Starting phenix.real_space_refine on Fri Dec 27 12:00:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oot_17028/12_2024/8oot_17028.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oot_17028/12_2024/8oot_17028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oot_17028/12_2024/8oot_17028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oot_17028/12_2024/8oot_17028.map" model { file = "/net/cci-nas-00/data/ceres_data/8oot_17028/12_2024/8oot_17028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oot_17028/12_2024/8oot_17028.cif" } resolution = 2.85 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= 0.009 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 20 5.16 5 C 2837 2.51 5 N 799 2.21 5 O 819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4479 Number of models: 1 Model: "" Number of chains: 3 Chain: "I" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 873 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain breaks: 1 Chain: "J" Number of atoms: 3574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3574 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 418} Chain breaks: 3 Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.15, per 1000 atoms: 0.93 Number of scatterers: 4479 At special positions: 0 Unit cell: (87.954, 87.132, 84.666, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 20 16.00 P 3 15.00 Mg 1 11.99 O 819 8.00 N 799 7.00 C 2837 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: 1.15 Conformation dependent library (CDL) restraints added in 547.8 milliseconds 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1036 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 45.5% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'I' and resid 7 through 21 Processing helix chain 'I' and resid 37 through 41 removed outlier: 4.294A pdb=" N ASN I 41 " --> pdb=" O GLN I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 50 Processing helix chain 'I' and resid 190 through 199 Processing helix chain 'I' and resid 203 through 212 removed outlier: 3.658A pdb=" N GLN I 207 " --> pdb=" O GLY I 203 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG I 212 " --> pdb=" O PHE I 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 22 Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.766A pdb=" N ARG J 46 " --> pdb=" O GLN J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 143 Processing helix chain 'J' and resid 165 through 179 Processing helix chain 'J' and resid 189 through 198 Processing helix chain 'J' and resid 225 through 228 Processing helix chain 'J' and resid 234 through 250 Processing helix chain 'J' and resid 259 through 271 removed outlier: 3.715A pdb=" N HIS J 265 " --> pdb=" O SER J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 283 removed outlier: 4.191A pdb=" N GLY J 283 " --> pdb=" O ARG J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 294 Processing helix chain 'J' and resid 603 through 606 Processing helix chain 'J' and resid 607 through 615 removed outlier: 3.990A pdb=" N ALA J 611 " --> pdb=" O SER J 607 " (cutoff:3.500A) Processing helix chain 'J' and resid 634 through 639 removed outlier: 3.579A pdb=" N VAL J 639 " --> pdb=" O GLU J 635 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 643 Processing helix chain 'J' and resid 645 through 651 Processing helix chain 'J' and resid 656 through 667 Processing helix chain 'J' and resid 667 through 672 removed outlier: 3.538A pdb=" N SER J 671 " --> pdb=" O GLN J 667 " (cutoff:3.500A) Processing helix chain 'J' and resid 679 through 684 Processing helix chain 'J' and resid 690 through 694 Processing helix chain 'J' and resid 697 through 710 removed outlier: 3.834A pdb=" N LEU J 709 " --> pdb=" O GLY J 705 " (cutoff:3.500A) Processing helix chain 'J' and resid 726 through 736 Processing helix chain 'J' and resid 738 through 745 Processing helix chain 'J' and resid 748 through 755 Processing sheet with id=AA1, first strand: chain 'I' and resid 179 through 180 removed outlier: 3.707A pdb=" N TYR I 179 " --> pdb=" O TYR I 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 27 through 29 Processing sheet with id=AA3, first strand: chain 'J' and resid 80 through 82 removed outlier: 4.365A pdb=" N ASN J 63 " --> pdb=" O THR J 159 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 97 through 100 Processing sheet with id=AA5, first strand: chain 'J' and resid 222 through 223 Processing sheet with id=AA6, first strand: chain 'J' and resid 222 through 223 removed outlier: 6.341A pdb=" N VAL J 686 " --> pdb=" O ARG J 719 " (cutoff:3.500A) 180 hydrogen bonds defined for protein. 