Starting phenix.real_space_refine on Tue Feb 11 22:25:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sj1_25152/02_2025/7sj1_25152.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sj1_25152/02_2025/7sj1_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_25152/02_2025/7sj1_25152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sj1_25152/02_2025/7sj1_25152.map" model { file = "/net/cci-nas-00/data/ceres_data/7sj1_25152/02_2025/7sj1_25152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sj1_25152/02_2025/7sj1_25152.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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, 'GLU:plan': 2, 'ARG:plan': 1, '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, 'GLU:plan': 2, 'ARG:plan': 1, '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, 'GLU:plan': 2, 'ARG:plan': 1, '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, 'GLU:plan': 2, 'ARG:plan': 1, '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-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 67 Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.54, per 1000 atoms: 0.70 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: 1.56 Conformation dependent library (CDL) restraints added in 780.3 milliseconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1480 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 86.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 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: 1.82 Time building geometry restraints manager: 1.81 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: 1.240 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.380 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.020 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:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.800 ------------------------------------------------------------------------------- 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= 0.731 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (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 TRP 0.005 0.001 TRP B 454 HIS 0.001 0.000 HIS B 486 PHE 0.029 0.002 PHE A 433 TYR 0.022 0.002 TYR D 485 ARG 0.002 0.000 ARG D 227 *********************** 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 : 0.632 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: 0.6159 (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: 0.6103 (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: 1.0981 time to fit residues: 197.8009 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 : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 0.4980 chunk 19 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 0.0030 chunk 23 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 = 0.4203 r_free = 0.4203 target = 0.179479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.133607 restraints weight = 6748.846| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.22 r_work: 0.3408 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2312 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= 0.214 Angle : 0.578 8.383 8804 Z= 0.299 Chirality : 0.040 0.131 1072 Planarity : 0.005 0.037 1016 Dihedral : 13.185 83.900 1060 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.06 % Allowed : 16.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.31), residues: 752 helix: 2.49 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 1.14 (0.63), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 435 HIS 0.002 0.001 HIS A 486 PHE 0.020 0.002 PHE D 433 TYR 0.014 0.002 TYR C 323 ARG 0.003 0.001 ARG B 487 *********************** 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: 7 poor density : 122 time to evaluate : 0.682 Fit side-chains REVERT: A 285 LEU cc_start: 0.7491 (mm) cc_final: 0.7122 (tp) REVERT: B 285 LEU cc_start: 0.7493 (mm) cc_final: 0.7111 (tp) REVERT: C 312 MET cc_start: 0.6267 (mtt) cc_final: 0.5803 (mmt) outliers start: 7 outliers final: 6 residues processed: 126 average time/residue: 1.3013 time to fit residues: 171.6149 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 : 0.617 ------------------------------------------------------------------------------- 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 D residue 393 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 0.0980 chunk 18 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.0670 chunk 50 optimal weight: 2.9990 overall best weight: 0.4720 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.175161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.129212 restraints weight = 6585.065| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.33 r_work: 0.3427 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2749 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= 0.193 Angle : 0.516 5.975 8804 Z= 0.267 Chirality : 0.038 0.123 1072 Planarity : 0.004 0.035 1016 Dihedral : 11.530 75.424 1060 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.67 % Allowed : 18.33 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.51 (0.31), residues: 752 helix: 2.69 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.80 (0.60), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 435 HIS 0.001 0.000 HIS D 486 PHE 0.012 0.001 PHE A 433 TYR 0.009 0.001 TYR C 485 ARG 0.002 0.000 ARG A 371 *********************** 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 126 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.746 Fit side-chains REVERT: A 284 THR cc_start: 0.8267 (m) cc_final: 0.8015 (p) REVERT: A 312 MET cc_start: 0.6358 (mtt) cc_final: 0.5947 (mmt) REVERT: B 284 THR cc_start: 0.8270 (m) cc_final: 0.8012 (p) REVERT: B 312 MET cc_start: 0.6285 (mtt) cc_final: 0.5898 (mmt) REVERT: C 284 THR cc_start: 0.8288 (m) cc_final: 0.8037 (p) REVERT: C 312 MET cc_start: 0.6242 (mtt) cc_final: 0.5934 (mmt) REVERT: D 284 THR cc_start: 0.8308 (m) cc_final: 0.8057 (p) REVERT: D 312 MET cc_start: 