Starting phenix.real_space_refine on Tue Mar 3 15:45:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sj1_25152/03_2026/7sj1_25152.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sj1_25152/03_2026/7sj1_25152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sj1_25152/03_2026/7sj1_25152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sj1_25152/03_2026/7sj1_25152.map" model { file = "/net/cci-nas-00/data/ceres_data/7sj1_25152/03_2026/7sj1_25152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sj1_25152/03_2026/7sj1_25152.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 4456 2.51 5 N 956 2.21 5 O 1021 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6463 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1527 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1527 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1527 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1527 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 90 Unusual residues: {' K': 2, 'POV': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 6, 'POV:plan-3': 6} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 6, 'POV:plan-3': 6} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 6, 'POV:plan-3': 6} Unresolved non-hydrogen planarities: 67 Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 6, 'POV:plan-3': 6} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.47, per 1000 atoms: 0.23 Number of scatterers: 6463 At special positions: 0 Unit cell: (95.46, 95.46, 64.5, 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 1021 8.00 N 956 7.00 C 4456 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 179.2 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 86.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 226 through 247 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 378 Processing helix chain 'A' and resid 380 through 392 Processing helix chain 'A' and resid 392 through 418 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: 4.374A pdb=" N ILE A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 247 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 378 Processing helix chain 'B' and resid 380 through 392 Processing helix chain 'B' and resid 392 through 418 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: 4.375A pdb=" N ILE B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 247 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 378 Processing helix chain 'C' and resid 380 through 392 Processing helix chain 'C' and resid 392 through 418 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: 4.375A pdb=" N ILE C 477 " --> pdb=" O PRO C 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 247 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 378 Processing helix chain 'D' and resid 380 through 392 Processing helix chain 'D' and resid 392 through 418 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: 4.374A pdb=" N ILE D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) 489 hydrogen bonds defined for protein. 1383 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 888 1.31 - 1.44: 1768 1.44 - 1.56: 3799 1.56 - 1.68: 69 1.68 - 1.81: 44 Bond restraints: 6568 Sorted by residual: bond pdb=" C21 POV C 706 " pdb=" O22 POV C 706 " ideal model delta sigma weight residual 1.205 1.415 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C21 POV B 707 " pdb=" O22 POV B 707 " ideal model delta sigma weight residual 1.205 1.414 -0.209 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C21 POV A 705 " pdb=" O22 POV A 705 " ideal model delta sigma weight residual 1.205 1.414 -0.209 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C21 POV D 708 " pdb=" O22 POV D 708 " ideal model delta sigma weight residual 1.205 1.414 -0.209 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C21 POV A 705 " pdb=" O21 POV A 705 " ideal model delta sigma weight residual 1.330 1.199 0.131 2.00e-02 2.50e+03 4.31e+01 ... (remaining 6563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 8437 1.97 - 3.94: 180 3.94 - 5.91: 151 5.91 - 7.88: 16 7.88 - 9.85: 20 Bond angle restraints: 8804 Sorted by residual: angle pdb=" C THR B 449 " pdb=" N PRO B 450 " pdb=" CA PRO B 450 " ideal model delta sigma weight residual 119.56 115.15 4.41 1.02e+00 9.61e-01 1.87e+01 angle pdb=" C THR D 449 " pdb=" N PRO D 450 " pdb=" CA PRO D 450 " ideal model delta sigma weight residual 119.56 115.16 4.40 1.02e+00 9.61e-01 1.86e+01 angle pdb=" C THR A 449 " pdb=" N PRO A 450 " pdb=" CA PRO A 450 " ideal model delta sigma weight residual 119.56 115.18 4.38 1.02e+00 9.61e-01 1.84e+01 angle pdb=" C THR C 449 " pdb=" N PRO C 450 " pdb=" CA PRO C 450 " ideal model delta sigma weight residual 119.56 115.20 4.36 1.02e+00 9.61e-01 1.82e+01 angle pdb=" C32 POV B 708 " pdb=" C31 POV B 708 " pdb=" O31 POV B 708 " ideal model delta sigma weight residual 110.66 120.51 -9.85 3.00e+00 1.11e-01 1.08e+01 ... (remaining 8799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.19: 3548 24.19 - 48.38: 232 48.38 - 72.57: 52 72.57 - 96.76: 0 96.76 - 120.95: 4 Dihedral angle restraints: 3836 sinusoidal: 1568 harmonic: 2268 Sorted by residual: 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 51.66 120.95 1 3.00e+01 1.11e-03 1.62e+01 