: D 487 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7368 (ttp-170) outliers start: 8 outliers final: 4 residues processed: 114 average time/residue: 1.3726 time to fit residues: 163.4758 Evaluate side-chains 115 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 19 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.0870 overall best weight: 0.9160 ------------------------------------------------------------------------------- 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 = 0.120587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.091342 restraints weight = 7313.733| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.67 r_work: 0.2846 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2389 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= 0.199 Angle : 0.494 5.860 8868 Z= 0.260 Chirality : 0.040 0.141 1072 Planarity : 0.004 0.030 1020 Dihedral : 7.926 58.449 1060 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.51 % Allowed : 14.76 % 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 (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: 3.63 (0.32), residues: 752 helix: 2.78 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.41 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 454 HIS 0.002 0.001 HIS A 378 PHE 0.017 0.001 PHE B 244 TYR 0.006 0.001 TYR A 323 ARG 0.002 0.000 ARG B 362 ********************** 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 122 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.556 Fit side-chains REVERT: A 380 LYS cc_start: 0.8655 (tppp) cc_final: 0.8150 (tptp) REVERT: A 487 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7354 (ttp-170) REVERT: B 247 GLU cc_start: 0.8275 (pt0) cc_final: 0.7961 (pt0) REVERT: B 380 LYS cc_start: 0.8666 (tppp) cc_final: 0.8121 (tptp) REVERT: B 487 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7348 (ttp-170) REVERT: C 380 LYS cc_start: 0.8646 (tppp) cc_final: 0.8145 (tptp) REVERT: C 487 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7364 (ttp-170) REVERT: D 380 LYS cc_start: 0.8665 (tppp) cc_final: 0.8154 (tptp) REVERT: D 487 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7357 (ttp-170) outliers start: 10 outliers final: 6 residues processed: 116 average time/residue: 1.4178 time to fit residues: 171.6348 Evaluate side-chains 121 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 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 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: 0.2980 chunk 47 optimal weight: 0.8980 chunk 63 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.092609 restraints weight = 7370.856| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.72 r_work: 0.2864 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2386 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= 0.159 Angle : 0.467 5.204 8868 Z= 0.245 Chirality : 0.039 0.136 1072 Planarity : 0.004 0.030 1020 Dihedral : 7.695 59.425 1060 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.66 % Allowed : 14.61 % 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 (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: 3.66 (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 TRP 0.006 0.001 TRP B 454 HIS 0.002 0.001 HIS A 378 PHE 0.019 0.001 PHE B 244 TYR 0.005 0.001 TYR A 323 ARG 0.003 0.000 ARG B 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6065.49 seconds wall clock time: 107 minutes 26.60 seconds (6446.60 seconds total)