Starting phenix.real_space_refine on Thu Jul 2 04:46:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sj1_25152/07_2026/7sj1_25152.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sj1_25152/07_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_25152/07_2026/7sj1_25152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sj1_25152/07_2026/7sj1_25152.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7sj1_25152/07_2026/7sj1_25152.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sj1_25152/07_2026/7sj1_25152.cif" model { file = "/net/cci-nas-00/data/ceres_data/7sj1_25152/07_2026/7sj1_25152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sj1_25152/07_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-6108/lib/python3.11/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: 248 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: 248 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: 248 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: 248 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: 1.62, per 1000 atoms: 0.25 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: 0.55 Conformation dependent library (CDL) restraints added in 340.2 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: 0.16 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: 0.78 Time building geometry restraints manager: 0.72 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: 3532 24.19 - 48.38: 232 48.38 - 72.57: 52 72.57 - 96.76: 0 96.76 - 120.95: 4 Dihedral angle restraints: 3820 sinusoidal: 1552 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 3817 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: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.960 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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 : 16.654 120.953 2340 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/Z covalent geometry : bond 0.01087 / 0.55 ( 6568) covalent geometry : angle 1.00696 / 0.42 ( 8804) hydrogen bonds : bond 0.17624 / 11.78 ( 489) hydrogen bonds : angle 4.43313 / 3.21 ( 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 : 0.199 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: 0.4425 time to fit residues: 79.7398 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 : 0.222 ------------------------------------------------------------------------------- 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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.179386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.134466 restraints weight = 6808.381| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.39 r_work: 0.3407 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2264 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= 0.142 Angle : 0.578 8.455 8804 Z= 0.300 Chirality : 0.041 0.131 1072 Planarity : 0.005 0.036 1016 Dihedral : 13.385 85.748 1044 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.36 % Allowed : 16.82 % Favored : 81.82 % 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: 3.30 (0.31), residues: 752 helix: 2.48 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 1.07 (0.62), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 487 TYR 0.014 0.002 TYR C 323 PHE 0.020 0.002 PHE C 433 TRP 0.004 0.001 TRP A 435 HIS 0.002 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 6568) covalent geometry : angle 0.57837 / 0.30 ( 8804) hydrogen bonds : bond 0.05157 / 3.32 ( 489) hydrogen bonds : angle 3.44307 / 2.49 ( 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 130 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.225 Fit side-chains REVERT: A 285 LEU cc_start: 0.7500 (mm) cc_final: 0.7119 (tp) REVERT: B 285 LEU cc_start: 0.7484 (mm) cc_final: 0.7108 (tp) REVERT: C 312 MET cc_start: 0.6251 (mtt) cc_final: 0.5791 (mmt) outliers start: 9 outliers final: 9 residues processed: 126 average time/residue: 0.5222 time to fit residues: 68.8310 Evaluate side-chains 125 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 392 SER 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: 0.1980 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 56 optimal weight: 0.0000 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.175997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.134804 restraints weight = 6586.914| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.58 r_work: 0.3404 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6568 Z= 0.120 Angle : 0.512 6.010 8804 Z= 0.265 Chirality : 0.038 0.123 1072 Planarity : 0.004 0.035 1016 Dihedral : 11.597 73.521 1044 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.67 % Allowed : 18.18 % Favored : 80.15 % 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: 3.51 (0.31), residues: 752 helix: 