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 51.68 120.93 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" C3 POV A 701 " pdb=" C31 POV A 701 " pdb=" O31 POV A 701 " pdb=" C32 POV A 701 " ideal model delta sinusoidal sigma weight residual 172.61 51.69 120.92 1 3.00e+01 1.11e-03 1.61e+01 ... (remaining 3833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 645 0.029 - 0.057: 252 0.057 - 0.086: 125 0.086 - 0.114: 29 0.114 - 0.143: 21 Chirality restraints: 1072 Sorted by residual: chirality pdb=" CA THR C 449 " pdb=" N THR C 449 " pdb=" C THR C 449 " pdb=" CB THR C 449 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA THR D 449 " pdb=" N THR D 449 " pdb=" C THR D 449 " pdb=" CB THR D 449 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA THR B 449 " pdb=" N THR B 449 " pdb=" C THR B 449 " pdb=" CB THR B 449 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 1069 not shown) Planarity restraints: 1016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 433 " -0.013 2.00e-02 2.50e+03 1.27e-02 2.80e+00 pdb=" CG PHE A 433 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 433 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 433 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 433 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 433 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 433 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 433 " -0.013 2.00e-02 2.50e+03 1.26e-02 2.78e+00 pdb=" CG PHE B 433 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE B 433 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 433 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 433 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 433 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 433 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 433 " -0.013 2.00e-02 2.50e+03 1.25e-02 2.72e+00 pdb=" CG PHE C 433 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 433 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 433 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 433 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 433 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 433 " 0.000 2.00e-02 2.50e+03 ... (remaining 1013 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.91: 2430 2.91 - 3.47: 7619 3.47 - 4.02: 10797 4.02 - 4.58: 16371 4.58 - 5.14: 22722 Nonbonded interactions: 59939 Sorted by model distance: nonbonded pdb=" O VAL B 407 " pdb=" OG SER B 411 " model vdw 2.351 3.040 nonbonded pdb=" O VAL A 407 " pdb=" OG SER A 411 " model vdw 2.351 3.040 nonbonded pdb=" O VAL D 407 " pdb=" OG SER D 411 " model vdw 2.351 3.040 nonbonded pdb=" O VAL C 407 " pdb=" OG SER C 411 " model vdw 2.351 3.040 nonbonded pdb=" O THR C 441 " pdb=" OG1 THR C 442 " model vdw 2.365 3.040 ... (remaining 59934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 226 through 489 or (resid 702 and (name C31 or name C32 or \ name C33 or name C34 or name C35)) or (resid 703 through 704 and (name C32 or n \ ame C33 or name C34 or name C35)))) selection = (chain 'B' and (resid 226 through 489 or (resid 702 and (name C31 or name C32 or \ name C33 or name C34 or name C35)) or (resid 703 through 704 and (name C32 or n \ ame C33 or name C34 or name C35)))) selection = (chain 'C' and (resid 226 through 489 or (resid 702 and (name C31 or name C32 or \ name C33 or name C34 or name C35)) or (resid 703 through 704 and (name C32 or n \ ame C33 or name C34 or name C35)))) selection = (chain 'D' and (resid 226 through 489 or (resid 702 and (name C31 or name C32 or \ name C33 or name C34 or name C35)) or (resid 703 through 704 and (name C32 or n \ ame C33 or name C34 or name C35)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.700 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 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 : 0.011 0.210 6568 Z= 0.549 Angle : 1.007 9.847 8804 Z= 0.418 Chirality : 0.041 0.143 1072 Planarity : 0.004 0.037 1016 Dihedral : 16.624 120.953 2356 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.61 % Allowed : 0.15 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.31), residues: 752 helix: 2.17 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.63 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 227 TYR 0.022 0.002 TYR D 485 PHE 0.029 0.002 PHE A 433 TRP 0.005 0.001 TRP B 454 HIS 0.001 0.000 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.01087 ( 6568) covalent geometry : angle 1.00696 ( 8804) hydrogen bonds : bond 0.17624 ( 489) hydrogen bonds : angle 4.43313 ( 1383) *********************** 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 171 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 167 time to evaluate : 0.243 Fit side-chains REVERT: A 285 LEU cc_start: 0.7714 (mm) cc_final: 0.7489 (tp) REVERT: A 312 MET cc_start: 0.6708 (mtt) cc_final: 0.6090 (tpp) REVERT: A 485 TYR cc_start: 0.6842 (t80) cc_final: 0.6158 (t80) REVERT: B 285 LEU cc_start: 0.7702 (mm) cc_final: 0.7491 (tp) REVERT: B 312 MET cc_start: 0.6717 (mtt) cc_final: 0.6102 (tpp) REVERT: B 485 TYR cc_start: 0.6825 (t80) cc_final: 0.6178 (t80) REVERT: C 312 MET cc_start: 0.6700 (mtt) cc_final: 0.6162 (tpp) REVERT: C 485 TYR cc_start: 0.6837 (t80) cc_final: 0.6182 (t80) REVERT: D 312 MET