Starting phenix.real_space_refine on Mon May 12 14:15:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u5c_41916/05_2025/8u5c_41916.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u5c_41916/05_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_41916/05_2025/8u5c_41916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u5c_41916/05_2025/8u5c_41916.map" model { file = "/net/cci-nas-00/data/ceres_data/8u5c_41916/05_2025/8u5c_41916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u5c_41916/05_2025/8u5c_41916.cif" } resolution = 2.68 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= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'ASP:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'ASP:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} 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: 5.73, per 1000 atoms: 0.63 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: 2.51 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.89 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: 2.64 Time building geometry restraints manager: 2.86 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: 0.05 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.470 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.700 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.085 0.022 TRP F 679 HIS 0.010 0.004 HIS E 310 PHE 0.093 0.013 PHE F 695 TYR 0.099 0.011 TYR F 151 ARG 0.011 0.001 ARG F 657 Details of bonding type rmsd hydrogen bonds : bond 0.14629 ( 751) hydrogen bonds : angle 6.83931 ( 2217) covalent geometry : bond 0.00987 ( 9252) covalent geometry : angle 1.58357 (12610) *********************** 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 : 1.017 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: 0.9431 time to fit residues: 123.5469 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 : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.095329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.074746 restraints weight = 21150.207| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.62 r_work: 0.3142 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9252 Z= 0.173 Angle : 0.642 6.476 12610 Z= 0.331 Chirality : 0.043 0.204 1536 Planarity : 0.005 0.039 1510 Dihedral : 7.394 59.489 1492 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.23 % Allowed : 9.75 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.70 (0.25), residues: 1142 helix: 1.36 (0.16), residues: 926 sheet: None (None), residues: 0 loop : 0.46 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 679 HIS 0.002 0.001 HIS E 505 PHE 0.028 0.002 PHE E 221 TYR 0.019 0.001 TYR E 451 ARG 0.003 0.001 ARG E 61 Details of bonding type rmsd hydrogen bonds : bond 0.05305 ( 751) hydrogen bonds : angle 5.04827 ( 2217) covalent geometry : bond 0.00377 ( 9252) covalent geometry : angle 0.64229 (12610) *********************** 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 87 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 1.038 Fit side-chains REVERT: E 216 GLN cc_start: 0.8700 (mt0) cc_final: 0.8361 (mt0) REVERT: F 288 LEU cc_start: 0.8243 (tp) cc_final: 0.7971 (mt) REVERT: F 297 MET cc_start: 0.8878 (mmt) cc_final: 0.8649 (mmp) REVERT: F 429 MET cc_start: 0.8756 (tpp) cc_final: 0.8503 (tpp) outliers start: 12 outliers final: 1 residues processed: 83 average time/residue: 0.9611 time to fit residues: 88.2259 Evaluate side-chains 62 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 93 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 67 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 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 = 0.3676 r_free = 0.3676 target = 0.094997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.074617 restraints weight = 21576.497| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.63 r_work: 0.3140 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9252 Z= 0.157 Angle : 0.584 6.477 12610 Z= 0.297 Chirality : 0.042 0.230 1536 Planarity : 0.004 0.033 1510 Dihedral : 7.069 57.903 1492 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.64 % Allowed : 10.99 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.36 (0.25), residues: 1142 helix: 1.84 (0.17), residues: 930 sheet: None (None), residues: 0 loop : 0.53 (0.48), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 363 HIS 0.001 0.000 