2.68 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.82 (0.60), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 371 TYR 0.009 0.001 TYR C 485 PHE 0.012 0.001 PHE A 433 TRP 0.004 0.001 TRP D 289 HIS 0.001 0.000 HIS C 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 6568) covalent geometry : angle 0.51231 / 0.27 ( 8804) hydrogen bonds : bond 0.04286 / 2.77 ( 489) hydrogen bonds : angle 3.22638 / 2.33 ( 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 127 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.228 Fit side-chains REVERT: A 284 THR cc_start: 0.8236 (m) cc_final: 0.8007 (p) REVERT: A 312 MET cc_start: 0.6317 (mtt) cc_final: 0.5908 (mmt) REVERT: B 284 THR cc_start: 0.8251 (m) cc_final: 0.8036 (p) REVERT: B 312 MET cc_start: 0.6299 (mtt) cc_final: 0.5860 (mmt) REVERT: C 284 THR cc_start: 0.8278 (m) cc_final: 0.8032 (p) REVERT: C 312 MET cc_start: 0.6273 (mtt) cc_final: 0.5863 (mmt) REVERT: D 284 THR cc_start: 0.8286 (m) cc_final: 0.8038 (p) REVERT: D 312 MET cc_start: 0.6280 (mtt) cc_final: 0.5857 (mmt) outliers start: 11 outliers final: 0 residues processed: 125 average time/residue: 0.5481 time to fit residues: 71.7217 Evaluate side-chains 105 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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: 0.9990 chunk 63 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 74 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.172635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.124636 restraints weight = 6652.222| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.19 r_work: 0.3398 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3067 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 : 0.566 8.878 8804 Z= 0.294 Chirality : 0.042 0.208 1072 Planarity : 0.005 0.045 1016 Dihedral : 10.363 59.034 1044 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.82 % Allowed : 19.70 % Favored : 78.48 % 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: 3.42 (0.31), residues: 752 helix: 2.67 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.55 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 487 TYR 0.014 0.001 TYR C 323 PHE 0.012 0.001 PHE B 433 TRP 0.006 0.001 TRP D 289 HIS 0.002 0.001 HIS C 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 6568) covalent geometry : angle 0.56607 / 0.29 ( 8804) hydrogen bonds : bond 0.04841 / 3.09 ( 489) hydrogen bonds : angle 3.26345 / 2.34 ( 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 133 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.168 Fit side-chains REVERT: A 312 MET cc_start: 0.6262 (mtt) cc_final: 0.5825 (mmt) REVERT: B 284 THR cc_start: 0.8261 (m) cc_final: 0.8050 (p) REVERT: B 312 MET cc_start: 0.6268 (mtt) cc_final: 0.5828 (mmt) REVERT: C 312 MET cc_start: 0.6220 (mtt) cc_final: 0.5796 (mmt) REVERT: D 312 MET cc_start: 0.6313 (mtt) cc_final: 0.5855 (mmt) outliers start: 12 outliers final: 1 residues processed: 133 average time/residue: 0.5654 time to fit residues: 78.7296 Evaluate side-chains 100 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 ILE 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: 5.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.171496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.124081 restraints weight = 6843.432| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.45 r_work: 0.3376 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6568 Z= 0.147 Angle : 0.572 12.587 8804 Z= 0.294 Chirality : 0.042 0.135 1072 Planarity : 0.004 0.035 1016 Dihedral : 9.724 56.862 1044 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.21 % Allowed : 21.06 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.31), residues: 752 helix: 2.51 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.54 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 377 TYR 0.017 0.002 TYR D 485 PHE 0.011 0.001 PHE C 324 TRP 0.004 0.001 TRP C 435 HIS 0.002 0.001 HIS D 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 6568) covalent geometry : angle 0.57203 / 0.29 ( 8804) hydrogen bonds : bond 0.04811 / 3.08 ( 489) hydrogen bonds : angle 3.28314 / 2.36 ( 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 123 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.244 Fit side-chains REVERT: A 312 MET cc_start: 0.6290 (mtt) cc_final: 0.5859 (mmt) REVERT: B 281 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8318 (tm) REVERT: B 284 THR cc_start: 0.8237 (m) cc_final: 0.8016 (p) REVERT: B 312 MET cc_start: 0.6296 (mtt) cc_final: 0.5859 (mmt) REVERT: C 312 MET cc_start: 0.6259 (mtt) cc_final: 0.5843 (mmt) outliers start: 8 outliers final: 0 residues processed: 123 average time/residue: 0.6088 time to fit residues: 78.1368 Evaluate side-chains 105 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 