cc_start: 0.6679 (mtt) cc_final: 0.6152 (tpp) REVERT: D 485 TYR cc_start: 0.6858 (t80) cc_final: 0.6268 (t80) outliers start: 4 outliers final: 0 residues processed: 171 average time/residue: 0.5452 time to fit residues: 97.9062 Evaluate side-chains 131 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.1980 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 = 0.4202 r_free = 0.4202 target = 0.179288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134248 restraints weight = 6809.655| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.42 r_work: 0.3405 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6568 Z= 0.145 Angle : 0.576 8.565 8804 Z= 0.299 Chirality : 0.040 0.132 1072 Planarity : 0.005 0.036 1016 Dihedral : 13.270 84.571 1060 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.21 % Allowed : 16.82 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.34 (0.31), residues: 752 helix: 2.48 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 1.18 (0.64), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 487 TYR 0.015 0.002 TYR C 323 PHE 0.020 0.002 PHE C 433 TRP 0.004 0.001 TRP B 435 HIS 0.002 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6568) covalent geometry : angle 0.57612 ( 8804) hydrogen bonds : bond 0.05115 ( 489) hydrogen bonds : angle 3.43907 ( 1383) *********************** 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 129 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.231 Fit side-chains REVERT: A 285 LEU cc_start: 0.7464 (mm) cc_final: 0.7102 (tp) REVERT: B 285 LEU cc_start: 0.7480 (mm) cc_final: 0.7104 (tp) REVERT: C 312 MET cc_start: 0.6236 (mtt) cc_final: 0.5763 (mmt) REVERT: D 312 MET cc_start: 0.6292 (mtt) cc_final: 0.5809 (mmt) outliers start: 8 outliers final: 8 residues processed: 125 average time/residue: 0.6334 time to fit residues: 82.6659 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 : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 393 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.184334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.149109 restraints weight = 6673.880| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.57 r_work: 0.3378 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6568 Z= 0.143 Angle : 0.550 6.476 8804 Z= 0.285 Chirality : 0.040 0.132 1072 Planarity : 0.004 0.037 1016 Dihedral : 11.640 74.964 1060 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.82 % Allowed : 18.64 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.32 (0.31), residues: 752 helix: 2.58 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.64 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 487 TYR 0.008 0.001 TYR A 323 PHE 0.011 0.001 PHE B 433 TRP 0.004 0.001 TRP C 435 HIS 0.002 0.001 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6568) covalent geometry : angle 0.55007 ( 8804) hydrogen bonds : bond 0.04865 ( 489) hydrogen bonds : angle 3.34141 ( 1383) *********************** 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 137 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.230 Fit side-chains REVERT: C 312 MET cc_start: 0.6293 (mtt) cc_final: 0.5874 (mmt) outliers start: 12 outliers final: 0 residues processed: 134 average time/residue: 0.6364 time to fit residues: 89.0338 Evaluate side-chains 109 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.185210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.144692 restraints weight = 6623.703| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.19 r_work: 0.3411 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6568 Z= 0.137 Angle : 0.547 7.634 8804 Z= 0.283 Chirality : 0.040 0.194 1072 Planarity : 0.004 0.037 1016 Dihedral : 10.523 66.098 1060 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.67 % Allowed : 20.45 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.31), residues: 752 helix: 2.65 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.49 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 487 TYR 0.014 0.001 TYR C 323 PHE 0.013 0.001 PHE B 433 TRP 0.004 0.001 TRP B 289 HIS 0.002 0.001 HIS C 486 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6568) covalent geometry : angle 0.54724 ( 8804) hydrogen bonds : bond 0.04625 ( 489) hydrogen bonds : angle 3.28804 ( 1383) *********************** 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 118 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.189 Fit side-chains REVERT: A 312 MET cc_start: 0.6331 (mtt) cc_final: 0.5906 (mmt) REVERT: B 312 MET cc_start: 0.6316 (mtt) cc_final: 0.5886 (mmt) REVERT: C 312 MET cc_start: 0.6304 (mtt) cc_final: 0.5865 (mmt) outliers start: 11 outliers final: 0 residues processed: 118 average time/residue: 0.6940 time to fit residues: 85.0883 Evaluate side-chains 100 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.170915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.124973 restraints weight = 6834.136| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.32 r_work: 0.3384 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6568 Z= 0.144 Angle : 0.568 10.425 8804 Z= 0.292 Chirality : 0.043 0.215 1072 Planarity : 0.005 0.036 1016 Dihedral : 9.771 59.011 1060 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.67 % Allowed : 21.06 