HIS E 412 PHE 0.024 0.002 PHE E 221 TYR 0.015 0.001 TYR F 451 ARG 0.001 0.000 ARG E 61 Details of bonding type rmsd hydrogen bonds : bond 0.04871 ( 751) hydrogen bonds : angle 4.74511 ( 2217) covalent geometry : bond 0.00351 ( 9252) covalent geometry : angle 0.58439 (12610) *********************** 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 85 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.990 Fit side-chains REVERT: E 216 GLN cc_start: 0.8693 (mt0) cc_final: 0.8345 (mt0) REVERT: E 337 ASN cc_start: 0.9172 (t0) cc_final: 0.8845 (t0) REVERT: E 338 MET cc_start: 0.7283 (mtt) cc_final: 0.6820 (mtp) REVERT: E 429 MET cc_start: 0.8700 (tpp) cc_final: 0.8497 (tpp) REVERT: F 288 LEU cc_start: 0.8229 (tp) cc_final: 0.7975 (mt) REVERT: F 420 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8673 (mp) outliers start: 16 outliers final: 2 residues processed: 80 average time/residue: 0.7949 time to fit residues: 70.8323 Evaluate side-chains 66 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 0.0270 chunk 84 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 = 0.095416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.075126 restraints weight = 21381.545| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.63 r_work: 0.3155 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2908 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= 0.145 Angle : 0.568 6.950 12610 Z= 0.284 Chirality : 0.041 0.218 1536 Planarity : 0.004 0.030 1510 Dihedral : 7.012 58.389 1492 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.64 % Allowed : 11.19 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.60 (0.25), residues: 1142 helix: 2.04 (0.17), residues: 930 sheet: None (None), residues: 0 loop : 0.42 (0.45), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 363 HIS 0.001 0.000 HIS F 412 PHE 0.023 0.001 PHE E 221 TYR 0.015 0.001 TYR E 451 ARG 0.001 0.000 ARG F 61 Details of bonding type rmsd hydrogen bonds : bond 0.04571 ( 751) hydrogen bonds : angle 4.60508 ( 2217) covalent geometry : bond 0.00324 ( 9252) covalent geometry : angle 0.56831 (12610) *********************** 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: 16 poor density : 65 time to evaluate : 0.989 Fit side-chains REVERT: E 337 ASN cc_start: 0.9151 (t0) cc_final: 0.8834 (t0) REVERT: E 338 MET cc_start: 0.7279 (mtt) cc_final: 0.6751 (mtp) REVERT: E 420 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8702 (mp) REVERT: E 429 MET cc_start: 0.8702 (tpp) cc_final: 0.8495 (tpp) REVERT: F 288 LEU cc_start: 0.8211 (tp) cc_final: 0.7982 (mt) REVERT: F 337 ASN cc_start: 0.9235 (t0) cc_final: 0.8732 (t0) REVERT: F 420 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8693 (mp) REVERT: F 429 MET cc_start: 0.8758 (tpp) cc_final: 0.8545 (tpp) outliers start: 16 outliers final: 1 residues processed: 75 average time/residue: 0.8212 time to fit residues: 68.4765 Evaluate side-chains 64 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain F residue 420 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 67 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.094849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.074498 restraints weight = 21520.607| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.64 r_work: 0.3137 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9252 Z= 0.155 Angle : 0.567 6.742 12610 Z= 0.283 Chirality : 0.042 0.222 1536 Planarity : 0.004 0.030 1510 Dihedral : 6.930 58.034 1492 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.44 % Allowed : 12.94 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.68 (0.25), residues: 1142 helix: 2.11 (0.17), residues: 930 sheet: None (None), residues: 0 loop : 0.37 (0.45), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 363 HIS 0.001 0.000 HIS F 658 PHE 0.019 0.001 PHE E 221 TYR 0.014 0.001 TYR E 451 ARG 0.001 0.000 ARG E 61 Details of bonding type rmsd hydrogen bonds : bond 0.04546 ( 751) hydrogen bonds : angle 4.55410 ( 2217) covalent geometry : bond 0.00354 ( 9252) covalent geometry : angle 0.56727 (12610) *********************** 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 80 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 1.084 Fit side-chains REVERT: E 337 ASN cc_start: 0.9153 (t0) cc_final: 0.8823 (t0) REVERT: E 338 MET cc_start: 0.7283 (mtt) cc_final: 0.6813 (mtp) REVERT: E 