Starting phenix.real_space_refine on Sat Aug 23 01:56:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u5c_41916/08_2025/8u5c_41916.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u5c_41916/08_2025/8u5c_41916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u5c_41916/08_2025/8u5c_41916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u5c_41916/08_2025/8u5c_41916.map" model { file = "/net/cci-nas-00/data/ceres_data/8u5c_41916/08_2025/8u5c_41916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u5c_41916/08_2025/8u5c_41916.cif" } resolution = 2.68 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= -0.001 sd= 0.027 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 6066 2.51 5 N 1378 2.21 5 O 1532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9032 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 4446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4446 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 552} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 4446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4446 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 552} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.99, per 1000 atoms: 0.22 Number of scatterers: 9032 At special positions: 0 Unit cell: (98.6209, 125.215, 75.3508, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1532 8.00 N 1378 7.00 C 6066 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: 0.64 Conformation dependent library (CDL) restraints added in 350.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 0 sheets defined 89.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'E' and resid 38 through 40 No H-bonds generated for 'chain 'E' and resid 38 through 40' Processing helix chain 'E' and resid 41 through 62 Processing helix chain 'E' and resid 66 through 80 removed outlier: 3.636A pdb=" N LYS E 71 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU E 73 " --> pdb=" O GLN E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 93 Processing helix chain 'E' and resid 94 through 98 Processing helix chain 'E' and resid 99 through 125 Processing helix chain 'E' and resid 129 through 143 Proline residue: E 138 - end of helix Processing helix chain 'E' and resid 149 through 159 Processing helix chain 'E' and resid 162 through 165 Processing helix chain 'E' and resid 166 through 196 removed outlier: 4.229A pdb=" N TYR E 170 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Proline residue: E 174 - end of helix Proline residue: E 182 - end of helix Processing helix chain 'E' and resid 202 through 216 Processing helix chain 'E' and resid 217 through 234 Processing helix chain 'E' and resid 238 through 264 removed outlier: 3.888A pdb=" N ASN E 243 " --> pdb=" O VAL E 239 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE E 244 " --> pdb=" O TYR E 240 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER E 253 " --> pdb=" O GLY E 249 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY E 254 " --> pdb=" O ASN E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 288 Processing helix chain 'E' and resid 288 through 302 Processing helix chain 'E' and resid 306 through 323 removed outlier: 3.635A pdb=" N PHE E 323 " --> pdb=" O LEU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 337 removed outlier: 4.140A pdb=" N ALA E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 367 removed outlier: 3.709A pdb=" N ALA E 355 " --> pdb=" O THR E 351 " (cutoff:3.500A) Proline residue: E 356 - end of helix Processing helix chain 'E' and resid 368 through 370 No H-bonds generated for 'chain 'E' and resid 368 through 370' Processing helix chain 'E' and resid 371 through 404 Processing helix chain 'E' and resid 405 through 409 removed outlier: 3.675A pdb=" N LYS E 408 " --> pdb=" O LYS E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 436 Processing helix chain 'E' and resid 439 through 473 Processing helix chain 'E' and resid 480 through 503 Proline residue: E 492 - end of helix Processing helix chain 'E' and resid 511 