Starting phenix.real_space_refine on Sun Apr 27 05:06:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oot_17028/04_2025/8oot_17028.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oot_17028/04_2025/8oot_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_17028/04_2025/8oot_17028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oot_17028/04_2025/8oot_17028.map" model { file = "/net/cci-nas-00/data/ceres_data/8oot_17028/04_2025/8oot_17028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oot_17028/04_2025/8oot_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-5669/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: 3.82, per 1000 atoms: 0.85 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: 1.07 Conformation dependent library (CDL) restraints added in 507.1 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: 0.53 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: 1.23 Time building geometry restraints manager: 1.29 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: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.610 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:15.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.520 ------------------------------------------------------------------------------- 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= 0.141 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 Details of bonding type rmsd hydrogen bonds : bond 0.18559 ( 178) hydrogen bonds : angle 8.47820 ( 498) covalent geometry : bond 0.00320 ( 4594) covalent geometry : angle 0.64492 ( 6233) *********************** 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 : 0.728 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: 1.8148 time to fit residues: 156.6592 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 : 0.579 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.058308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.046895 restraints weight = 12944.351| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.76 r_work: 0.2727 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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= 0.139 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 Details of bonding type rmsd hydrogen bonds : bond 0.04251 ( 178) hydrogen bonds : angle 5.95322 ( 498) covalent geometry : bond 0.00316 ( 4594) covalent geometry : angle 0.60675 ( 6233) *********************** 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 : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 167 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8107 (mtpp) REVERT: I 191 LYS cc_start: 0.8606 (ptmm) cc_final: 0.8256 (mmtm) REVERT: J 106 TYR cc_start: 0.7365 (m-80) cc_final: 0.7094 (m-80) REVERT: J 154 MET cc_start: 0.8883 (tpp) cc_final: 0.8166 (mtm) outliers start: 13 outliers final: 3 residues processed: 61 average time/residue: 1.5217 time to fit residues: 95.8317 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 : 0.539 ------------------------------------------------------------------------------- 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 40 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 0.0040 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 12 optimal weight: 5.9990 chunk 4 optimal weight: 0.0370 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 overall best weight: 0.3870 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.058469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.046995 restraints weight = 12897.127| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.76 r_work: 0.2726 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4594 Z= 0.116 Angle : 0.551 6.274 6233 Z= 0.289 Chirality : 0.042 0.148 654 Planarity : 0.004 0.045 811 Dihedral : 7.510 71.043 649 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.50 % Allowed : 10.28 % Favored : 88.22 % 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: 0.80 (0.36), residues: 544 helix: 0.81 (0.36), residues: 214 sheet: 0.55 (0.70), residues: 48 loop : 0.48 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 129 HIS 0.004 0.001 HIS J 628 PHE 0.011 0.001 PHE J 695 TYR 0.010 0.001 TYR I 188 ARG 0.008 0.001 ARG J 279 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 178) hydrogen bonds : angle 5.61474 ( 498) covalent geometry : bond 0.00260 ( 4594) covalent geometry : angle 0.55115 ( 6233) *********************** 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 62 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: I 20 LEU cc_start: 0.9160 (mt) cc_final: 0.8929 (mp) REVERT: I 167 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8088 (mtpp) REVERT: I 191 LYS cc_start: 0.8684 (ptmm) cc_final: 0.8241 (mmtm) REVERT: J 154 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8239 (mtm) REVERT: J 238 MET cc_start: 0.8578 (mmm) cc_final: 0.7982 (mtm) outliers start: 7 outliers