498 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: 1.21 Time building geometry restraints manager: 1.30 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: 1486 1.34 - 1.46: 822 1.46 - 1.58: 2247 1.58 - 1.69: 5 1.69 - 1.81: 34 Bond restraints: 4594 Sorted by residual: bond pdb=" CB THR J 689 " pdb=" CG2 THR J 689 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.10e+00 bond pdb=" N ASN J 232 " pdb=" CA ASN J 232 " ideal model delta sigma weight residual 1.461 1.473 -0.012 1.49e-02 4.50e+03 6.03e-01 bond pdb=" CB CYS J 105 " pdb=" SG CYS J 105 " ideal model delta sigma weight residual 1.808 1.784 0.024 3.30e-02 9.18e+02 5.23e-01 bond pdb=" CB GLU J 635 " pdb=" CG GLU J 635 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.19e-01 bond pdb=" C GLN J 298 " pdb=" N TYR J 299 " ideal model delta sigma weight residual 1.331 1.312 0.019 2.83e-02 1.25e+03 4.31e-01 ... (remaining 4589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 5594 0.99 - 1.98: 517 1.98 - 2.98: 93 2.98 - 3.97: 23 3.97 - 4.96: 6 Bond angle restraints: 6233 Sorted by residual: angle pdb=" N VAL J 634 " pdb=" CA VAL J 634 " pdb=" C VAL J 634 " ideal model delta sigma weight residual 110.62 113.19 -2.57 1.02e+00 9.61e-01 6.33e+00 angle pdb=" N ALA J 736 " pdb=" CA ALA J 736 " pdb=" C ALA J 736 " ideal model delta sigma weight residual 111.37 115.31 -3.94 1.65e+00 3.67e-01 5.69e+00 angle pdb=" N ARG J 221 " pdb=" CA ARG J 221 " pdb=" C ARG J 221 " ideal model delta sigma weight residual 110.80 115.68 -4.88 2.13e+00 2.20e-01 5.26e+00 angle pdb=" C TRP J 735 " pdb=" N ALA J 736 " pdb=" CA ALA J 736 " ideal model delta sigma weight residual 120.82 124.19 -3.37 1.50e+00 4.44e-01 5.05e+00 angle pdb=" C LEU J 290 " pdb=" N GLU J 291 " pdb=" CA GLU J 291 " ideal model delta sigma weight residual 120.38 123.38 -3.00 1.46e+00 4.69e-01 4.22e+00 ... (remaining 6228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 2497 15.24 - 30.48: 197 30.48 - 45.71: 44 45.71 - 60.95: 23 60.95 - 76.19: 9 Dihedral angle restraints: 2770 sinusoidal: 1160 harmonic: 1610 Sorted by residual: dihedral pdb=" CA GLU J 626 " pdb=" C GLU J 626 " pdb=" N THR J 627 " pdb=" CA THR J 627 " ideal model delta harmonic sigma weight residual 180.00 149.95 30.05 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA CYS J 105 " pdb=" C CYS J 105 " pdb=" N TYR J 106 " pdb=" CA TYR J 106 " ideal model delta harmonic sigma weight residual -180.00 -151.30 -28.70 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ASP J 292 " pdb=" C ASP J 292 " pdb=" N ARG J 293 " pdb=" CA ARG J 293 " ideal model delta harmonic sigma weight residual 180.00 153.34 26.66 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 2767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 404 0.037 - 0.075: 176 0.075 - 0.112: 58 0.112 - 0.149: 15 0.149 - 0.186: 1 Chirality restraints: 654 Sorted by residual: chirality pdb=" CA GLU J 635 " pdb=" N GLU J 635 " pdb=" C GLU J 635 " pdb=" CB GLU J 635 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.67e-01 chirality pdb=" CA ARG J 221 " pdb=" N ARG J 221 " pdb=" C ARG J 221 " pdb=" CB ARG J 221 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CB ILE J 39 " pdb=" CA ILE J 39 " pdb=" CG1 ILE J 39 " pdb=" CG2 ILE J 39 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 651 not shown) Planarity restraints: 811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 720 " -0.213 9.50e-02 1.11e+02 9.61e-02 7.07e+00 pdb=" NE ARG J 720 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG J 720 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG J 720 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG J 720 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 293 " -0.168 9.50e-02 1.11e+02 7.58e-02 4.73e+00 pdb=" NE ARG J 293 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG J 293 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG J 293 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG J 293 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 284 " -0.003 2.00e-02 2.50e+03 1.52e-02 4.65e+00 pdb=" CG TYR J 284 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR J 284 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR J 284 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR J 284 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR J 284 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR J 284 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR J 284 " -0.023 2.00e-02 2.50e+03 ... (remaining 808 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 7 2.37 - 3.01: 2423 3.01 - 3.64: 6664 3.64 - 4.27: 10601 4.27 - 4.90: 17554 Nonbonded interactions: 37249 Sorted by model distance: nonbonded pdb=" O1G ATP J 801 " pdb="MG MG J 802 " model vdw 1.743 2.170 nonbonded pdb=" O1B ATP J 801 " pdb="MG MG J 802 " model vdw 1.886 2.170 nonbonded pdb=" OD2 ASP J 190 " pdb="MG MG J 802 " model vdw 2.170 2.170 nonbonded pdb=" OD1 ASP I 171 " pdb=" NH1 ARG I 212 " model vdw 2.223 3.120 nonbonded pdb=" OE1 GLN J 42 " pdb=" NH1 ARG J 79 " model