0.6278 (mtt) cc_final: 0.5838 (mmt) outliers start: 11 outliers final: 0 residues processed: 124 average time/residue: 1.2754 time to fit residues: 165.5910 Evaluate side-chains 104 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 39 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 62 optimal weight: 0.0060 overall best weight: 0.7996 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.173523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.125230 restraints weight = 6702.551| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.21 r_work: 0.3405 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3024 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= 0.225 Angle : 0.553 8.973 8804 Z= 0.286 Chirality : 0.041 0.191 1072 Planarity : 0.005 0.035 1016 Dihedral : 10.479 66.963 1060 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.82 % Allowed : 20.00 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.31), residues: 752 helix: 2.66 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.63 (0.59), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 289 HIS 0.002 0.001 HIS C 486 PHE 0.011 0.001 PHE B 433 TYR 0.012 0.001 TYR B 323 ARG 0.010 0.001 ARG D 487 *********************** 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 132 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.722 Fit side-chains REVERT: A 312 MET cc_start: 0.6258 (mtt) cc_final: 0.5857 (mmt) REVERT: B 312 MET cc_start: 0.6290 (mtt) cc_final: 0.5881 (mmt) REVERT: C 312 MET cc_start: 0.6255 (mtt) cc_final: 0.5877 (mmt) REVERT: D 284 THR cc_start: 0.8291 (m) cc_final: 0.8082 (p) REVERT: D 312 MET cc_start: 0.6297 (mtt) cc_final: 0.5869 (mmt) outliers start: 12 outliers final: 1 residues processed: 131 average time/residue: 1.3583 time to fit residues: 186.0500 Evaluate side-chains 102 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 393 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 36 optimal weight: 0.0980 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.172507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.124585 restraints weight = 6698.458| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.19 r_work: 0.3400 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3265 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= 0.220 Angle : 0.555 12.314 8804 Z= 0.285 Chirality : 0.041 0.136 1072 Planarity : 0.005 0.036 1016 Dihedral : 9.670 60.399 1060 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.52 % Allowed : 20.91 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.31), residues: 752 helix: 2.56 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.56 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 289 HIS 0.002 0.001 HIS C 486 PHE 0.009 0.001 PHE C 433 TYR 0.019 0.002 TYR D 485 ARG 0.010 0.001 ARG A 487 *********************** 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 122 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.631 Fit side-chains REVERT: A 281 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8280 (tm) REVERT: A 312 MET cc_start: 0.6285 (mtt) cc_final: 0.5886 (mmt) REVERT: B 312 MET cc_start: 0.6309 (mtt) cc_final: 0.5906 (mmt) REVERT: C 281 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8359 (tm) REVERT: C 312 MET cc_start: 0.6218 (mtt) cc_final: 0.5852 (mmt) REVERT: D 284 THR cc_start: 0.8236 (m) cc_final: 0.8013 (p) REVERT: D 312 MET cc_start: 0.6327 (mtt) cc_final: 0.5899 (mmt) outliers start: 10 outliers final: 2 residues processed: 120 average time/residue: 1.3869 time to fit residues: 173.7166 Evaluate side-chains 104 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain D residue 393 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.170926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.131014 restraints weight = 6744.689| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.39 r_work: 0.3363 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6568 Z= 0.247 Angle : 0.583 12.664 8804 Z= 0.299 Chirality : 0.043 0.149 1072 Planarity : 0.005 0.037 1016 Dihedral : 9.204 54.811 1060 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.21 % Allowed : 22.88 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.31), residues: 752 helix: 2.52 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.61 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 289 HIS 0.003 0.001 HIS A 486 PHE 0.010 0.001 PHE B 433 TYR 0.019 0.002 TYR D 485 ARG 0.008 0.001 ARG D 487 *********************** 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 123 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.682 Fit side-chains REVERT: A 312 MET cc_start: 0.6263 (mtt) cc_final: 0.5813 (mmt) REVERT: C 312 MET cc_start: 0.6201 (mtt) cc_final: 0.5761 (mmt) REVERT: D 284 THR cc_start: 0.8213 (m) cc_final: 0.7963 (p) outliers start: 8 outliers final: 3 residues processed: 120 average time/residue: 1.3804 time to fit residues: 172.9202 Evaluate side-chains 115 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 18 optimal weight: 0.9980 chunk 50 optimal weight: 0.0170 chunk 49 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.172557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.126444 restraints weight = 6714.394| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.28 r_work: 0.3403 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3575 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= 0.214 Angle : 0.562 13.466 8804 Z= 0.287 Chirality : 0.041 0.141 1072 Planarity : 0.004 0.037 1016 Dihedral : 8.668 51.540 1060 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.21 % Allowed : 21.82 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.31), residues: 752 helix: 2.58 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.80 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 454 HIS 0.002 0.000 HIS C 486 PHE 0.009 0.001 PHE C 324 TYR 0.019 0.001 TYR D 485 ARG 0.008 0.001 ARG D 487 