Starting phenix.real_space_refine on Thu Jul 2 00:18:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8oot_17028/07_2026/8oot_17028.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oot_17028/07_2026/8oot_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 { model { file = "/net/cci-nas-00/data/ceres_data/8oot_17028/07_2026/8oot_17028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oot_17028/07_2026/8oot_17028.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8oot_17028/07_2026/8oot_17028.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8oot_17028/07_2026/8oot_17028.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oot_17028/07_2026/8oot_17028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oot_17028/07_2026/8oot_17028.map" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 1.24, per 1000 atoms: 0.28 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: 0.36 Conformation dependent library (CDL) restraints added in 184.6 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: 0.10 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: 0.55 Time building geometry restraints manager: 0.46 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: 2489 15.24 - 30.48: 195 30.48 - 45.71: 38 45.71 - 60.95: 10 60.95 - 76.19: 7 Dihedral angle restraints: 2739 sinusoidal: 1129 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 2736 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: 4.510 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.440 Find NCS groups from input model: 0.010 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: 0.000 Load rotamer database and sin/cos tables:8.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 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 : 12.474 76.185 1703 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.021 0.003 ARG J 720 TYR 0.023 0.004 TYR J 284 PHE 0.015 0.002 PHE J 687 TRP 0.022 0.002 TRP J 129 HIS 0.003 0.001 HIS I 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 4594) covalent geometry : angle 0.64492 / 0.38 ( 6233) hydrogen bonds : bond 0.18559 / 13.06 ( 178) hydrogen bonds : angle 8.47820 / 6.10 ( 498) *********************** 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 : 0.128 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: 0.6718 time to fit residues: 57.8500 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 : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.0670 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.0770 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3167 r_free = 0.3167 target = 0.058135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.046592 restraints weight = 13189.612| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.79 r_work: 0.2709 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4594 Z= 0.145 Angle : 0.608 5.292 6233 Z= 0.325 Chirality : 0.044 0.147 654 Planarity : 0.005 0.045 811 Dihedral : 6.581 73.840 618 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.78 % Allowed : 8.35 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.36), residues: 544 helix: 0.60 (0.37), residues: 208 sheet: 0.39 (0.63), residues: 59 loop : 0.44 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 279 TYR 0.012 0.001 TYR I 188 PHE 0.011 0.001 PHE J 612 TRP 0.015 0.002 TRP J 129 HIS 0.004 0.001 HIS J 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 4594) covalent geometry : angle 0.60755 / 0.33 ( 6233) hydrogen bonds : bond 0.04173 / 2.85 ( 178) hydrogen bonds : angle 5.95157 / 4.34 ( 498) *********************** 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 69 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 167 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8116 (mtpp) REVERT: I 191 LYS cc_start: 0.8607 (ptmm) cc_final: 0.8246 (mmtm) REVERT: J 106 TYR cc_start: 0.7389 (m-80) cc_final: 0.7105 (m-80) REVERT: J 154 MET cc_start: 0.8889 (tpp) cc_final: 0.8176 (mtm) outliers start: 13 outliers final: 4 residues processed: 60 average time/residue: 0.6084 time to fit residues: 37.5859 Evaluate side-chains 56 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 259 ASN 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 46 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.057469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.045966 restraints weight = 12919.483| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.74 r_work: 0.2692 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4594 Z= 0.155 Angle : 0.571 5.996 6233 Z= 0.299 Chirality : 0.043 0.147 654 Planarity : 0.004 0.046 811 Dihedral : 6.168 72.370 618 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.93 % Allowed : 9.64 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.36), residues: 544 