through 515 Processing helix chain 'E' and resid 516 through 544 Processing helix chain 'E' and resid 655 through 682 Processing helix chain 'E' and resid 687 through 703 removed outlier: 3.614A pdb=" N PHE E 699 " --> pdb=" O PHE E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 703 through 712 Processing helix chain 'F' and resid 38 through 40 No H-bonds generated for 'chain 'F' and resid 38 through 40' Processing helix chain 'F' and resid 41 through 62 Processing helix chain 'F' and resid 66 through 80 removed outlier: 3.636A pdb=" N LYS F 71 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU F 73 " --> pdb=" O GLN F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 93 Processing helix chain 'F' and resid 94 through 98 Processing helix chain 'F' and resid 99 through 125 Processing helix chain 'F' and resid 129 through 143 Proline residue: F 138 - end of helix Processing helix chain 'F' and resid 149 through 159 removed outlier: 3.547A pdb=" N ILE F 153 " --> pdb=" O LEU F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 165 Processing helix chain 'F' and resid 166 through 196 removed outlier: 4.163A pdb=" N TYR F 170 " --> pdb=" O LEU F 166 " (cutoff:3.500A) Proline residue: F 174 - end of helix Proline residue: F 182 - end of helix Processing helix chain 'F' and resid 202 through 216 Processing helix chain 'F' and resid 217 through 234 Processing helix chain 'F' and resid 238 through 265 removed outlier: 3.884A pdb=" N ASN F 243 " --> pdb=" O VAL F 239 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE F 244 " --> pdb=" O TYR F 240 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER F 253 " --> pdb=" O GLY F 249 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLY F 254 " --> pdb=" O ASN F 250 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL F 265 " --> pdb=" O GLY F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 288 Processing helix chain 'F' and resid 288 through 302 Processing helix chain 'F' and resid 306 through 322 Processing helix chain 'F' and resid 326 through 337 removed outlier: 4.063A pdb=" N ALA F 330 " --> pdb=" O ALA F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 367 removed outlier: 3.704A pdb=" N ALA F 355 " --> pdb=" O THR F 351 " (cutoff:3.500A) Proline residue: F 356 - end of helix Processing helix chain 'F' and resid 368 through 370 No H-bonds generated for 'chain 'F' and resid 368 through 370' Processing helix chain 'F' and resid 371 through 404 Processing helix chain 'F' and resid 405 through 409 removed outlier: 3.614A pdb=" N LYS F 408 " --> pdb=" O LYS F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 436 Processing helix chain 'F' and resid 439 through 473 Processing helix chain 'F' and resid 480 through 503 Proline residue: F 492 - end of helix Processing helix chain 'F' and resid 511 through 515 Processing helix chain 'F' and resid 516 through 544 Processing helix chain 'F' and resid 655 through 682 Processing helix chain 'F' and resid 687 through 703 removed outlier: 3.598A pdb=" N PHE F 699 " --> pdb=" O PHE F 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 703 through 712 751 hydrogen bonds defined for protein. 2217 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: 1.40 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1780 1.33 - 1.45: 2055 1.45 - 1.57: 5313 1.57 - 1.69: 14 1.69 - 1.81: 90 Bond restraints: 9252 Sorted by residual: bond pdb=" CZ ARG E 657 " pdb=" NH2 ARG E 657 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.55e+00 bond pdb=" N ARG F 41 " pdb=" CA ARG F 41 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.31e-02 5.83e+03 7.77e+00 bond pdb=" N TYR F 455 " pdb=" CA TYR F 455 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.21e-02 6.83e+03 7.68e+00 bond pdb=" N ARG E 41 " pdb=" CA ARG E 41 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.33e-02 5.65e+03 7.63e+00 bond pdb=" CZ ARG F 657 " pdb=" NH2 ARG F 657 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.52e+00 ... (remaining 9247 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 