vdw 2.291 3.120 ... (remaining 37244 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.930 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.870 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 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 : 0.003 0.035 4594 Z= 0.208 Angle : 0.645 4.958 6233 Z= 0.375 Chirality : 0.046 0.186 654 Planarity : 0.009 0.096 811 Dihedral : 13.623 76.185 1734 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.61 (0.34), residues: 544 helix: -0.91 (0.33), residues: 196 sheet: 0.52 (0.72), residues: 51 loop : -0.07 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 129 HIS 0.003 0.001 HIS I 189 PHE 0.015 0.002 PHE J 687 TYR 0.023 0.004 TYR J 284 ARG 0.021 0.003 ARG J 720 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 16 LEU cc_start: 0.9200 (tp) cc_final: 0.8956 (tp) REVERT: I 191 LYS cc_start: 0.8519 (ptmm) cc_final: 0.8296 (tptt) REVERT: J 106 TYR cc_start: 0.7549 (m-80) cc_final: 0.7131 (m-80) REVERT: J 238 MET cc_start: 0.8849 (mtt) cc_final: 0.8515 (mtm) REVERT: J 707 MET cc_start: 0.9280 (ttp) cc_final: 0.9079 (ttp) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 1.8529 time to fit residues: 159.8336 Evaluate side-chains 55 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 8.9990 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 chunk 25 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN J 42 GLN J 63 ASN J 628 HIS J 654 GLN J 692 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4594 Z= 0.209 Angle : 0.607 5.269 6233 Z= 0.326 Chirality : 0.044 0.154 654 Planarity : 0.005 0.045 811 Dihedral : 8.893 73.102 649 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.78 % Allowed : 8.14 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.66 (0.36), residues: 544 helix: 0.65 (0.37), residues: 208 sheet: 0.41 (0.63), residues: 59 loop : 0.46 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 129 HIS 0.004 0.001 HIS J 610 PHE 0.012 0.001 PHE J 612 TYR 0.013 0.001 TYR I 188 ARG 0.008 0.001 ARG J 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 167 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8053 (mtpp) REVERT: J 106 TYR cc_start: 0.7409 (m-80) cc_final: 0.7094 (m-80) REVERT: J 154 MET cc_start: 0.9017 (tpp) cc_final: 0.8309 (mtm) outliers start: 13 outliers final: 3 residues processed: 61 average time/residue: 1.6139 time to fit residues: 101.6191 Evaluate side-chains 56 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain I residue 210 GLU Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 622 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 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 0.025 4594 Z= 0.254 Angle : 0.578 5.989 6233 Z= 0.304 Chirality : 0.043 0.146 654 Planarity : 0.004 0.046 811 Dihedral : 7.787 69.432 649 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.93 % Allowed : 10.06 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.73 (0.36), residues: 544 helix: 0.73 (0.36), residues: 214 sheet: 0.19 (0.68), residues: 54 loop : 0.54 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 129 HIS 0.004 0.001 HIS I 189 PHE 0.009 0.001 PHE J 612 TYR 0.011 0.001 TYR J 180 ARG 0.007 0.001 ARG J 279 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 20 LEU cc_start: 0.9283 (mt) cc_final: 0.9045 (mp) REVERT: I 167 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8071 (mtpp) REVERT: J 106 TYR cc_start: 0.7501 (m-80) cc_final: 0.7279 (m-10) REVERT: J 154 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8401 (mtm) REVERT: J 279 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8240 (ttp80) outliers start: 9 outliers final: 4 residues processed: 58 average time/residue: 1.6934 time to fit residues: 101.2334 Evaluate side-chains 56 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 259 ASN Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 622 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4594 Z= 0.238 Angle : 0.566 6.242 6233 Z= 0.301 Chirality : 0.043 0.145 654 Planarity : 0.005 0.042 811 Dihedral : 7.509 69.758 649 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.78 % Allowed : 10.28 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.73 (0.36), residues: 544 helix: 0.80 (0.36), residues: 214 sheet: 0.02 (0.67), residues: 54 loop : 0.51 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 129 HIS 0.003 0.001 HIS I 189 PHE 0.008 0.001 PHE J 695 TYR 0.011 0.001 TYR I 188 ARG 0.008 0.001 ARG J 748 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: I 20 LEU cc_start: 0.9283 (mt) cc_final: 0.9016 (mp) REVERT: I 22 LEU cc_start: 0.8969 (mp) cc_final: 0.8511 (mp) REVERT: I 39 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7995 (mtt180) REVERT: I 167 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8082 (mtpp) REVERT: J 154 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8412 (mtm) REVERT: J 279 ARG cc_start: 0.8457 (ttp80) cc_final: 0.7954 (tmt-80) outliers start: 13 outliers final: 4 residues processed: 61 average time/residue: 1.6925 time to fit residues: 106.4359 Evaluate side-chains 59 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 259 ASN Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 622 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.0670 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4594 Z= 0.235 Angle : 0.560 7.025 6233 Z= 0.295 Chirality : 0.042 0.144 654 Planarity : 0.005 0.044 811 Dihedral : 7.376 69.119 649 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.78 % Allowed : 10.49 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.67 (0.37), residues: 544 helix: 0.90 (0.36), residues: 214 sheet: -0.29 (0.66), residues: 56 loop : 0.41 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 129 HIS 0.003 0.001 HIS I 189 PHE 0.008 0.001 PHE J 612 TYR 0.011 0.001 TYR J 106 ARG 0.007 0.001 ARG J 748 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 20 LEU cc_start: 0.9281 (mt) cc_final: 0.9019 (mp) REVERT: I 22 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8535 (mp) REVERT: I 167 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8060 (mtpp) REVERT: J 154 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8375 (mtm) outliers start: 13 outliers final: 5 residues processed: 59 average time/residue: 1.7280 time to fit residues: 105.0590 Evaluate side-chains 58 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 259 ASN Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 622 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.0570 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4594 Z= 0.212 Angle : 0.569 7.932 6233 Z= 0.301 Chirality : 0.042 0.143 654 Planarity : 0.005 0.041 811 Dihedral : 7.179 69.415 649 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.36 % Allowed : 12.21 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.67 (0.37), residues: 544 helix: 0.89 (0.36), residues: 214 sheet: 0.15 (0.64), residues: 55 loop : 0.31 (0.40), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 129 HIS 0.003 0.001 HIS J 628 PHE 0.007 0.001 PHE J 35 TYR 0.011 0.001 TYR J 251 ARG 0.010 0.001 ARG J 279 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: I 22 LEU cc_start: 0.8977 (mp) cc_final: 0.8511 (mp) REVERT: I 167 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8040 (mtpp) REVERT: J 93 LYS cc_start: 0.8880 (tmmt) cc_final: 0.8400 (tmmt) REVERT: J 94 MET cc_start: 0.8603 (mtp) cc_final: 0.8354 (mtp) REVERT: J 154 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8383 (mtm) outliers start: 11 outliers final: 5 residues processed: 61 average time/residue: 1.6517 time to fit residues: 103.9472 Evaluate side-chains 60 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain I residue 210 GLU Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 259 ASN Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 622 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 43 optimal weight: 0.0770 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 overall best weight: 0.3138 ------------------------------------------------------------------------------- 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: 0.8606 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4594 Z= 0.177 Angle : 0.554 7.466 6233 Z= 0.290 Chirality : 0.041 0.146 654 Planarity : 0.004 0.042 811 Dihedral : 6.890 70.166 649 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.71 % Allowed : 13.92 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.75 (0.37), residues: 544 helix: 0.86 (0.36), residues: 220 sheet: 0.03 (0.63), residues: 55 loop : 0.47 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 129 HIS 0.003 0.001 HIS J 628 PHE 0.008 0.001 PHE J 35 TYR 0.009 0.001 TYR I 188 ARG 0.010 0.001 ARG J 279 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: I 20 LEU cc_start: 0.9234 (mt) cc_final: 0.9001 (mp) REVERT: I 167 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8020 (mtpp) REVERT: J 93 LYS cc_start: 0.8853 (tmmt) cc_final: 0.8505 (tmmt) REVERT: J 154 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8409 (mtm) outliers start: 8 outliers final: 1 residues processed: 58 average time/residue: 1.6616 time to fit residues: 99.3315 Evaluate side-chains 55 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 297 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 38 optimal weight: 0.0470 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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: 0.8618 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4594 Z= 0.220 Angle : 0.579 8.377 6233 Z= 0.305 Chirality : 0.041 0.137 654 Planarity : 0.005 0.044 811 Dihedral : 6.892 69.312 649 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.50 % Allowed : 14.78 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.76 (0.37), residues: 544 helix: 0.86 (0.36), residues: 220 sheet: 0.08 (0.64), residues: 55 loop : 0.47 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 129 HIS 0.003 0.001 HIS J 628 PHE 0.006 0.001 PHE J 612 TYR 0.027 0.001 TYR J 251 ARG 0.011 0.001 ARG J 279 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: I 22 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8497 (mp) REVERT: I 167 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8007 (mtpp) REVERT: I 204 MET cc_start: 0.8173 (mtm) cc_final: 0.7923 (mmm) REVERT: I 206 GLU cc_start: 0.8032 (pm20) cc_final: 0.7629 (tp30) REVERT: J 154 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8413 (mtm) outliers start: 7 outliers final: 2 residues processed: 58 average time/residue: 1.6673 time to fit residues: 99.6870 Evaluate side-chains 58 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain I residue 210 GLU Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 297 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 35 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8619 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4594 Z= 0.216 Angle : 0.585 7.900 6233 Z= 0.306 Chirality : 0.042 0.141 654 Planarity : 0.005 0.044 811 Dihedral : 6.909 69.055 649 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.28 % Allowed : 14.99 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.77 (0.37), residues: 544 helix: 0.89 (0.36), residues: 221 sheet: -0.04 (0.63), residues: 55 loop : 0.49 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 129 HIS 0.003 0.001 HIS J 628 PHE 0.007 0.001 PHE J 612 TYR 0.010 0.001 TYR I 188 ARG 0.012 0.001 ARG J 279 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: I 22 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8522 (mp) REVERT: I 167 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8215 (mtpp) REVERT: I 206 GLU cc_start: 0.8014 (pm20) cc_final: 0.7639 (tp30) REVERT: I 207 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8493 (tt0) REVERT: J 154 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8409 (mtm) outliers start: 6 outliers final: 3 residues processed: 57 average time/residue: 1.8258 time to fit residues: 107.0763 Evaluate side-chains 61 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain I residue 210 GLU Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 259 ASN Chi-restraints excluded: chain J residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 0.0050 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 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: 0.8615 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4594 Z= 0.216 Angle : 0.594 9.193 6233 Z= 0.312 Chirality : 0.042 0.146 654 Planarity : 0.005 0.048 811 Dihedral : 6.865 69.070 649 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.28 % Allowed : 15.20 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.79 (0.37), residues: 544 helix: 0.92 (0.36), residues: 221 sheet: 0.01 (0.63), residues: 55 loop : 0.47 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 129 HIS 0.003 0.001 HIS J 628 PHE 0.006 0.001 PHE J 612 TYR 0.011 0.001 TYR J 251 ARG 0.014 0.001 ARG J 279 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: I 22 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8516 (mp) REVERT: I 167 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8212 (mtpp) REVERT: I 206 GLU cc_start: 0.7955 (pm20) cc_final: 0.7571 (tp30) REVERT: I 207 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8493 (tt0) REVERT: J 154 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8404 (mtm) outliers start: 6 outliers final: 3 residues processed: 57 average time/residue: 1.7097 time to fit residues: 100.4655 Evaluate side-chains 61 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain I residue 210 GLU Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.057479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.046282 restraints weight = 13202.758| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.76 r_work: 0.2702 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4594 Z= 0.236 Angle : 0.604 8.539 6233 Z= 0.314 Chirality : 0.042 0.132 654 Planarity : 0.005 0.049 811 Dihedral : 6.919 69.331 649 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.71 % Allowed : 13.92 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.81 (0.37), residues: 544 helix: 0.94 (0.36), residues: 221 sheet: 0.09 (0.64), residues: 55 loop : 0.48 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 129 HIS 0.002 0.001 HIS I 189 PHE 0.007 0.001 PHE J 612 TYR 0.012 0.001 TYR J 251 ARG 0.013 0.001 ARG J 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2455.28 seconds wall clock time: 44 minutes 39.43 seconds (2679.43 seconds total)