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.31), residues: 752 helix: 2.66 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.46 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 487 TYR 0.010 0.001 TYR C 323 PHE 0.012 0.001 PHE A 433 TRP 0.005 0.001 TRP A 289 HIS 0.002 0.001 HIS D 486 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6568) covalent geometry : angle 0.56819 ( 8804) hydrogen bonds : bond 0.04705 ( 489) hydrogen bonds : angle 3.28389 ( 1383) *********************** 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 118 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.249 Fit side-chains REVERT: A 312 MET cc_start: 0.6336 (mtt) cc_final: 0.5887 (mmt) REVERT: B 281 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8211 (tm) REVERT: B 312 MET cc_start: 0.6301 (mtt) cc_final: 0.5852 (mmt) REVERT: C 312 MET cc_start: 0.6270 (mtt) cc_final: 0.5851 (mmt) outliers start: 11 outliers final: 5 residues processed: 117 average time/residue: 0.7006 time to fit residues: 85.1785 Evaluate side-chains 104 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain D residue 288 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.0970 chunk 73 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.4268 r_free = 0.4268 target = 0.183132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.145734 restraints weight = 6753.938| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.64 r_work: 0.3370 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6568 Z= 0.125 Angle : 0.546 13.261 8804 Z= 0.276 Chirality : 0.041 0.147 1072 Planarity : 0.004 0.036 1016 Dihedral : 9.078 54.873 1060 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.21 % Allowed : 21.67 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.52 (0.31), residues: 752 helix: 2.72 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.68 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 377 TYR 0.019 0.001 TYR D 485 PHE 0.011 0.001 PHE D 433 TRP 0.006 0.001 TRP D 289 HIS 0.001 0.001 HIS D 486 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6568) covalent geometry : angle 0.54612 ( 8804) hydrogen bonds : bond 0.04338 ( 489) hydrogen bonds : angle 3.18224 ( 1383) *********************** 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 126 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.242 Fit side-chains REVERT: A 281 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8267 (mt) REVERT: A 312 MET cc_start: 0.6220 (mtt) cc_final: 0.5730 (mmt) REVERT: B 312 MET cc_start: 0.6155 (mtt) cc_final: 0.5665 (mmt) REVERT: C 312 MET cc_start: 0.6107 (mtt) cc_final: 0.5736 (mmt) REVERT: D 312 MET cc_start: 0.6162 (mtt) cc_final: 0.5637 (mmt) outliers start: 8 outliers final: 2 residues processed: 124 average time/residue: 0.6628 time to fit residues: 85.5898 Evaluate side-chains 113 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain D residue 393 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 0.0070 chunk 23 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 0.0010 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 overall best weight: 0.4604 ------------------------------------------------------------------------------- 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 = 0.4281 r_free = 0.4281 target = 0.184288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.141509 restraints weight = 6712.145| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.18 r_work: 0.3428 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6568 Z= 0.121 Angle : 0.544 13.465 8804 Z= 0.275 Chirality : 0.040 0.143 1072 Planarity : 0.004 0.035 1016 Dihedral : 8.299 50.288 1060 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.52 % Allowed : 21.36 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.68 (0.31), residues: 752 helix: 2.81 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.83 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 377 TYR 0.020 0.001 TYR D 485 PHE 0.011 0.001 PHE A 433 TRP 0.007 0.001 TRP A 289 HIS 0.001 0.000 HIS C 486 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6568) covalent geometry : angle 0.54432 ( 8804) hydrogen bonds : bond 0.04121 ( 489) hydrogen bonds : angle 3.14000 ( 1383) *********************** 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 135 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.145 Fit side-chains REVERT: A 312 MET cc_start: 0.5927 (mtt) cc_final: 0.5700 (mmt) outliers start: 10 outliers final: 5 residues processed: 131 average time/residue: 0.5613 time to fit residues: 77.0533 Evaluate side-chains 119 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain D residue 486 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 42 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 0.0870 chunk 55 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 5 optimal weight: 0.0050 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.5372 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.181952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.138158 restraints weight = 6997.850| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.18 r_work: 0.3438 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6568 Z= 0.130 Angle : 0.561 13.687 8804 Z= 0.287 Chirality : 0.041 