helix: 0.74 (0.36), residues: 214 sheet: 0.13 (0.68), residues: 54 loop : 0.54 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 279 TYR 0.011 0.001 TYR J 210 PHE 0.010 0.001 PHE J 695 TRP 0.014 0.001 TRP J 129 HIS 0.003 0.001 HIS I 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 4594) covalent geometry : angle 0.57140 / 0.30 ( 6233) hydrogen bonds : bond 0.03824 / 2.62 ( 178) hydrogen bonds : angle 5.67099 / 4.12 ( 498) *********************** 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 : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 20 LEU cc_start: 0.9202 (mt) cc_final: 0.8972 (mp) REVERT: I 167 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8097 (mtpp) REVERT: I 191 LYS cc_start: 0.8649 (ptmm) cc_final: 0.8183 (tptt) REVERT: J 154 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8240 (mtm) REVERT: J 279 ARG cc_start: 0.8640 (ttp80) cc_final: 0.8386 (ttp80) outliers start: 9 outliers final: 4 residues processed: 58 average time/residue: 0.6348 time to fit residues: 37.9009 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 : 0.130 ------------------------------------------------------------------------------- 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 12 optimal weight: 0.0070 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 0.0570 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.057720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.046174 restraints weight = 13069.603| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.77 r_work: 0.2698 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4594 Z= 0.132 Angle : 0.550 6.876 6233 Z= 0.290 Chirality : 0.042 0.144 654 Planarity : 0.005 0.041 811 Dihedral : 5.900 71.856 618 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.57 % Allowed : 10.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.36), residues: 544 helix: 0.86 (0.36), residues: 214 sheet: 0.40 (0.70), residues: 48 loop : 0.42 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 748 TYR 0.011 0.001 TYR J 106 PHE 0.009 0.001 PHE J 695 TRP 0.013 0.001 TRP J 129 HIS 0.003 0.001 HIS J 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 4594) covalent geometry : angle 0.55026 / 0.29 ( 6233) hydrogen bonds : bond 0.03417 / 2.35 ( 178) hydrogen bonds : angle 5.49064 / 3.99 ( 498) *********************** 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 66 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: I 22 LEU cc_start: 0.8962 (mp) cc_final: 0.8514 (mp) REVERT: I 39 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8296 (mtt180) REVERT: I 167 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8071 (mtpp) REVERT: I 191 LYS cc_start: 0.8730 (ptmm) cc_final: 0.8255 (tptt) REVERT: J 154 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8249 (mtm) REVERT: J 279 ARG cc_start: 0.8645 (ttp80) cc_final: 0.8396 (ttp80) outliers start: 12 outliers final: 3 residues processed: 61 average time/residue: 0.6481 time to fit residues: 40.7347 Evaluate side-chains 58 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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 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 19 optimal weight: 0.0970 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 2 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.057326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.045799 restraints weight = 13152.295| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.75 r_work: 0.2690 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4594 Z= 0.134 Angle : 0.540 6.885 6233 Z= 0.283 Chirality : 0.042 0.144 654 Planarity : 0.004 0.043 811 Dihedral : 5.748 71.345 618 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.14 % Allowed : 11.35 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.36), residues: 544 helix: 0.95 (0.36), residues: 214 sheet: 0.09 (0.69), residues: 50 loop : 0.33 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 748 TYR 0.010 0.001 TYR I 188 PHE 0.007 0.001 PHE J 612 TRP 0.012 0.001 TRP J 129 HIS 0.003 0.001 HIS J 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 4594) covalent geometry : angle 0.54018 / 0.28 ( 6233) hydrogen bonds : bond 0.03333 / 2.31 ( 178) hydrogen bonds : angle 5.40769 / 3.92 ( 498) *********************** 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: 10 poor density : 56 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 20 LEU cc_start: 0.9168 (mt) cc_final: 0.8889 (mp) REVERT: I 22 LEU cc_start: 0.8974 (mp) cc_final: 0.8518 (mp) REVERT: I 167 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8093 (mtpp) REVERT: I 191 LYS cc_start: 0.8784 (ptmm) cc_final: 0.8327 (mmtt) REVERT: J 154 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8252 (mtm) REVERT: J 279 ARG cc_start: 0.8637 (ttp80) cc_final: 0.8364 (ttp80) outliers start: 10 outliers final: 5 residues processed: 61 average time/residue: 0.6718 time to fit residues: 42.2091 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 : 0.158 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 34 optimal weight: 0.2980 chunk 16 optimal weight: 0.0000 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.057707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.046284 restraints weight = 13211.498| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.75 r_work: 0.2704 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4594 Z= 0.124 Angle : 0.548 7.377 6233 Z= 0.290 Chirality : 0.042 0.143 654 Planarity : 0.004 0.041 811 Dihedral : 5.601 71.850 618 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.78 % Allowed : 11.99 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.37), residues: 544 helix: 0.86 (0.36), residues: 220 sheet: 0.12 (0.64), residues: 55 loop : 0.48 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 35 TYR 0.010 0.001 TYR I 188 PHE 0.007 0.001 PHE J 35 TRP 0.012 0.001 TRP J 129 HIS 0.002 0.001 HIS J 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 4594) covalent geometry : angle 0.54834 / 0.29 ( 6233) hydrogen bonds : bond 0.03177 / 2.19 ( 178) hydrogen bonds : angle 5.33600 / 3.86 ( 498) *********************** 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: 13 poor density : 55 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: I 20 LEU cc_start: 0.9174 (mt) cc_final: 0.8867 (mp) REVERT: I 22 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8495 (mp) REVERT: I 167 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8045 (mtpp) REVERT: I 191 LYS cc_start: 0.8793 (ptmm) cc_final: 0.8331 (mmtt) REVERT: I 199 ASN cc_start: 0.8562 (t0) cc_final: 0.8357 (m-40) REVERT: J 93 LYS cc_start: 0.8863 (tmmt) cc_final: 0.8502 (tmmt) REVERT: J 94 MET cc_start: 0.8606 (mtp) cc_final: 0.8393 (mtp) REVERT: J 154 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8261 (mtm) REVERT: J 279 ARG cc_start: 0.8628 (ttp80) cc_final: 0.8350 (ttp80) outliers start: 13 outliers final: 6 residues processed: 61 average time/residue: 0.6448 time to fit residues: 40.4435 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 : 0.109 ------------------------------------------------------------------------------- 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 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 52 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 0.0010 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.057863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.046332 restraints weight = 13135.023| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.78 r_work: 0.2703 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.3320 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= 0.122 Angle : 0.553 7.601 6233 Z= 0.291 Chirality : 0.041 0.142 654 Planarity : 0.004 0.040 811 Dihedral : 5.503 72.206 618 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.71 % Allowed : 13.06 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.37), residues: 544 helix: 0.89 (0.36), residues: 220 sheet: 0.07 (0.63), residues: 55 loop : 0.52 (0.41), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 35 TYR 0.009 0.001 TYR I 188 PHE 0.006 0.001 PHE J 35 TRP 0.011 0.001 TRP J 129 HIS 0.003 0.001 HIS J 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 4594) covalent geometry : angle 0.55265 / 0.29 ( 6233) hydrogen bonds : bond 0.03120 / 2.16 ( 178) hydrogen bonds : angle 5.28046 / 3.82 ( 498) *********************** 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 64 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: I 22 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8487 (mp) REVERT: I 167 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8040 (mtpp) REVERT: I 191 LYS cc_start: 0.8822 (ptmm) cc_final: 0.8322 (tptt) REVERT: I 199 ASN cc_start: 0.8623 (t0) cc_final: 0.8410 (m110) REVERT: J 93 LYS cc_start: 0.8853 (tmmt) cc_final: 0.8505 (tmmt) REVERT: J 154 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8277 (mtm) REVERT: J 279 ARG cc_start: 0.8623 (ttp80) cc_final: 0.8339 (ttp80) outliers start: 8 outliers final: 2 residues processed: 59 average time/residue: 0.5394 time to fit residues: 32.7958 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 : 0.147 ------------------------------------------------------------------------------- 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 259 ASN 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 7 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.057100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.045678 restraints