final: 1 residues processed: 58 average time/residue: 1.6188 time to fit residues: 96.8917 Evaluate side-chains 54 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.057212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.045731 restraints weight = 13114.817| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.77 r_work: 0.2687 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2895 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= 0.160 Angle : 0.565 6.342 6233 Z= 0.299 Chirality : 0.043 0.145 654 Planarity : 0.005 0.045 811 Dihedral : 7.427 70.609 649 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: 0.76 (0.36), residues: 544 helix: 0.85 (0.36), residues: 214 sheet: 0.40 (0.70), residues: 48 loop : 0.41 (0.38), residues: 282 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 0.009 0.001 PHE J 612 TYR 0.012 0.001 TYR J 106 ARG 0.009 0.001 ARG J 748 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 178) hydrogen bonds : angle 5.53295 ( 498) covalent geometry : bond 0.00369 ( 4594) covalent geometry : angle 0.56455 ( 6233) *********************** 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 : 0.567 Fit side-chains revert: symmetry clash REVERT: I 20 LEU cc_start: 0.9226 (mt) cc_final: 0.8907 (mp) REVERT: I 22 LEU cc_start: 0.8957 (mp) cc_final: 0.8517 (mp) REVERT: I 167 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8081 (mtpp) REVERT: I 191 LYS cc_start: 0.8737 (ptmm) cc_final: 0.8266 (tptt) REVERT: J 154 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8248 (mtm) REVERT: J 279 ARG cc_start: 0.8641 (ttp80) cc_final: 0.8120 (tmt-80) outliers start: 13 outliers final: 5 residues processed: 61 average time/residue: 1.5841 time to fit residues: 99.7842 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 : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.056756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.045234 restraints weight = 13260.998| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.77 r_work: 0.2671 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3016 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= 0.172 Angle : 0.576 7.094 6233 Z= 0.302 Chirality : 0.043 0.143 654 Planarity : 0.005 0.043 811 Dihedral : 7.405 69.071 649 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.78 % Allowed : 9.85 % Favored : 87.37 % 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: 0.62 (0.36), residues: 544 helix: 0.84 (0.36), residues: 214 sheet: 0.09 (0.61), residues: 66 loop : 0.31 (0.40), residues: 264 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 0.009 0.001 PHE J 612 TYR 0.012 0.001 TYR J 180 ARG 0.007 0.001 ARG J 748 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 178) hydrogen bonds : angle 5.49111 ( 498) covalent geometry : bond 0.00402 ( 4594) covalent geometry : angle 0.57551 ( 6233) *********************** 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 : 0.545 Fit side-chains revert: symmetry clash REVERT: I 22 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8523 (mp) REVERT: I 167 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8106 (mtpp) REVERT: I 191 LYS cc_start: 0.8799 (ptmm) cc_final: 0.8310 (tptt) REVERT: J 93 LYS cc_start: 0.8851 (tmmt) cc_final: 0.8202 (tmmt) REVERT: J 94 MET cc_start: 0.8547 (mtp) cc_final: 0.8051 (mtp) REVERT: J 154 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8261 (mtm) outliers start: 13 outliers final: 3 residues processed: 58 average time/residue: 1.6184 time to fit residues: 96.8811 Evaluate side-chains 57 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 22 LEU 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 225 LEU Chi-restraints excluded: chain J residue 297 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.057004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.045541 restraints weight = 13120.991| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.75 r_work: 0.2680 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3181 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= 0.149 Angle : 0.575 7.286 6233 Z= 0.306 Chirality : 0.042 0.142 654 Planarity : 0.005 0.042 811 Dihedral : 7.266 69.349 649 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.57 % Allowed : 11.99 % 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: 0.61 (0.36), residues: 544 helix: 0.87 (0.36), residues: 214 sheet: -0.28 (0.62), residues: 61 loop : 0.36 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 129 HIS 0.002 0.001 HIS J 628 PHE 0.007 0.001 PHE J 612 TYR 0.011 0.001 TYR I 188 ARG 0.010 0.001 ARG J 279 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 178) hydrogen bonds : angle 5.42764 ( 498) covalent geometry : bond 0.00349 ( 4594) covalent geometry : angle 0.57458 ( 6233) *********************** 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 67 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: I 20 LEU cc_start: 0.9156 (mt) cc_final: 0.8878 (mp) REVERT: I 22 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8523 (mp) REVERT: I 167 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8068 (mtpp) REVERT: I 191 LYS cc_start: 0.8837 (ptmm) cc_final: 0.8340 (tptt) REVERT: J 93 LYS cc_start: 0.8835 (tmmt) cc_final: 0.8289 (tmmt) REVERT: J 94 MET cc_start: 0.8510 (mtp) cc_final: 0.8139 (mtp) REVERT: J 154 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8225 (mtm) outliers start: 12 outliers final: 4 residues processed: 59 average time/residue: 1.5769 time to fit residues: 96.0582 Evaluate side-chains 58 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 163 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 0 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.0570 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.5100 ------------------------------------------------------------------------------- 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 = 0.3146 r_free = 0.3146 target = 0.057369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.046015 restraints weight = 13098.791| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.74 r_work: 0.2694 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4594 Z= 0.131 Angle : 0.569 9.917 6233 Z= 0.296 Chirality : 0.042 0.139 654 Planarity : 0.004 0.041 811 Dihedral : 7.087 69.661 649 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.71 % Allowed : 13.49 % Favored : 84.80 % 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: 0.71 (0.37), residues: 544 helix: 0.93 (0.36), residues: 214 sheet: -0.22 (0.62), residues: 61 loop : 0.43 (0.41), 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 0.007 0.001 PHE J 35 TYR 0.011 0.001 TYR J 251 ARG 0.010 0.001 ARG J 279 Details of bonding type rmsd hydrogen bonds : bond 0.03287 ( 178) hydrogen bonds : angle 5.34710 ( 498) covalent geometry : bond 0.00310 ( 4594) covalent geometry : angle 0.56929 ( 6233) *********************** 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 62 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: I 20 LEU cc_start: 0.9193 (mt) cc_final: 0.8895 (mp) REVERT: I 22 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8502 (mp) REVERT: I 167 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8065 (mtpp) REVERT: I 191 LYS cc_start: 0.8851 (ptmm) cc_final: 0.8369 (tptt) REVERT: J 93 LYS cc_start: 0.8884 (tmmt) cc_final: 0.8557 (tmmt) REVERT: J 94 MET cc_start: 0.8619 (mtp) cc_final: 0.8271 (mtp) REVERT: J 154 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8255 (mtm) outliers start: 8 outliers final: 1 residues processed: 57 average time/residue: 1.7001 time to fit residues: 99.9478 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 : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 22 LEU 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 3 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 32 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3149 r_free = 0.3149 target = 0.057432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.046169 restraints weight = 13043.757| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.73 r_work: 0.2703 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4594 Z= 0.135 Angle : 0.572 7.791 6233 Z= 0.303 Chirality : 0.042 0.153 654 Planarity : 0.005 0.041 811 Dihedral : 6.993 69.434 649 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.71 % Allowed : 14.35 % Favored : 83.94 % 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: 0.76 (0.37), residues: 544 helix: 0.89 (0.36), residues: 219 sheet: 0.21 (0.65), residues: 55 loop : 0.42 (0.41), residues: 270 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 0.009 0.001 TYR I 188 ARG 0.012 0.001 ARG J 279 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 178) hydrogen bonds : angle 5.35158 ( 498) covalent geometry : bond 0.00319 ( 4594) covalent geometry : angle 0.57235 ( 6233) *********************** 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 63 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: I 22 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8489 (mp) REVERT: I 167 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8024 (mtpp) REVERT: I 191 LYS cc_start: 0.8852 (ptmm) cc_final: 0.8353 (tptt) REVERT: I 199 ASN cc_start: 0.8613 (t0) cc_final: 0.8365 (m-40) REVERT: I 206 GLU cc_start: 0.8040 (pm20) cc_final: 0.7659 (tp30) REVERT: J 93 LYS cc_start: 0.8872 (tmmt) cc_final: 0.8209 (tmmt) REVERT: J 154 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8258 (mtm) outliers start: 8 outliers final: 2 residues processed: 57 average time/residue: 1.8346 time to fit residues: 107.5615 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 : 0.560 ------------------------------------------------------------------------------- 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 45 