0.148 1072 Planarity : 0.005 0.046 1016 Dihedral : 7.985 47.685 1060 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.36 % Allowed : 23.03 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.69 (0.31), residues: 752 helix: 2.80 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.92 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 377 TYR 0.020 0.001 TYR D 485 PHE 0.010 0.001 PHE A 433 TRP 0.008 0.001 TRP A 289 HIS 0.000 0.000 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6568) covalent geometry : angle 0.56063 ( 8804) hydrogen bonds : bond 0.04238 ( 489) hydrogen bonds : angle 3.20663 ( 1383) *********************** 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 129 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.206 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 126 average time/residue: 0.5819 time to fit residues: 76.7051 Evaluate side-chains 114 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain D residue 288 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 64 optimal weight: 0.0170 chunk 53 optimal weight: 0.0770 chunk 48 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 overall best weight: 0.3376 ------------------------------------------------------------------------------- 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 = 0.4303 r_free = 0.4303 target = 0.187206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.141984 restraints weight = 7007.135| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.24 r_work: 0.3689 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6568 Z= 0.122 Angle : 0.563 13.279 8804 Z= 0.283 Chirality : 0.041 0.143 1072 Planarity : 0.005 0.036 1016 Dihedral : 7.569 50.536 1060 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.91 % Allowed : 23.48 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.74 (0.31), residues: 752 helix: 2.83 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 1.00 (0.59), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 377 TYR 0.023 0.002 TYR B 485 PHE 0.029 0.001 PHE A 481 TRP 0.008 0.001 TRP D 289 HIS 0.001 0.000 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6568) covalent geometry : angle 0.56316 ( 8804) hydrogen bonds : bond 0.03986 ( 489) hydrogen bonds : angle 3.17813 ( 1383) *********************** 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: 6 poor density : 116 time to evaluate : 0.254 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 121 average time/residue: 0.5306 time to fit residues: 67.3140 Evaluate side-chains 118 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain D residue 288 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.1980 chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4261 r_free = 0.4261 target = 0.183055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.137448 restraints weight = 6914.342| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.21 r_work: 0.3631 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6568 Z= 0.147 Angle : 0.612 14.265 8804 Z= 0.310 Chirality : 0.043 0.151 1072 Planarity : 0.005 0.052 1016 Dihedral : 7.872 57.203 1060 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.91 % Allowed : 24.85 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.68 (0.31), residues: 752 helix: 2.81 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.86 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 377 TYR 0.022 0.002 TYR D 485 PHE 0.010 0.001 PHE A 324 TRP 0.010 0.002 TRP A 289 HIS 0.001 0.000 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 6568) covalent geometry : angle 0.61209 ( 8804) hydrogen bonds : bond 0.04622 ( 489) hydrogen bonds : angle 3.30691 ( 1383) ********************** 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 130 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.223 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 129 average time/residue: 0.5746 time to fit residues: 77.5747 Evaluate side-chains 121 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain D residue 288 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 18 optimal weight: 0.0770 chunk 71 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.4270 r_free = 0.4270 target = 0.183960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.139740 restraints weight = 6926.262| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.16 r_work: 0.3582 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6568 Z= 0.134 Angle : 0.625 15.703 8804 Z= 0.307 Chirality : 0.042 0.147 1072 Planarity : 0.005 0.047 1016 Dihedral : 7.686 56.745 1060 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.61 % Allowed : 24.70 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.68 (0.31), residues: 752 helix: 2.83 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.75 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 377 TYR 0.022 0.002 TYR B 485 PHE 0.030 0.001 PHE C 481 TRP 0.009 0.001 TRP A 289 HIS 0.001 0.000 HIS C 486 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6568) covalent geometry : angle 0.62521 ( 8804) hydrogen bonds : bond 0.04404 ( 489) hydrogen bonds : angle 3.28128 ( 1383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2427.41 seconds wall clock time: 41 minutes 59.39 seconds (2519.39 seconds total)