Starting phenix.real_space_refine on Tue Sep 24 01:25:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4n_25681/09_2024/7t4n_25681.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4n_25681/09_2024/7t4n_25681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4n_25681/09_2024/7t4n_25681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4n_25681/09_2024/7t4n_25681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4n_25681/09_2024/7t4n_25681.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4n_25681/09_2024/7t4n_25681.cif" } resolution = 2.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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 44 5.16 5 C 4148 2.51 5 N 1090 2.21 5 O 1194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6476 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3264 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3255 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 385} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 404, 3255 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 385} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3308 Chain: "B" Number of atoms: 3212 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 3203 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 399, 3203 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3255 Time building chain proxies: 7.76, per 1000 atoms: 1.20 Number of scatterers: 6476 At special positions: 0 Unit cell: (115.787, 78.302, 74.97, 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 44 16.00 O 1194 8.00 N 1090 7.00 C 4148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 1.6 seconds 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1564 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 44.3% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 119 through 137 Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 307 through 328 Processing helix chain 'A' and resid 357 through 361 removed outlier: 4.566A pdb=" N CYS A 360 " --> pdb=" O ALA A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 406 through 420 removed outlier: 3.589A pdb=" N TYR A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 471 through 485 Processing helix chain 'A' and resid 486 through 491 removed outlier: 3.990A pdb=" N LEU A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 515 Processing helix chain 'A' and resid 542 through 554 Processing helix chain 'A' and resid 557 through 574 removed outlier: 4.022A pdb=" N HIS A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 573 " --> pdb=" O GLN A 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 137 removed outlier: 4.164A pdb=" N GLY B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 removed outlier: 3.724A pdb=" N GLU B 158 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 215 Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 307 through 328 removed outlier: 3.587A pdb=" N HIS B 328 " --> pdb=" O HIS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 removed outlier: 4.536A pdb=" N CYS B 360 " --> pdb=" O ALA B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 393 Processing helix chain 'B' and resid 406 through 420 removed outlier: 3.733A pdb=" N TYR B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 removed outlier: 3.515A pdb=" N LEU B 443 " --> pdb=" O GLU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 471 through 485 Processing helix chain 'B' and resid 486 through 491 removed outlier: 3.779A pdb=" N LEU B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 515 Processing helix chain 'B' and resid 542 through 554 Processing helix chain 'B' and resid 557 through 574 removed outlier: 3.819A pdb=" N HIS B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 160 removed outlier: 3.573A pdb=" N SER A 251 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LYS A 291 " --> pdb=" O MET A 249 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N MET A 249 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AA4, first strand: chain 'A' and resid 330 through 331 Processing sheet with id=AA5, first strand: chain 'A' and resid 370 through 372 Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 166 removed outlier: 7.056A pdb=" N LYS B 291 " --> pdb=" O MET B 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET B 249 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 295 through 296 removed outlier: 3.528A pdb=" N CYS B 295 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 370 through 372 293 hydrogen bonds defined for protein. 841 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.73 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2087 1.34 - 1.46: 1313 1.46 - 1.58: 3139 1.58 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 6607 Sorted by residual: bond pdb=" CB ASP B 428 " pdb=" CG ASP B 428 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.24e-01 bond pdb=" C ILE A 233 " pdb=" O ILE A 233 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.19e-02 7.06e+03 8.44e-01 bond pdb=" CB LYS B 432 " pdb=" CG LYS B 432 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.51e-01 bond pdb=" CG LYS B 432 " pdb=" CD LYS B 432 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 4.98e-01 bond pdb=" CA ASP B 428 " pdb=" CB ASP B 428 " ideal model delta sigma weight residual 1.528 1.540 -0.012 1.66e-02 3.63e+03 4.92e-01 ... (remaining 6602 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 8755 1.16 - 2.32: 146 2.32 - 3.48: 36 3.48 - 4.64: 6 4.64 - 5.80: 3 Bond angle restraints: 8946 Sorted by residual: angle pdb=" CB LYS B 432 " pdb=" CG LYS B 432 " pdb=" CD LYS B 432 " ideal model delta sigma weight residual 111.30 117.10 -5.80 2.30e+00 