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3123 r_free = 0.3123 target = 0.056649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.045248 restraints weight = 13252.303| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.77 r_work: 0.2671 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4594 Z= 0.174 Angle : 0.614 10.591 6233 Z= 0.320 Chirality : 0.043 0.136 654 Planarity : 0.005 0.048 811 Dihedral : 7.134 69.068 649 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: 0.26 (0.66), residues: 55 loop : 0.41 (0.41), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 129 HIS 0.002 0.001 HIS J 628 PHE 0.008 0.001 PHE J 612 TYR 0.011 0.001 TYR I 188 ARG 0.013 0.001 ARG J 279 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 178) hydrogen bonds : angle 5.41067 ( 498) covalent geometry : bond 0.00412 ( 4594) covalent geometry : angle 0.61377 ( 6233) *********************** 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: 8 poor density : 53 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: I 22 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8500 (mp) REVERT: I 167 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8061 (mtpp) REVERT: I 191 LYS cc_start: 0.8897 (ptmm) cc_final: 0.8397 (tptt) REVERT: I 199 ASN cc_start: 0.8597 (t0) cc_final: 0.8355 (m-40) REVERT: I 206 GLU cc_start: 0.8182 (pm20) cc_final: 0.7631 (tp30) REVERT: I 207 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8396 (tt0) REVERT: J 154 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8242 (mtm) outliers start: 8 outliers final: 3 residues processed: 56 average time/residue: 1.8223 time to fit residues: 105.1689 Evaluate side-chains 59 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 163 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 0.0870 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.3143 r_free = 0.3143 target = 0.057446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.046125 restraints weight = 13194.083| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.75 r_work: 0.2697 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 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 0.042 4594 Z= 0.132 Angle : 0.594 9.443 6233 Z= 0.311 Chirality : 0.042 0.132 654 Planarity : 0.005 0.049 811 Dihedral : 6.916 68.971 649 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.07 % Allowed : 14.56 % 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: 0.95 (0.36), residues: 220 sheet: 0.22 (0.66), residues: 55 loop : 0.43 (0.41), 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 0.010 0.001 TYR I 188 ARG 0.012 0.001 ARG J 279 Details of bonding type rmsd hydrogen bonds : bond 0.03159 ( 178) hydrogen bonds : angle 5.33768 ( 498) covalent geometry : bond 0.00314 ( 4594) covalent geometry : angle 0.59383 ( 6233) ********************** 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 61 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: I 191 LYS cc_start: 0.8948 (ptmm) cc_final: 0.8395 (tptt) REVERT: I 199 ASN cc_start: 0.8616 (t0) cc_final: 0.8386 (m110) REVERT: I 206 GLU cc_start: 0.8156 (pm20) cc_final: 0.7544 (tp30) REVERT: I 207 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8364 (tt0) REVERT: J 154 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8267 (mtm) outliers start: 5 outliers final: 2 residues processed: 58 average time/residue: 1.7039 time to fit residues: 101.8543 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 : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 24 SER 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 45 optimal weight: 2.9990 chunk 2 optimal weight: 0.0370 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- 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 = 0.3121 r_free = 0.3121 target = 0.056541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.045194 restraints weight = 13297.620| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.77 r_work: 0.2668 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3510 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= 0.176 Angle : 0.628 8.315 6233 Z= 0.327 Chirality : 0.043 0.134 654 Planarity : 0.005 0.049 811 Dihedral : 7.103 69.566 649 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.28 % Allowed : 14.35 % 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: 0.77 (0.37), residues: 544 helix: 0.90 (0.36), residues: 220 sheet: 0.21 (0.66), residues: 55 loop : 0.41 (0.41), residues: 269 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 0.009 0.001 PHE J 612 TYR 0.011 0.001 TYR J 180 ARG 0.013 0.001 ARG J 279 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 178) hydrogen bonds : angle 5.40738 ( 498) covalent geometry : bond 0.00419 ( 4594) covalent geometry : angle 0.62756 ( 6233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4121.50 seconds wall clock time: 70 minutes 40.89 seconds (4240.89 seconds total)