Starting phenix.real_space_refine on Fri Oct 11 03:26:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5c_41916/10_2024/8u5c_41916.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5c_41916/10_2024/8u5c_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5c_41916/10_2024/8u5c_41916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5c_41916/10_2024/8u5c_41916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5c_41916/10_2024/8u5c_41916.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5c_41916/10_2024/8u5c_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-5477/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: 5.86, per 1000 atoms: 0.65 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: 2.28 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: 0.85 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: 2.68 Time building geometry restraints manager: 2.61 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: 0.00 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: 1.340 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: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.110 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.580 ------------------------------------------------------------------------------- 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= 0.637 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 *********************** 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 fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 1.030 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: 0.9830 time to fit residues: 128.7306 Evaluate side-chains 65 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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= 0.236 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 *********************** 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 fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 0.980 Fit side-chains outliers start: 12 outliers final: 1 residues processed: 83 average time/residue: 0.8978 time to fit residues: 82.3922 Evaluate side-chains 60 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 57 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2578 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= 0.225 Angle : 0.588 6.491 12610 Z= 0.298 Chirality : 0.042 0.230 1536 Planarity : 0.004 0.032 1510 Dihedral : 7.085 57.903 1492 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.95 % Allowed : 10.88 % 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: 2.32 (0.25), residues: 1142 helix: 1.81 (0.17), residues: 930 sheet: None (None), residues: 0 loop : 0.52 (0.48), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 363 HIS 0.001 0.000 HIS E 412 PHE 0.024 0.002 PHE F 221 TYR 0.015 0.001 TYR F 451 ARG 0.001 0.000 ARG E 61 *********************** 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 fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 1.111 Fit side-chains REVERT: E 338 MET cc_start: 0.7479 (mtt) cc_final: 0.7244 (mtp) REVERT: E 521 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6884 (mmt) outliers start: 19 outliers final: 3 residues processed: 80 average time/residue: 0.8396 time to fit residues: 74.6786 Evaluate side-chains 65 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 521 MET 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 102 optimal weight: 0.0970 chunk 77 optimal weight: 0.0060 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 0.0050 chunk 110 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 overall best weight: 0.3008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9252 Z= 0.161 Angle : 0.556 7.420 12610 Z= 0.279 Chirality : 0.040 0.212 1536 Planarity : 0.004 0.031 1510 Dihedral : 7.012 58.658 1492 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.23 % Allowed : 11.91 % Favored : 86.86 % 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: 2.66 (0.25), residues: 1142 helix: 2.10 (0.17), residues: 930 sheet: None (None), residues: 0 loop : 0.38 (0.45), residues: 212 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 0.022 0.001 PHE E 221 TYR 0.015 0.001 TYR E 451 ARG 0.001 0.000 ARG F 61 *********************** 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 82 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 1.089 Fit side-chains REVERT: F 494 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8206 (tp) outliers start: 12 outliers final: 0 residues processed: 76 average time/residue: 0.8521 time to fit residues: 72.0363 Evaluate side-chains 59 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 494 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 0.0770 chunk 94 optimal weight: 0.1980 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9252 Z= 0.190 Angle : 0.561 7.556 12610 Z= 0.279 Chirality : 0.041 0.219 1536 Planarity : 0.004 0.030 1510 Dihedral : 6.927 58.034 1492 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.23 % Allowed : 13.66 % 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 (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: 2.69 (0.25), residues: 1142 helix: 2.13 (0.17), residues: 934 sheet: None (None), residues: 0 loop : 0.31 (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 F 658 PHE 0.020 0.001 PHE E 221 TYR 0.014 0.001 TYR E 451 ARG 0.001 0.000 ARG F 61 *********************** 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 78 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 1.036 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 74 average time/residue: 0.8685 time to fit residues: 71.4721 Evaluate side-chains 66 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 466 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3215 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= 0.207 Angle : 0.568 7.990 