1.89e-01 6.35e+00 angle pdb=" CA ASP B 428 " pdb=" CB ASP B 428 " pdb=" CG ASP B 428 " ideal model delta sigma weight residual 112.60 114.61 -2.01 1.00e+00 1.00e+00 4.03e+00 angle pdb=" CB ASP B 428 " pdb=" CG ASP B 428 " pdb=" OD1 ASP B 428 " ideal model delta sigma weight residual 118.40 122.72 -4.32 2.30e+00 1.89e-01 3.53e+00 angle pdb=" C ASP B 428 " pdb=" CA ASP B 428 " pdb=" CB ASP B 428 " ideal model delta sigma weight residual 109.65 112.58 -2.93 1.71e+00 3.42e-01 2.93e+00 angle pdb=" C SER B 175 " pdb=" N ALA B 176 " pdb=" CA ALA B 176 " ideal model delta sigma weight residual 122.29 119.88 2.41 1.65e+00 3.67e-01 2.13e+00 ... (remaining 8941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 3537 17.59 - 35.18: 377 35.18 - 52.78: 110 52.78 - 70.37: 15 70.37 - 87.96: 11 Dihedral angle restraints: 4050 sinusoidal: 1652 harmonic: 2398 Sorted by residual: dihedral pdb=" CA ASP B 121 " pdb=" CB ASP B 121 " pdb=" CG ASP B 121 " pdb=" OD1 ASP B 121 " ideal model delta sinusoidal sigma weight residual -30.00 -89.26 59.26 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CB GLU A 133 " pdb=" CG GLU A 133 " pdb=" CD GLU A 133 " pdb=" OE1 GLU A 133 " ideal model delta sinusoidal sigma weight residual 0.00 -87.96 87.96 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CA GLN B 189 " pdb=" C GLN B 189 " pdb=" N LEU B 190 " pdb=" CA LEU B 190 " ideal model delta harmonic sigma weight residual 180.00 -164.22 -15.78 0 5.00e+00 4.00e-02 9.97e+00 ... (remaining 4047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 581 0.026 - 0.051: 274 0.051 - 0.077: 102 0.077 - 0.102: 29 0.102 - 0.128: 23 Chirality restraints: 1009 Sorted by residual: chirality pdb=" CA ILE B 450 " pdb=" N ILE B 450 " pdb=" C ILE B 450 " pdb=" CB ILE B 450 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE A 165 " pdb=" N ILE A 165 " pdb=" C ILE A 165 " pdb=" CB ILE A 165 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA VAL B 252 " pdb=" N VAL B 252 " pdb=" C VAL B 252 " pdb=" CB VAL B 252 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 1006 not shown) Planarity restraints: 1134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 401 " 0.008 2.00e-02 2.50e+03 7.94e-03 1.58e+00 pdb=" CG TRP A 401 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP A 401 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 401 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 401 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 401 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 401 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 401 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 401 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 401 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 450 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO A 451 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 451 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 451 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 450 " -0.019 5.00e-02 4.00e+02 2.93e-02 1.38e+00 pdb=" N PRO B 451 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 451 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 451 " -0.016 5.00e-02 4.00e+02 ... (remaining 1131 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 571 2.75 - 3.28: 6256 3.28 - 3.82: 10918 3.82 - 4.36: 14131 4.36 - 4.90: 22842 Nonbonded interactions: 54718 Sorted by model distance: nonbonded pdb=" OH TYR B 438 " pdb=" O LEU B 462 " model vdw 2.207 3.040 nonbonded pdb=" O ARG B 132 " pdb=" OG SER B 136 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR A 438 " pdb=" O LEU A 462 " model vdw 2.224 3.040 nonbonded pdb=" O GLY A 382 " pdb=" OG1 THR B 205 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASP B 428 " pdb=" N THR B 430 " model vdw 2.299 3.120 ... (remaining 54713 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 120 and (name N or name CA or name C or name O or name CB \ )) or resid 121 through 179 or resid 188 through 211 or resid 213 through 267 o \ r (resid 282 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 83 through 573 or (resid 574 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'B' and (resid 120 through 211 or resid 213 through 574)) } 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=0.50 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: 4.920 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.180 Find NCS groups from input model: 0.260 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:10.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 : 0.002 0.032 6607 Z= 0.149 Angle : 0.423 5.798 8946 Z= 0.222 Chirality : 0.038 0.128 1009 Planarity : 0.003 0.030 1134 Dihedral : 16.225 87.960 2486 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.25 % Allowed : 17.48 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.28), residues: 785 helix: 1.35 (0.28), residues: 320 sheet: 0.50 (0.51), residues: 105 loop : -0.01 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 401 HIS 0.002 0.001 HIS B 328 PHE 0.011 0.001 PHE A 253 TYR 0.009 0.001 TYR B 482 ARG 0.005 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.766 Fit side-chains REVERT: B 150 GLN cc_start: 0.6982 (pm20) cc_final: 0.6336 (pm20) outliers start: 9 outliers final: 5 residues processed: 110 average time/residue: 1.2814 time to fit residues: 147.8531 Evaluate side-chains 108 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 560 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 71 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 189 GLN A 283 ASN A 366 GLN B 569 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6607 Z= 0.187 Angle : 0.488 4.702 8946 Z= 0.262 