9650 1.76 - 3.51: 2460 3.51 - 5.27: 442 5.27 - 7.02: 47 7.02 - 8.78: 11 Bond angle restraints: 12610 Sorted by residual: angle pdb=" N ILE F 491 " pdb=" CA ILE F 491 " pdb=" CB ILE F 491 " ideal model delta sigma weight residual 110.50 114.10 -3.60 6.30e-01 2.52e+00 3.27e+01 angle pdb=" OE1 GLN E 443 " pdb=" CD GLN E 443 " pdb=" NE2 GLN E 443 " ideal model delta sigma weight residual 122.60 116.94 5.66 1.00e+00 1.00e+00 3.20e+01 angle pdb=" OE1 GLN F 443 " pdb=" CD GLN F 443 " pdb=" NE2 GLN F 443 " ideal model delta sigma weight residual 122.60 117.10 5.50 1.00e+00 1.00e+00 3.03e+01 angle pdb=" C ALA F 427 " pdb=" N GLY F 428 " pdb=" CA GLY F 428 " ideal model delta sigma weight residual 119.98 125.54 -5.56 1.11e+00 8.12e-01 2.51e+01 angle pdb=" OE1 GLN F 143 " pdb=" CD GLN F 143 " pdb=" NE2 GLN F 143 " ideal model delta sigma weight residual 122.60 117.93 4.67 1.00e+00 1.00e+00 2.18e+01 ... (remaining 12605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 5196 17.53 - 35.06: 329 35.06 - 52.59: 71 52.59 - 70.12: 6 70.12 - 87.65: 12 Dihedral angle restraints: 5614 sinusoidal: 2276 harmonic: 3338 Sorted by residual: dihedral pdb=" C LEU F 319 " pdb=" N LEU F 319 " pdb=" CA LEU F 319 " pdb=" CB LEU F 319 " ideal model delta harmonic sigma weight residual -122.60 -136.61 14.01 0 2.50e+00 1.60e-01 3.14e+01 dihedral pdb=" CA ALA F 199 " pdb=" C ALA F 199 " pdb=" N SER F 200 " pdb=" CA SER F 200 " ideal model delta harmonic sigma weight residual 180.00 152.47 27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" C TYR E 451 " pdb=" N TYR E 451 " pdb=" CA TYR E 451 " pdb=" CB TYR E 451 " ideal model delta harmonic sigma weight residual -122.60 -136.29 13.69 0 2.50e+00 1.60e-01 3.00e+01 ... (remaining 5611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1170 0.098 - 0.197: 301 0.197 - 0.295: 51 0.295 - 0.393: 11 0.393 - 0.491: 3 Chirality restraints: 1536 Sorted by residual: chirality pdb=" CA LEU F 319 " pdb=" N LEU F 319 " pdb=" C LEU F 319 " pdb=" CB LEU F 319 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.04e+00 chirality pdb=" CA TYR E 451 " pdb=" N TYR E 451 " pdb=" C TYR E 451 " pdb=" CB TYR E 451 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.70e+00 chirality pdb=" CA LEU E 319 " pdb=" N LEU E 319 " pdb=" C LEU E 319 " pdb=" CB LEU E 319 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.29e+00 ... (remaining 1533 not shown) Planarity restraints: 1510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 151 " -0.096 2.00e-02 2.50e+03 5.75e-02 6.61e+01 pdb=" CG TYR F 151 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR F 151 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR F 151 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR F 151 " 0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR F 151 " 0.030 2.00e-02 2.50e+03 pdb=" CZ TYR F 151 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR F 151 " -0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 679 " -0.071 2.00e-02 2.50e+03 5.05e-02 6.38e+01 pdb=" CG TRP F 679 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP F 679 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP F 679 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP F 679 " 0.056 2.00e-02 2.50e+03 pdb=" CE2 TRP F 679 " -0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP F 679 " 0.085 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 679 " -0.053 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 679 " 0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP F 679 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 695 " -0.093 2.00e-02 2.50e+03 5.68e-02 5.65e+01 pdb=" CG PHE F 695 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE F 695 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 PHE F 695 " 0.053 2.00e-02 2.50e+03 pdb=" CE1 PHE F 695 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE F 695 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE F 695 " -0.055 2.00e-02 2.50e+03 ... (remaining 1507 not shown) Histogram of nonbonded