12610 Z= 0.280 Chirality : 0.042 0.220 1536 Planarity : 0.004 0.030 1510 Dihedral : 6.892 58.672 1492 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.33 % Allowed : 13.76 % 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 (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: 2.76 (0.25), residues: 1142 helix: 2.18 (0.17), residues: 934 sheet: None (None), residues: 0 loop : 0.29 (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 0.015 0.001 TYR E 451 ARG 0.001 0.000 ARG F 61 *********************** 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 76 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 1.037 Fit side-chains outliers start: 13 outliers final: 3 residues processed: 74 average time/residue: 0.8921 time to fit residues: 73.0584 Evaluate side-chains 63 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 466 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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= 0.192 Angle : 0.571 8.467 12610 Z= 0.279 Chirality : 0.041 0.243 1536 Planarity : 0.003 0.030 1510 Dihedral : 6.854 59.910 1492 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.23 % Allowed : 13.96 % 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: 2.88 (0.25), residues: 1142 helix: 2.27 (0.17), residues: 926 sheet: None (None), residues: 0 loop : 0.37 (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 E 412 PHE 0.015 0.001 PHE E 221 TYR 0.013 0.001 TYR F 451 ARG 0.001 0.000 ARG F 61 *********************** 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 77 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 1.076 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 74 average time/residue: 0.9705 time to fit residues: 79.1018 Evaluate side-chains 66 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 215 LEU 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 43 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 10 optimal weight: 0.0030 chunk 86 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9252 Z= 0.179 Angle : 0.585 9.795 12610 Z= 0.285 Chirality : 0.042 0.280 1536 Planarity : 0.003 0.030 1510 Dihedral : 6.820 59.436 1492 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.72 % Allowed : 14.27 % 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: 2.29 (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 E 412 PHE 0.032 0.001 PHE F 221 TYR 0.013 0.001 TYR F 451 ARG 0.001 0.000 ARG E 213 *********************** 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 74 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 1.048 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 73 average time/residue: 0.8692 time to fit residues: 70.4492 Evaluate side-chains 63 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain F residue 136 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 0.0050 chunk 80 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3478 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= 0.182 Angle : 0.592 10.245 12610 Z= 0.286 Chirality : 0.042 0.270 1536 Planarity : 0.003 0.030 1510 Dihedral : 6.772 58.476 1492 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.72 % Allowed : 14.78 % Favored : 84.50 % 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: 2.30 (0.17), residues: 924 sheet: None (None), residues: 0 loop : 0.38 (0.44), residues: 218 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 0.028 0.001 PHE E 221 TYR 0.014 0.001 TYR F 451 ARG 0.001 0.000 ARG E 61 *********************** 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 72 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 1.143 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 71 average time/residue: 1.0200 time to fit residues: 79.5395 Evaluate side-chains 63 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain F residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9252 Z= 0.225 Angle : 0.622 11.463 12610 Z= 0.299 Chirality : 0.043 0.260 1536 Planarity : 0.004 0.029 1510 Dihedral : 6.767 58.329 1492 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.72 % Allowed : 14.99 % Favored : 84.29 % 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: 2.23 (0.17), residues: 926 sheet: None (None), residues: 0 loop : 0.56 (0.46), 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 0.002 PHE F 221 TYR 0.013 0.001 TYR E 320 ARG 0.001 0.000 ARG F 687 ********************** 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 67 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 1.085 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 65 average time/residue: 0.9621 time to fit residues: 68.7932 Evaluate side-chains 62 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain F residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 chunk 37 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 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 = 0.3705 r_free = 0.3705 target = 0.096654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.076640 restraints weight = 21467.176| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.62 r_work: 0.3179 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3586 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= 0.193 Angle : 0.613 11.472 12610 Z= 0.293 Chirality : 0.042 0.299 1536 Planarity : 0.004 0.029 1510 Dihedral : 6.716 56.556 1492 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.72 % Allowed : 14.89 % Favored : 84.39 % 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: 2.24 (0.17), residues: 926 sheet: None (None), residues: 0 loop : 0.64 (0.46), 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 0.025 0.001 PHE F 221 TYR 0.011 0.001 TYR E 320 ARG 0.001 0.000 ARG F 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2394.34 seconds wall clock time: 44 minutes 17.03 seconds (2657.03 seconds total)