420 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8728 (mp) REVERT: E 429 MET cc_start: 0.8732 (tpp) cc_final: 0.8500 (tpp) REVERT: E 540 MET cc_start: 0.8350 (pp-130) cc_final: 0.8048 (ppp) REVERT: F 288 LEU cc_start: 0.8298 (tp) cc_final: 0.7987 (mt) REVERT: F 337 ASN cc_start: 0.9238 (t0) cc_final: 0.8752 (t0) REVERT: F 338 MET cc_start: 0.7443 (mtm) cc_final: 0.7219 (mtp) REVERT: F 420 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8699 (mp) REVERT: F 429 MET cc_start: 0.8732 (tpp) cc_final: 0.8469 (tpp) outliers start: 14 outliers final: 6 residues processed: 77 average time/residue: 0.7846 time to fit residues: 67.3593 Evaluate side-chains 69 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 420 ILE 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 521 MET Chi-restraints excluded: chain F residue 533 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 67 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 0.0770 chunk 105 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.095844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.075759 restraints weight = 21378.337| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.62 r_work: 0.3144 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3216 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= 0.134 Angle : 0.552 6.431 12610 Z= 0.274 Chirality : 0.041 0.221 1536 Planarity : 0.004 0.030 1510 Dihedral : 6.887 59.978 1492 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.54 % Allowed : 13.04 % 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 (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: 2.78 (0.25), residues: 1142 helix: 2.20 (0.17), residues: 934 sheet: None (None), residues: 0 loop : 0.26 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 363 HIS 0.001 0.000 HIS E 412 PHE 0.017 0.001 PHE E 221 TYR 0.014 0.001 TYR E 451 ARG 0.001 0.000 ARG F 61 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 751) hydrogen bonds : angle 4.48745 ( 2217) covalent geometry : bond 0.00299 ( 9252) covalent geometry : angle 0.55210 (12610) *********************** 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 84 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 1.017 Fit side-chains REVERT: E 337 ASN cc_start: 0.9185 (t0) cc_final: 0.8835 (t0) REVERT: E 338 MET cc_start: 0.7269 (mtt) cc_final: 0.6778 (mtp) REVERT: E 420 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8715 (mp) REVERT: E 429 MET cc_start: 0.8747 (tpp) cc_final: 0.8490 (tpp) REVERT: F 288 LEU cc_start: 0.8266 (tp) cc_final: 0.7976 (mt) REVERT: F 337 ASN cc_start: 0.9230 (t0) cc_final: 0.8728 (t0) REVERT: F 420 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8684 (mp) REVERT: F 429 MET cc_start: 0.8759 (tpp) cc_final: 0.8496 (tpp) outliers start: 15 outliers final: 4 residues processed: 81 average time/residue: 0.7863 time to fit residues: 70.8661 Evaluate side-chains 70 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 521 MET Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 466 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 65 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 94 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.095957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.075624 restraints weight = 21746.858| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.68 r_work: 0.3166 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3287 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= 0.134 Angle : 0.563 7.263 12610 Z= 0.277 Chirality : 0.041 0.245 1536 Planarity : 0.004 0.030 1510 Dihedral : 6.844 59.971 1492 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.33 % Allowed : 13.35 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.87 (0.25), residues: 1142 helix: 2.25 (0.17), residues: 926 sheet: None (None), residues: 0 loop : 0.42 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 363 HIS 0.001 0.000 HIS F 412 PHE 0.027 0.001 PHE E 221 TYR 0.013 0.001 TYR E 451 ARG 0.001 0.000 ARG F 61 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 751) hydrogen bonds : angle 4.46729 ( 2217) covalent geometry : bond 0.00300 ( 9252) covalent geometry : angle 0.56296 (12610) *********************** 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 79 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 1.008 Fit side-chains REVERT: E 337 ASN cc_start: 0.9188 (t0) cc_final: 0.8814 (t0) REVERT: E 338 MET cc_start: 0.7298 (mtt) cc_final: 0.6810 (mtp) REVERT: E 420 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8704 (mp) REVERT: E 429 MET cc_start: 0.8751 (tpp) cc_final: 0.8526 (tpp) REVERT: F 92 VAL cc_start: 0.9053 (t) cc_final: 0.8782 (m) REVERT: F 288 LEU cc_start: 0.8278 (tp) cc_final: 0.7994 (mt) REVERT: F 337 ASN cc_start: 0.9170 (t0) cc_final: 0.8706 (t0) REVERT: F 420 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8697 (mp) REVERT: F 429 MET cc_start: 0.8759 (tpp) cc_final: 0.8493 (tpp) outliers start: 13 outliers final: 4 residues processed: 76 average time/residue: 0.7989 time to fit residues: 67.8967 Evaluate side-chains 68 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 420 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.095943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.075841 restraints weight = 21953.707| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.64 r_work: 0.3165 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3350 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= 0.141 Angle : 0.573 7.024 12610 Z= 0.280 Chirality : 0.042 0.280 1536 Planarity : 0.003 0.030 1510 Dihedral : 6.810 59.157 1492 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.13 % Allowed : 13.45 % 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 (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: 2.91 (0.25), residues: 1142 helix: 2.28 (0.17), residues: 926 sheet: None (None), residues: 0 loop : 0.45 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 363 HIS 0.001 0.000 HIS F 412 PHE 0.028 0.001 PHE F 221 TYR 0.014 0.001 TYR E 320 ARG 0.001 0.000 ARG F 61 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 751) hydrogen bonds : angle 4.46848 ( 2217) covalent geometry : bond 0.00322 ( 9252) covalent geometry : angle 0.57250 (12610) *********************** 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 79 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 1.069 Fit side-chains REVERT: E 337 ASN cc_start: 0.9225 (t0) cc_final: 0.8849 (t0) REVERT: E 338 MET cc_start: 0.7248 (mtt) cc_final: 0.6755 (mtp) REVERT: E 420 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8690 (mp) REVERT: E 429 MET cc_start: 0.8758 (tpp) cc_final: 0.8530 (tpp) REVERT: E 540 MET cc_start: 0.8262 (pp-130) cc_final: 0.8008 (ppp) REVERT: F 92 VAL cc_start: 0.9038 (t) cc_final: 0.8758 (m) REVERT: F 288 LEU cc_start: 0.8237 (tp) cc_final: 0.7948 (mt) REVERT: F 337 ASN cc_start: 0.9248 (t0) cc_final: 0.8728 (t0) REVERT: F 420 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8692 (mp) REVERT: F 429 MET cc_start: 0.8758 (tpp) cc_final: 0.8495 (tpp) outliers start: 11 outliers final: 4 residues processed: 77 average time/residue: 0.8687 time to fit residues: 74.0798 Evaluate side-chains 70 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 420 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 533 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.095677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.075433 restraints weight = 21544.378| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.63 r_work: 0.3152 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3367 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= 0.150 Angle : 0.586 8.929 12610 Z= 0.286 Chirality : 0.042 0.272 1536 Planarity : 0.003 0.029 1510 Dihedral : 6.788 58.505 1492 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.33 % Allowed : 13.66 % 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 (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: 2.88 (0.25), residues: 1142 helix: 2.25 (0.17), residues: 926 sheet: None (None), residues: 0 loop : 0.48 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 363 HIS 0.001 0.000 HIS F 412 PHE 0.027 0.001 PHE E 221 TYR 0.015 0.001 TYR E 320 ARG 0.001 0.000 ARG E 687 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 751) hydrogen bonds : angle 4.47459 ( 2217) covalent geometry : bond 0.00347 ( 9252) covalent geometry : angle 0.58626 (12610) *********************** 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 75 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.994 Fit side-chains REVERT: E 337 ASN cc_start: 0.9221 (t0) cc_final: 0.8890 (t0) REVERT: E 338 MET cc_start: 0.7229 (mtt) cc_final: 0.6766 (mtp) REVERT: E 420 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8701 (mp) REVERT: E 429 MET cc_start: 0.8755 (tpp) cc_final: 0.8521 (tpp) REVERT: F 288 LEU cc_start: 0.8251 (tp) cc_final: 0.7951 (mt) REVERT: F 337 ASN cc_start: 0.9260 (t0) cc_final: 0.8753 (t0) REVERT: F 420 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8689 (mp) REVERT: F 429 MET cc_start: 0.8756 (tpp) cc_final: 0.8500 (tpp) REVERT: F 540 MET cc_start: 0.8268 (pp-130) cc_final: 0.8037 (ppp) outliers start: 13 outliers final: 6 residues processed: 72 average time/residue: 0.8794 time to fit residues: 70.1338 Evaluate side-chains 69 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 420 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 Chi-restraints excluded: chain F residue 533 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 61 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.096188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.075980 restraints weight = 21765.209| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.64 r_work: 0.3159 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3499 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= 0.137 Angle : 0.590 8.566 12610 Z= 0.285 Chirality : 0.042 0.296 1536 Planarity : 0.003 0.030 1510 Dihedral : 6.747 57.345 1492 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.03 % Allowed : 13.96 % 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 (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: 2.92 (0.25), residues: 1142 helix: 2.26 (0.17), residues: 926 sheet: None (None), residues: 0 loop : 0.59 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 363 HIS 0.001 0.000 HIS E 412 PHE 0.027 0.001 PHE E 221 TYR 0.013 0.001 TYR E 320 ARG 0.001 0.000 ARG F 687 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 751) hydrogen bonds : angle 4.45989 ( 2217) covalent geometry : bond 0.00311 ( 9252) covalent geometry : angle 0.59028 (12610) ********************** 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 77 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 1.054 Fit side-chains REVERT: E 337 ASN cc_start: 0.9209 (t0) cc_final: 0.8853 (t0) REVERT: E 338 MET cc_start: 0.7235 (mtt) cc_final: 0.6728 (mtp) REVERT: E 420 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8712 (mp) REVERT: E 429 MET cc_start: 0.8787 (tpp) cc_final: 0.8558 (tpp) REVERT: F 92 VAL cc_start: 0.9049 (t) cc_final: 0.8763 (m) REVERT: F 288 LEU cc_start: 0.8268 (tp) cc_final: 0.7981 (mt) REVERT: F 337 ASN cc_start: 0.9239 (t0) cc_final: 0.8721 (t0) REVERT: F 420 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8716 (mp) REVERT: F 540 MET cc_start: 0.8262 (pp-130) cc_final: 0.8022 (ppp) outliers start: 10 outliers final: 6 residues processed: 75 average time/residue: 0.8548 time to fit residues: 71.1062 Evaluate side-chains 71 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 420 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 Chi-restraints excluded: chain F residue 533 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 15 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 104 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 101 optimal weight: 0.0050 chunk 41 optimal weight: 0.7980 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.096681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.076650 restraints weight = 21590.589| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.61 r_work: 0.3175 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9252 Z= 0.131 Angle : 0.605 14.954 12610 Z= 0.289 Chirality : 0.042 0.298 1536 Planarity : 0.004 0.030 1510 Dihedral : 6.725 56.487 1492 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.92 % Allowed : 14.27 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.98 (0.25), residues: 1142 helix: 2.30 (0.17), residues: 926 sheet: None (None), residues: 0 loop : 0.59 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 363 HIS 0.001 0.000 HIS F 412 PHE 0.027 0.001 PHE E 221 TYR 0.012 0.001 TYR F 451 ARG 0.002 0.000 ARG F 213 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 751) hydrogen bonds : angle 4.43229 ( 2217) covalent geometry : bond 0.00294 ( 9252) covalent geometry : angle 0.60512 (12610) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4440.02 seconds wall clock time: 77 minutes 48.74 seconds (4668.74 seconds total)