281 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.173667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.133343 restraints weight = 6800.030| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.54 r_work: 0.3376 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3449 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= 0.126 Angle : 0.552 13.302 8804 Z= 0.279 Chirality : 0.041 0.143 1072 Planarity : 0.004 0.035 1016 Dihedral : 8.878 50.776 1044 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 0.76 % Allowed : 23.18 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.40 (0.31), residues: 752 helix: 2.63 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.67 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 377 TYR 0.019 0.001 TYR D 485 PHE 0.011 0.001 PHE C 433 TRP 0.004 0.001 TRP D 289 HIS 0.002 0.001 HIS C 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 6568) covalent geometry : angle 0.55209 / 0.28 ( 8804) hydrogen bonds : bond 0.04351 / 2.80 ( 489) hydrogen bonds : angle 3.18076 / 2.30 ( 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 121 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.213 Fit side-chains REVERT: A 312 MET cc_start: 0.6113 (mtt) cc_final: 0.5640 (mmt) REVERT: B 284 THR cc_start: 0.8196 (m) cc_final: 0.7915 (p) REVERT: B 312 MET cc_start: 0.6121 (mtt) cc_final: 0.5649 (mmt) REVERT: C 312 MET cc_start: 0.6039 (mtt) cc_final: 0.5623 (mmt) REVERT: D 312 MET cc_start: 0.6173 (mtt) cc_final: 0.5728 (mmt) outliers start: 5 outliers final: 1 residues processed: 119 average time/residue: 0.5427 time to fit residues: 67.6789 Evaluate side-chains 110 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B 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: 2.9990 chunk 2 optimal weight: 0.4980 chunk 23 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 17 optimal weight: 0.0970 chunk 20 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.173755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.133252 restraints weight = 6793.296| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.45 r_work: 0.3382 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3609 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= 0.126 Angle : 0.554 13.684 8804 Z= 0.280 Chirality : 0.041 0.145 1072 Planarity : 0.004 0.034 1016 Dihedral : 8.332 48.505 1044 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.91 % Allowed : 22.42 % Favored : 76.67 % 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: 3.53 (0.31), residues: 752 helix: 2.70 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.85 (0.59), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 377 TYR 0.020 0.001 TYR D 485 PHE 0.011 0.001 PHE B 433 TRP 0.004 0.001 TRP D 289 HIS 0.002 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 6568) covalent geometry : angle 0.55447 / 0.28 ( 8804) hydrogen bonds : bond 0.04350 / 2.79 ( 489) hydrogen bonds : angle 3.15802 / 2.27 ( 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 124 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.243 Fit side-chains REVERT: B 284 THR cc_start: 0.8119 (m) cc_final: 0.7843 (p) REVERT: D 312 MET cc_start: 0.6077 (mtt) cc_final: 0.5813 (mmt) outliers start: 6 outliers final: 1 residues processed: 122 average time/residue: 0.5418 time to fit residues: 69.3785 Evaluate side-chains 114 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 42 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 5 optimal weight: 0.0570 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.182237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.138159 restraints weight = 6968.388| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.14 r_work: 0.3620 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6568 Z= 0.142 Angle : 0.585 13.964 8804 Z= 0.298 Chirality : 0.041 0.156 1072 Planarity : 0.005 0.048 1016 Dihedral : 8.243 48.353 1044 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.67 % Allowed : 23.33 % Favored : 75.00 % 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: 3.41 (0.31), residues: 752 helix: 2.60 (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 0.001 ARG B 377 TYR 0.021 0.001 TYR D 485 PHE 0.029 0.002 PHE B 481 TRP 0.005 0.001 TRP D 289 HIS 0.002 0.000 HIS C 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 6568) covalent geometry : angle 0.58477 / 0.30 ( 8804) hydrogen bonds : bond 0.04634 / 2.96 ( 489) hydrogen bonds : angle 3.27103 / 2.35 ( 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 126 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.252 Fit side-chains REVERT: B 281 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8410 (tm) REVERT: B 284 THR cc_start: 0.8124 (m) cc_final: 0.7898 (p) REVERT: D 312 MET cc_start: 