Chirality : 0.040 0.143 1009 Planarity : 0.004 0.028 1134 Dihedral : 4.818 59.251 880 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.22 % Allowed : 15.53 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.29), residues: 785 helix: 1.94 (0.28), residues: 327 sheet: 0.64 (0.51), residues: 99 loop : -0.03 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 401 HIS 0.003 0.001 HIS A 324 PHE 0.013 0.002 PHE A 253 TYR 0.013 0.001 TYR B 482 ARG 0.005 0.000 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.794 Fit side-chains REVERT: A 155 ASN cc_start: 0.7571 (p0) cc_final: 0.6833 (p0) REVERT: B 150 GLN cc_start: 0.6951 (pm20) cc_final: 0.6371 (pm20) REVERT: B 167 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7203 (mppt) outliers start: 16 outliers final: 4 residues processed: 113 average time/residue: 1.3332 time to fit residues: 157.8159 Evaluate side-chains 104 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 560 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 48 optimal weight: 0.3980 chunk 19 optimal weight: 0.0070 chunk 71 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 366 GLN A 504 GLN B 569 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6607 Z= 0.177 Angle : 0.474 4.644 8946 Z= 0.253 Chirality : 0.040 0.142 1009 Planarity : 0.004 0.038 1134 Dihedral : 4.578 55.274 876 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.66 % Allowed : 16.23 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.29), residues: 785 helix: 2.11 (0.28), residues: 327 sheet: 0.64 (0.51), residues: 99 loop : -0.09 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 401 HIS 0.003 0.001 HIS A 324 PHE 0.014 0.002 PHE A 253 TYR 0.013 0.001 TYR B 482 ARG 0.010 0.000 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.776 Fit side-chains REVERT: B 150 GLN cc_start: 0.6927 (pm20) cc_final: 0.6341 (pm20) REVERT: B 167 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.7134 (mppt) REVERT: B 292 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7201 (ptp90) outliers start: 12 outliers final: 5 residues processed: 105 average time/residue: 1.4586 time to fit residues: 160.3263 Evaluate side-chains 105 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 560 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 0.2980 chunk 72 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 366 GLN A 504 GLN B 498 ASN B 569 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6607 Z= 0.207 Angle : 0.485 4.648 8946 Z= 0.259 Chirality : 0.040 0.140 1009 Planarity : 0.004 0.041 1134 Dihedral : 4.531 54.410 875 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.05 % Allowed : 14.56 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.29), residues: 785 helix: 2.13 (0.28), residues: 327 sheet: 0.45 (0.50), residues: 105 loop : -0.10 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 401 HIS 0.003 0.001 HIS A 559 PHE 0.015 0.002 PHE A 253 TYR 0.015 0.001 TYR B 482 ARG 0.009 0.001 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 99 time to evaluate : 0.714 Fit side-chains REVERT: A 157 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7706 (p0) REVERT: B 150 GLN cc_start: 0.6960 (pm20) cc_final: 0.6372 (pm20) REVERT: B 167 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7151 (mppt) REVERT: B 292 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7211 (ptp90) outliers start: 22 outliers final: 7 residues processed: 113 average time/residue: 1.4537 time to fit residues: 172.1315 Evaluate side-chains 109 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 560 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.0570 chunk 65 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 366 GLN A 504 GLN B 569 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6607 Z= 0.169 Angle : 0.464 4.590 8946 Z= 0.247 Chirality : 0.039 0.141 1009 Planarity : 0.004 0.037 1134 Dihedral : 4.439 52.614 875 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.22 % Allowed : 15.67 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.29), residues: 785 helix: 2.23 (0.28), residues: 327 sheet: 0.43 (0.49), residues: 105 loop : -0.11 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 401 HIS 0.003 0.001 HIS A 328 PHE 0.015 0.002 PHE A 253 TYR 0.019 0.001 TYR A 494 ARG 0.008 0.000 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 150 GLN cc_start: 0.6901 (pm20) cc_final: 0.6307 (pm20) REVERT: B 167 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7086 (mppt) outliers start: 16 outliers final: 9 residues processed: 112 average time/residue: 1.2864 time to fit residues: 151.2249 Evaluate side-chains 109 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 560 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 73 optimal weight: 0.0570 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 0.0970 chunk 55 optimal weight: 0.0980 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 366 GLN A 504 GLN B 569 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6607 Z= 0.136 Angle : 0.459 8.310 8946 Z= 0.241 Chirality : 0.039 0.140 1009 Planarity : 0.003 0.034 1134 Dihedral : 4.341 51.631 875 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.22 % Allowed : 15.26 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.29), residues: 785 helix: 2.34 (0.28), residues: 327 sheet: 0.09 (0.47), residues: 115 loop : 0.07 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 401 HIS 0.003 0.001 HIS A 328 PHE 0.015 0.001 PHE A 253 TYR 0.018 0.001 TYR A 494 ARG 0.008 0.000 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: B 150 GLN cc_start: 0.6883 (pm20) cc_final: 0.6258 (pm20) REVERT: B 167 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7130 (mppt) outliers start: 16 outliers final: 8 residues processed: 110 average time/residue: 1.2749 time to fit residues: 147.2001 Evaluate side-chains 105 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 560 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 189 GLN A 366 GLN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6607 Z= 0.225 Angle : 0.514 7.925 8946 Z= 0.271 Chirality : 0.041 0.138 1009 Planarity : 0.004 0.051 1134 Dihedral : 4.547 51.919 875 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.08 % Allowed : 15.95 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.29), residues: 785 helix: 2.20 (0.28), residues: 327 sheet: 0.33 (0.50), residues: 105 loop : -0.11 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 401 HIS 0.004 0.001 HIS A 328 PHE 0.016 0.002 PHE A 253 TYR 0.018 0.001 TYR A 494 ARG 0.007 0.000 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: B 150 GLN cc_start: 0.6929 (pm20) cc_final: 0.6316 (pm20) REVERT: B 167 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7139 (mppt) outliers start: 15 outliers final: 11 residues processed: 108 average time/residue: 1.3637 time to fit residues: 154.1075 Evaluate side-chains 107 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 560 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 69 optimal weight: 0.0980 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 189 GLN A 366 GLN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6607 Z= 0.208 Angle : 0.508 7.775 8946 Z= 0.268 Chirality : 0.040 0.139 1009 Planarity : 0.004 0.050 1134 Dihedral : 4.546 51.349 875 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.50 % Allowed : 15.53 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.29), residues: 785 helix: 2.19 (0.28), residues: 327 sheet: 0.28 (0.50), residues: 105 loop : -0.13 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 401 HIS 0.003 0.001 HIS A 328 PHE 0.016 0.002 PHE A 253 TYR 0.018 0.001 TYR A 494 ARG 0.007 0.000 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: B 150 GLN cc_start: 0.6894 (pm20) cc_final: 0.6254 (pm20) REVERT: B 167 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7132 (mppt) outliers start: 18 outliers final: 10 residues processed: 107 average time/residue: 1.2984 time to fit residues: 145.6203 Evaluate side-chains 107 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 560 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 75 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 366 GLN A 504 GLN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6607 Z= 0.199 Angle : 0.502 7.683 8946 Z= 0.265 Chirality : 0.040 0.138 1009 Planarity : 0.004 0.051 1134 Dihedral : 4.559 50.713 875 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.94 % Allowed : 15.95 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.29), residues: 785 helix: 2.21 (0.28), residues: 327 sheet: 0.27 (0.50), residues: 105 loop : -0.12 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 401 HIS 0.003 0.001 HIS A 328 PHE 0.016 0.002 PHE A 253 TYR 0.018 0.001 TYR A 494 ARG 0.007 0.000 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: B 167 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7127 (mppt) outliers start: 14 outliers final: 10 residues processed: 104 average time/residue: 1.3008 time to fit residues: 141.9394 Evaluate side-chains 104 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 560 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 48 optimal weight: 0.0060 chunk 38 optimal weight: 0.0870 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 366 GLN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6607 Z= 0.160 Angle : 0.477 7.698 8946 Z= 0.250 Chirality : 0.039 0.140 1009 Planarity : 0.004 0.031 1134 Dihedral : 4.438 50.088 875 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.94 % Allowed : 16.37 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.29), residues: 785 helix: 2.32 (0.28), residues: 327 sheet: -0.02 (0.48), residues: 115 loop : 0.05 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 401 HIS 0.003 0.001 HIS A 328 PHE 0.015 0.001 PHE A 253 TYR 0.018 0.001 TYR A 494 ARG 0.007 0.000 ARG B 541 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.795 Fit side-chains REVERT: B 167 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.7115 (mppt) REVERT: B 189 GLN cc_start: 0.6493 (tp40) cc_final: 0.5848 (mm-40) outliers start: 14 outliers final: 10 residues processed: 104 average time/residue: 1.3171 time to fit residues: 143.7104 Evaluate side-chains 105 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 560 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 3 optimal weight: 0.0870 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 366 GLN A 504 GLN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.139290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109621 restraints weight = 10723.533| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.04 r_work: 0.3135 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6607 Z= 0.190 Angle : 0.494 7.601 8946 Z= 0.260 Chirality : 0.040 0.138 1009 Planarity : 0.004 0.052 1134 Dihedral : 4.507 50.339 875 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.53 % Allowed : 16.78 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.29), residues: 785 helix: 2.26 (0.28), residues: 327 sheet: -0.00 (0.49), residues: 115 loop : 0.05 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 401 HIS 0.003 0.001 HIS A 328 PHE 0.016 0.002 PHE A 253 TYR 0.017 0.001 TYR A 494 ARG 0.007 0.000 ARG B 541 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3375.29 seconds wall clock time: 59 minutes 43.40 seconds (3583.40 seconds total)