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.740 Fit side-chains REVERT: A 312 MET cc_start: 0.6233 (mtt) cc_final: 0.5743 (mmt) REVERT: B 312 MET cc_start: 0.6236 (mtt) cc_final: 0.5740 (mmt) REVERT: C 312 MET cc_start: 0.6175 (mtt) cc_final: 0.5761 (mmt) REVERT: D 284 THR cc_start: 0.8231 (m) cc_final: 0.7944 (p) outliers start: 8 outliers final: 4 residues processed: 121 average time/residue: 1.3652 time to fit residues: 172.6211 Evaluate side-chains 117 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain D 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 3 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4183 r_free = 0.4183 target = 0.176440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.131627 restraints weight = 6924.736| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.14 r_work: 0.3370 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6568 Z= 0.275 Angle : 0.612 14.400 8804 Z= 0.313 Chirality : 0.043 0.165 1072 Planarity : 0.005 0.035 1016 Dihedral : 9.046 58.533 1060 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.67 % Allowed : 22.12 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.12 (0.31), residues: 752 helix: 2.42 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.63 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 289 HIS 0.001 0.000 HIS C 486 PHE 0.012 0.002 PHE D 324 TYR 0.024 0.002 TYR A 485 ARG 0.008 0.001 ARG A 377 *********************** 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: 11 poor density : 118 time to evaluate : 0.711 Fit side-chains REVERT: A 407 VAL cc_start: 0.8082 (p) cc_final: 0.7871 (t) REVERT: B 407 VAL cc_start: 0.8078 (p) cc_final: 0.7870 (t) REVERT: C 407 VAL cc_start: 0.8078 (p) cc_final: 0.7870 (t) REVERT: D 407 VAL cc_start: 0.8081 (p) cc_final: 0.7869 (t) outliers start: 11 outliers final: 9 residues processed: 123 average time/residue: 1.3124 time to fit residues: 168.9252 Evaluate side-chains 126 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 393 MET Chi-restraints excluded: chain D residue 486 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 75 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4241 r_free = 0.4241 target = 0.180947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.137142 restraints weight = 6956.827| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.11 r_work: 0.3400 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3811 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= 0.231 Angle : 0.578 13.697 8804 Z= 0.298 Chirality : 0.042 0.142 1072 Planarity : 0.004 0.036 1016 Dihedral : 8.566 53.094 1060 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.52 % Allowed : 22.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.31), residues: 752 helix: 2.43 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.57 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 454 HIS 0.001 0.000 HIS C 486 PHE 0.029 0.001 PHE B 292 TYR 0.021 0.002 TYR A 485 ARG 0.007 0.001 ARG B 377 *********************** 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 124 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.668 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 122 average time/residue: 1.3096 time to fit residues: 167.1795 Evaluate side-chains 116 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain D residue 393 MET 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 3 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 69 optimal weight: 0.0670 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.4253 r_free = 0.4253 target = 0.182544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.138609 restraints weight = 6874.426| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.10 r_work: 0.3516 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 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 0.050 6568 Z= 0.215 Angle : 0.567 13.413 8804 Z= 0.292 Chirality : 0.041 0.142 1072 Planarity : 0.004 0.035 1016 Dihedral : 7.941 50.155 1060 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.91 % Allowed : 24.24 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.31 (0.31), residues: 752 helix: 2.57 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.63 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 454 HIS 0.000 0.000 HIS A 378 PHE 0.029 0.001 PHE A 481 TYR 0.021 0.002 TYR B 485 ARG 0.008 0.000 ARG D 377 ********************** 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 126 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.669 Fit side-chains REVERT: A 312 MET cc_start: 0.6190 (mtt) cc_final: 0.5746 (mmt) REVERT: B 312 MET cc_start: 0.6195 (mtt) cc_final: 0.5806 (mmt) REVERT: C 312 MET cc_start: 0.6219 (mtt) cc_final: 0.5847 (mmt) outliers start: 6 outliers final: 4 residues processed: 124 average time/residue: 1.2856 time to fit residues: 166.9109 Evaluate side-chains 115 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain D residue 393 MET 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 65 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4259 r_free = 0.4259 target = 0.182640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.138508 restraints weight = 6966.025| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.11 r_work: 0.3563 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6568 Z= 0.232 Angle : 0.585 14.048 8804 Z= 0.304 Chirality : 0.041 0.153 1072 Planarity : 0.005 0.053 1016 Dihedral : 7.745 50.060 1060 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 10.21 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.31), residues: 752 helix: 2.54 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.57 (0.57), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 454 HIS 0.001 0.000 HIS D 378 PHE 0.030 0.001 PHE A 292 TYR 0.022 0.002 TYR A 485 ARG 0.009 0.001 ARG D 377 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4820.15 seconds wall clock time: 85 minutes 48.51 seconds (5148.51 seconds total)