0.6193 (mtt) cc_final: 0.5868 (mmt) outliers start: 11 outliers final: 2 residues processed: 123 average time/residue: 0.5317 time to fit residues: 68.3428 Evaluate side-chains 116 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 393 MET 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: 1.9990 chunk 47 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.180264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.136203 restraints weight = 7037.208| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.12 r_work: 0.3547 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6568 Z= 0.162 Angle : 0.614 14.188 8804 Z= 0.314 Chirality : 0.043 0.154 1072 Planarity : 0.005 0.044 1016 Dihedral : 8.499 49.107 1044 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.91 % Allowed : 23.94 % Favored : 75.15 % 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: 3.30 (0.31), residues: 752 helix: 2.54 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.73 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 377 TYR 0.024 0.002 TYR A 485 PHE 0.025 0.002 PHE B 481 TRP 0.005 0.002 TRP A 289 HIS 0.001 0.000 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.16 ( 6568) covalent geometry : angle 0.61438 / 0.31 ( 8804) hydrogen bonds : bond 0.05032 / 3.21 ( 489) hydrogen bonds : angle 3.39927 / 2.43 ( 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 123 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.145 Fit side-chains REVERT: A 407 VAL cc_start: 0.8034 (p) cc_final: 0.7786 (t) REVERT: B 281 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8450 (tm) REVERT: C 407 VAL cc_start: 0.8023 (p) cc_final: 0.7778 (t) outliers start: 6 outliers final: 5 residues processed: 122 average time/residue: 0.5073 time to fit residues: 64.6401 Evaluate side-chains 121 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 281 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.182475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.138426 restraints weight = 6885.874| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.12 r_work: 0.3578 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3898 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 : 0.606 13.571 8804 Z= 0.303 Chirality : 0.041 0.147 1072 Planarity : 0.004 0.039 1016 Dihedral : 8.287 49.731 1044 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.21 % Allowed : 24.09 % 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: 3.36 (0.31), residues: 752 helix: 2.59 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.71 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 377 TYR 0.021 0.002 TYR D 485 PHE 0.025 0.001 PHE B 481 TRP 0.005 0.001 TRP D 454 HIS 0.001 0.000 HIS C 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 6568) covalent geometry : angle 0.60581 / 0.30 ( 8804) hydrogen bonds : bond 0.04568 / 2.93 ( 489) hydrogen bonds : angle 3.32677 / 2.39 ( 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 128 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.266 Fit side-chains REVERT: A 281 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8328 (mt) REVERT: B 281 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8443 (tm) REVERT: D 312 MET cc_start: 0.6201 (mtt) cc_final: 0.5828 (mmt) outliers start: 8 outliers final: 5 residues processed: 126 average time/residue: 0.4978 time to fit residues: 65.7293 Evaluate side-chains 120 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 281 LEU 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 486 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 74 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.182810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.137966 restraints weight = 6960.817| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.16 r_work: 0.3641 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3990 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= 0.141 Angle : 0.620 14.307 8804 Z= 0.308 Chirality : 0.041 0.150 1072 Planarity : 0.005 0.051 1016 Dihedral : 8.254 54.648 1044 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.06 % Allowed : 24.39 % Favored : 74.55 % 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: 3.37 (0.31), residues: 752 helix: 2.61 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.66 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 377 TYR 0.022 0.002 TYR A 485 PHE 0.030 0.001 PHE C 481 TRP 0.005 0.001 TRP A 289 HIS 0.001 0.000 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 6568) covalent geometry : angle 0.61974 / 0.31 ( 8804) hydrogen bonds : bond 0.04655 / 2.98 ( 489) hydrogen bonds : angle 3.36277 / 2.40 ( 1383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2145.29 seconds wall clock time: 37 minutes 22.75 seconds (2242.75 seconds total)