interaction distances: 2.60 - 3.06: 5530 3.06 - 3.52: 10668 3.52 - 3.98: 15530 3.98 - 4.44: 18484 4.44 - 4.90: 28934 Nonbonded interactions: 79146 Sorted by model distance: nonbonded pdb=" O SER E 251 " pdb=" OG SER E 255 " model vdw 2.595 3.040 nonbonded pdb=" O SER F 251 " pdb=" OG SER F 255 " model vdw 2.597 3.040 nonbonded pdb=" O ASN E 682 " pdb=" OH TYR E 689 " model vdw 2.599 3.040 nonbonded pdb=" O ASN F 682 " pdb=" OH TYR F 689 " model vdw 2.600 3.040 nonbonded pdb=" OH TYR E 240 " pdb=" OD1 ASP F 385 " model vdw 2.604 3.040 ... (remaining 79141 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: 0.01 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' } 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: 1.440 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.640 Find NCS groups from input model: 0.040 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:5.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 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 : 0.010 0.046 9252 Z= 0.587 Angle : 1.584 8.779 12610 Z= 1.049 Chirality : 0.093 0.491 1536 Planarity : 0.012 0.063 1510 Dihedral : 13.021 87.647 3462 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.62 % Allowed : 3.39 % Favored : 96.00 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -0.60 (0.23), residues: 1142 helix: -0.28 (0.15), residues: 916 sheet: None (None), residues: 0 loop : -0.18 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 657 TYR 0.099 0.011 TYR F 151 PHE 0.093 0.013 PHE F 695 TRP 0.085 0.022 TRP F 679 HIS 0.010 0.004 HIS E 310 Details of bonding type rmsd covalent geometry : bond 0.00987 ( 9252) covalent geometry : angle 1.58357 (12610) hydrogen bonds : bond 0.14629 ( 751) hydrogen bonds : angle 6.83931 ( 2217) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.224 Fit side-chains REVERT: F 288 LEU cc_start: 0.8805 (tp) cc_final: 0.8588 (mt) REVERT: F 297 MET cc_start: 0.8429 (mmt) cc_final: 0.8206 (mmp) outliers start: 6 outliers final: 0 residues processed: 120 average time/residue: 0.3664 time to fit residues: 48.0697 Evaluate side-chains 65 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 143 GLN E 198 ASN E 243 ASN F 143 GLN F 198 ASN F 243 ASN F 422 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.095283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.074704 restraints weight = 21418.118| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.63 r_work: 0.3135 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9252 Z= 0.169 Angle : 0.646 6.272 12610 Z= 0.333 Chirality : 0.043 0.221 1536 Planarity : 0.005 0.040 1510 Dihedral : 7.363 59.885 1492 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.13 % Allowed : 9.75 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.70 (0.25), residues: 1142 helix: 1.36 (0.16), residues: 926 sheet: None (None), residues: 0 loop : 0.44 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 213 TYR 0.020 0.001 TYR E 451 PHE 0.029 0.002 PHE E 221 TRP 0.011 0.002 TRP F 679 HIS 0.002 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9252) covalent geometry : angle 0.64575 (12610) hydrogen bonds : bond 0.05489 ( 751) hydrogen bonds : angle 5.06879 ( 2217) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.246 Fit side-chains REVERT: E 216 GLN cc_start: 0.8703 (mt0) cc_final: 0.8351 (mt0) REVERT: F 288 LEU cc_start: 0.8258 (tp) cc_final: 0.7973 (mt) REVERT: F 297 MET cc_start: 0.8876 (mmt) cc_final: 0.8636 (mmp) REVERT: F 429 MET cc_start: 0.8749 (tpp) cc_final: 0.8481 (tpp) outliers start: 11 outliers final: 2 residues processed: 79 average time/residue: 0.3460 time to fit residues: 30.3582 Evaluate side-chains 65 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 215 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 54 optimal weight: 0.3980 chunk 56 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 113 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.095447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.075176 restraints weight = 21272.597| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.62 r_work: 0.3154 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9252 Z= 0.147 Angle : 0.577 6.911 12610 Z= 0.292 Chirality : 0.042 0.224 1536 Planarity : 0.004 0.032 1510 Dihedral : 7.090 57.854 1492 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.95 % Allowed : 10.78 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 2.36 (0.25), residues: 1142 helix: 1.85 (0.17), residues: 930 sheet: None (None), residues: 0 loop : 0.49 (0.47), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 61 TYR 0.016 0.001 TYR F 451 PHE 0.024 0.002 PHE E 221 TRP 0.012 0.001 TRP F 363 HIS 0.001 0.000 HIS E 412 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9252) covalent geometry : angle 0.57662 (12610) hydrogen bonds : bond 0.04798 ( 751) hydrogen bonds : angle 4.73062 ( 2217) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.233 Fit side-chains REVERT: E 216 GLN cc_start: 0.8687 (mt0) cc_final: 0.8353 (mt0) REVERT: E 337 ASN cc_start: 0.9165 (t0) cc_final: 0.8800 (t0) REVERT: E 338 MET cc_start: 0.7492 (mtt) cc_final: 0.6916 (mtp) REVERT: F 288 LEU cc_start: 0.8225 (tp) cc_final: 0.7989 (mt) REVERT: F 337 ASN cc_start: 0.9166 (t0) cc_final: 0.8769 (t0) REVERT: F 338 MET cc_start: 0.7518 (mtt) cc_final: 0.7243 (mtm) REVERT: F 420 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8679 (mp) REVERT: F 429 MET cc_start: 0.8775 (tpp) cc_final: 0.8511 (tpp) REVERT: F 486 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.7948 (pt) outliers start: 19 outliers final: 3 residues processed: 84 average time/residue: 0.3308 time to fit residues: 30.9579 Evaluate side-chains 68 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 521 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 27 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 90 optimal weight: 0.0770 chunk 57 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.095756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.075398 restraints weight = 21632.126| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.65 r_work: 0.3159 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9252 Z= 0.141 Angle : 0.566 7.398 12610 Z= 0.283 Chirality : 0.041 0.219 1536 Planarity : 0.004 0.030 1510 Dihedral : 6.995 57.734 1492 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.44 % Allowed : 12.01 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 2.61 (0.25), residues: 1142 helix: 2.05 (0.17), residues: 930 sheet: None (None), residues: 0 loop : 0.40 (0.45), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 61 TYR 0.015 0.001 TYR E 451 PHE 0.023 0.002 PHE E 221 TRP 0.011 0.001 TRP E 363 HIS 0.001 0.000 HIS F 412 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9252) covalent geometry : angle 0.56607 (12610) hydrogen bonds : bond 0.04540 ( 751) hydrogen bonds : angle 4.60272 ( 2217) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.275 Fit side-chains REVERT: E 337 ASN cc_start: 0.9143 (t0) cc_final: 0.8789 (t0) REVERT: E 338 MET cc_start: 0.7313 (mtt) cc_final: 0.6806 (mtp) REVERT: F 288 LEU cc_start: 0.8196 (tp) cc_final: 0.7972 (mt) REVERT: F 337 ASN cc_start: 0.9164 (t0) cc_final: 0.8757 (t0) REVERT: F 338 MET cc_start: 0.7421 (mtt) cc_final: 0.7151 (mtm) REVERT: F 420 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8691 (mp) REVERT: F 429 MET cc_start: 0.8760 (tpp) cc_final: 0.8513 (tpp) outliers start: 14 outliers final: 1 residues processed: 75 average time/residue: 0.3483 time to fit residues: 28.9206 Evaluate side-chains 63 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 521 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.094928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.074523 restraints weight = 21671.357| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.65 r_work: 0.3138 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9252 Z= 0.158 Angle : 0.574 7.627 12610 Z= 0.285 Chirality : 0.042 0.222 1536 Planarity : 0.004 0.030 1510 Dihedral : 6.947 58.064 1492 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.03 % Allowed : 13.55 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 2.66 (0.25), residues: 1142 helix: 2.11 (0.17), residues: 930 sheet: None (None), residues: 0 loop : 0.32 (0.45), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 61 TYR 0.014 0.001 TYR F 451 PHE 0.020 0.001 PHE E 221 TRP 0.012 0.001 TRP E 363 HIS 0.001 0.000 HIS F 505 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9252) covalent geometry : angle 0.57386 (12610) hydrogen bonds : bond 0.04556 ( 751) hydrogen bonds : angle 4.56251 ( 2217) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.294 Fit side-chains REVERT: E 337 ASN cc_start: 0.9160 (t0) cc_final: 0.8842 (t0) REVERT: E 338 MET cc_start: 0.7271 (mtt) cc_final: 0.6812 (mtp) REVERT: E 420 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8700 (mp) REVERT: F 288 LEU cc_start: 0.8307 (tp) cc_final: 0.7991 (mt) REVERT: F 337 ASN cc_start: 0.9179 (t0) cc_final: 0.8756 (t0) REVERT: F 338 MET cc_start: 0.7427 (mtt) cc_final: 0.7104 (mtm) REVERT: F 420 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8708 (mp) REVERT: F 429 MET cc_start: 0.8779 (tpp) cc_final: 0.8518 (tpp) REVERT: F 540 MET cc_start: 0.8369 (pp-130) cc_final: 0.8064 (ppp) outliers start: 10 outliers final: 3 residues processed: 74 average time/residue: 0.3525 time to fit residues: 29.0228 Evaluate side-chains 66 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 521 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 105 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.094752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.074434 restraints weight = 21595.423| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.64 r_work: 0.3136 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9252 Z= 0.160 Angle : 0.571 7.904 12610 Z= 0.282 Chirality : 0.042 0.223 1536 Planarity : 0.004 0.029 1510 Dihedral : 6.888 59.355 1492 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.33 % Allowed : 13.55 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 2.71 (0.25), residues: 1142 helix: 2.15 (0.17), residues: 930 sheet: None (None), residues: 0 loop : 0.29 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 61 TYR 0.014 0.001 TYR E 451 PHE 0.016 0.001 PHE E 221 TRP 0.011 0.001 TRP E 363 HIS 0.001 0.000 HIS F 412 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 9252) covalent geometry : angle 0.57123 (12610) hydrogen bonds : bond 0.04517 ( 751) hydrogen bonds : angle 4.52793 ( 2217) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.347 Fit side-chains REVERT: E 337 ASN cc_start: 0.9217 (t0) cc_final: 0.8877 (t0) REVERT: E 338 MET cc_start: 0.7259 (mtt) cc_final: 0.6803 (mtp) REVERT: F 288 LEU cc_start: 0.8304 (tp) cc_final: 0.7997 (mt) REVERT: F 337 ASN cc_start: 0.9184 (t0) cc_final: 0.8800 (t0) REVERT: F 338 MET cc_start: 0.7422 (mtt) cc_final: 0.7119 (mtm) REVERT: F 420 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8693 (mp) REVERT: F 429 MET cc_start: 0.8807 (tpp) cc_final: 0.8540 (tpp) outliers start: 13 outliers final: 4 residues processed: 77 average time/residue: 0.3512 time to fit residues: 29.8892 Evaluate side-chains 68 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 521 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 74 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 0.0570 chunk 65 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.095805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.075578 restraints weight = 21728.746| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.66 r_work: 0.3160 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9252 Z= 0.136 Angle : 0.569 8.287 12610 Z= 0.280 Chirality : 0.042 0.251 1536 Planarity : 0.004 0.030 1510 Dihedral : 6.850 59.622 1492 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.44 % Allowed : 13.55 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 2.80 (0.25), residues: 1142 helix: 2.21 (0.17), residues: 934 sheet: None (None), residues: 0 loop : 0.27 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 61 TYR 0.014 0.001 TYR E 451 PHE 0.031 0.001 PHE E 221 TRP 0.011 0.001 TRP E 363 HIS 0.001 0.000 HIS E 412 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9252) covalent geometry : angle 0.56867 (12610) hydrogen bonds : bond 0.04361 ( 751) hydrogen bonds : angle 4.49830 ( 2217) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.287 Fit side-chains REVERT: E 337 ASN cc_start: 0.9169 (t0) cc_final: 0.8854 (t0) REVERT: E 338 MET cc_start: 0.7281 (mtt) cc_final: 0.6800 (mtp) REVERT: F 288 LEU cc_start: 0.8293 (tp) cc_final: 0.8006 (mt) REVERT: F 337 ASN cc_start: 0.9172 (t0) cc_final: 0.8805 (t0) REVERT: F 338 MET cc_start: 0.7542 (mtt) cc_final: 0.7286 (mtm) REVERT: F 420 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8705 (mp) REVERT: F 429 MET cc_start: 0.8782 (tpp) cc_final: 0.8524 (tpp) outliers start: 14 outliers final: 4 residues processed: 80 average time/residue: 0.3274 time to fit residues: 29.2317 Evaluate side-chains 68 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 521 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 64 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 95 optimal weight: 0.4980 chunk 83 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.095775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.075672 restraints weight = 21618.232| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.62 r_work: 0.3158 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9252 Z= 0.144 Angle : 0.600 11.827 12610 Z= 0.289 Chirality : 0.042 0.284 1536 Planarity : 0.004 0.030 1510 Dihedral : 6.826 59.238 1492 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.92 % Allowed : 13.86 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 2.78 (0.25), residues: 1142 helix: 2.18 (0.17), residues: 934 sheet: None (None), residues: 0 loop : 0.36 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 61 TYR 0.015 0.001 TYR E 320 PHE 0.030 0.001 PHE F 221 TRP 0.011 0.001 TRP E 363 HIS 0.001 0.000 HIS E 412 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9252) covalent geometry : angle 0.60037 (12610) hydrogen bonds : bond 0.04362 ( 751) hydrogen bonds : angle 4.51174 ( 2217) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.327 Fit side-chains REVERT: E 337 ASN cc_start: 0.9242 (t0) cc_final: 0.8919 (t0) REVERT: E 338 MET cc_start: 0.7188 (mtt) cc_final: 0.6702 (mtp) REVERT: E 540 MET cc_start: 0.8234 (pp-130) cc_final: 0.7990 (ppp) REVERT: F 288 LEU cc_start: 0.8165 (tp) cc_final: 0.7878 (mt) REVERT: F 337 ASN cc_start: 0.9236 (t0) cc_final: 0.8867 (t0) REVERT: F 338 MET cc_start: 0.7437 (mtt) cc_final: 0.7169 (mtm) REVERT: F 420 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8642 (mp) REVERT: F 429 MET cc_start: 0.8696 (tpp) cc_final: 0.8427 (tpp) REVERT: F 540 MET cc_start: 0.8239 (pp-130) cc_final: 0.8001 (ppp) outliers start: 9 outliers final: 3 residues processed: 74 average time/residue: 0.3863 time to fit residues: 31.5510 Evaluate side-chains 68 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 521 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 87 optimal weight: 0.3980 chunk 88 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.095678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.075553 restraints weight = 21745.757| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.63 r_work: 0.3150 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9252 Z= 0.147 Angle : 0.603 11.925 12610 Z= 0.290 Chirality : 0.042 0.272 1536 Planarity : 0.004 0.029 1510 Dihedral : 6.793 58.354 1492 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.13 % Allowed : 13.76 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 2.86 (0.25), residues: 1142 helix: 2.24 (0.17), residues: 926 sheet: None (None), residues: 0 loop : 0.45 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 678 TYR 0.014 0.001 TYR E 320 PHE 0.027 0.001 PHE F 221 TRP 0.011 0.001 TRP E 363 HIS 0.001 0.000 HIS E 412 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9252) covalent geometry : angle 0.60261 (12610) hydrogen bonds : bond 0.04364 ( 751) hydrogen bonds : angle 4.48760 ( 2217) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.291 Fit side-chains REVERT: E 337 ASN cc_start: 0.9252 (t0) cc_final: 0.8928 (t0) REVERT: E 338 MET cc_start: 0.7106 (mtt) cc_final: 0.6609 (mtp) REVERT: E 521 MET cc_start: 0.5422 (OUTLIER) cc_final: 0.4907 (tpp) REVERT: F 288 LEU cc_start: 0.8179 (tp) cc_final: 0.7891 (mt) REVERT: F 337 ASN cc_start: 0.9240 (t0) cc_final: 0.8869 (t0) REVERT: F 338 MET cc_start: 0.7450 (mtt) cc_final: 0.7177 (mtm) REVERT: F 420 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8653 (mp) REVERT: F 429 MET cc_start: 0.8698 (tpp) cc_final: 0.8428 (tpp) outliers start: 11 outliers final: 5 residues processed: 75 average time/residue: 0.3478 time to fit residues: 28.7338 Evaluate side-chains 69 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 521 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 92 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 25 optimal weight: 0.0050 chunk 12 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.096116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075958 restraints weight = 21594.398| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.63 r_work: 0.3156 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9252 Z= 0.143 Angle : 0.619 15.332 12610 Z= 0.294 Chirality : 0.042 0.264 1536 Planarity : 0.004 0.030 1510 Dihedral : 6.730 56.221 1492 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.13 % Allowed : 13.96 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 2.89 (0.25), residues: 1142 helix: 2.24 (0.17), residues: 926 sheet: None (None), residues: 0 loop : 0.57 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 213 TYR 0.013 0.001 TYR E 320 PHE 0.026 0.001 PHE F 221 TRP 0.011 0.001 TRP F 363 HIS 0.001 0.000 HIS E 412 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9252) covalent geometry : angle 0.61910 (12610) hydrogen bonds : bond 0.04336 ( 751) hydrogen bonds : angle 4.48811 ( 2217) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.292 Fit side-chains REVERT: E 337 ASN cc_start: 0.9217 (t0) cc_final: 0.8898 (t0) REVERT: E 338 MET cc_start: 0.7194 (mtt) cc_final: 0.6716 (mtp) REVERT: E 521 MET cc_start: 0.5877 (OUTLIER) cc_final: 0.5365 (tpp) REVERT: F 288 LEU cc_start: 0.8256 (tp) cc_final: 0.7973 (mt) REVERT: F 337 ASN cc_start: 0.9203 (t0) cc_final: 0.8837 (t0) REVERT: F 338 MET cc_start: 0.7485 (mtt) cc_final: 0.7202 (mtm) REVERT: F 420 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8699 (mp) REVERT: F 429 MET cc_start: 0.8774 (tpp) cc_final: 0.8507 (tpp) outliers start: 11 outliers final: 5 residues processed: 73 average time/residue: 0.3310 time to fit residues: 26.8856 Evaluate side-chains 71 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 521 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 29 optimal weight: 0.4980 chunk 90 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 112 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.096314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.076322 restraints weight = 21379.647| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.60 r_work: 0.3168 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9252 Z= 0.136 Angle : 0.614 11.974 12610 Z= 0.291 Chirality : 0.042 0.294 1536 Planarity : 0.004 0.030 1510 Dihedral : 6.715 56.425 1492 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.82 % Allowed : 14.17 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 2.94 (0.25), residues: 1142 helix: 2.26 (0.17), residues: 926 sheet: None (None), residues: 0 loop : 0.67 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 678 TYR 0.011 0.001 TYR E 320 PHE 0.025 0.001 PHE F 221 TRP 0.011 0.001 TRP F 363 HIS 0.001 0.000 HIS E 412 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9252) covalent geometry : angle 0.61380 (12610) hydrogen bonds : bond 0.04293 ( 751) hydrogen bonds : angle 4.46484 ( 2217) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1915.28 seconds wall clock time: 33 minutes 31.56 seconds (2011.56 seconds total)