weight = 13324.392| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.76 r_work: 0.2682 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4594 Z= 0.140 Angle : 0.556 7.715 6233 Z= 0.292 Chirality : 0.042 0.139 654 Planarity : 0.004 0.039 811 Dihedral : 5.499 71.649 618 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.71 % Allowed : 13.70 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.37), residues: 544 helix: 0.87 (0.36), residues: 221 sheet: 0.04 (0.64), residues: 55 loop : 0.55 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 35 TYR 0.010 0.001 TYR I 188 PHE 0.007 0.001 PHE J 612 TRP 0.011 0.001 TRP J 129 HIS 0.002 0.001 HIS J 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 4594) covalent geometry : angle 0.55560 / 0.29 ( 6233) hydrogen bonds : bond 0.03287 / 2.26 ( 178) hydrogen bonds : angle 5.29754 / 3.84 ( 498) *********************** 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 62 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: I 22 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8493 (mp) REVERT: I 167 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8049 (mtpp) REVERT: I 191 LYS cc_start: 0.8859 (ptmm) cc_final: 0.8384 (tptt) REVERT: I 199 ASN cc_start: 0.8679 (t0) cc_final: 0.8449 (m110) REVERT: J 154 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8255 (mtm) REVERT: J 279 ARG cc_start: 0.8638 (ttp80) cc_final: 0.8420 (ttp80) outliers start: 8 outliers final: 3 residues processed: 57 average time/residue: 0.6412 time to fit residues: 37.5396 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 : 0.110 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 0 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 44 optimal weight: 0.0370 chunk 24 optimal weight: 2.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.057153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.045727 restraints weight = 13381.198| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.78 r_work: 0.2685 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.3417 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= 0.137 Angle : 0.570 7.885 6233 Z= 0.299 Chirality : 0.042 0.140 654 Planarity : 0.004 0.039 811 Dihedral : 5.474 71.584 618 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.93 % Allowed : 13.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.37), residues: 544 helix: 0.88 (0.36), residues: 221 sheet: 0.02 (0.64), residues: 55 loop : 0.52 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 35 TYR 0.010 0.001 TYR I 188 PHE 0.007 0.001 PHE J 612 TRP 0.012 0.001 TRP J 129 HIS 0.002 0.001 HIS J 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 4594) covalent geometry : angle 0.57013 / 0.30 ( 6233) hydrogen bonds : bond 0.03216 / 2.23 ( 178) hydrogen bonds : angle 5.29351 / 3.83 ( 498) *********************** 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 64 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: I 22 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8532 (mp) REVERT: I 191 LYS cc_start: 0.8936 (ptmm) cc_final: 0.8421 (tptt) REVERT: I 199 ASN cc_start: 0.8662 (t0) cc_final: 0.8425 (m110) REVERT: J 154 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8267 (mtm) REVERT: J 279 ARG cc_start: 0.8632 (ttp80) cc_final: 0.8412 (ttp80) outliers start: 9 outliers final: 4 residues processed: 58 average time/residue: 0.6233 time to fit residues: 37.1214 Evaluate side-chains 58 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 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 47 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.056786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.045530 restraints weight = 13293.758| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.72 r_work: 0.2680 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.3479 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= 0.147 Angle : 0.589 9.218 6233 Z= 0.307 Chirality : 0.042 0.139 654 Planarity : 0.004 0.039 811 Dihedral : 5.492 71.262 618 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.50 % Allowed : 13.92 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.37), residues: 544 helix: 0.88 (0.36), residues: 221 sheet: -0.36 (0.62), residues: 61 loop : 0.63 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 35 TYR 0.010 0.001 TYR I 188 PHE 0.007 0.001 PHE J 612 TRP 0.013 0.001 TRP J 129 HIS 0.002 0.001 HIS J 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 4594) covalent geometry : angle 0.58865 / 0.31 ( 6233) hydrogen bonds : bond 0.03320 / 2.31 ( 178) hydrogen bonds : angle 5.31564 / 3.86 ( 498) ********************** 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: 7 poor density : 55 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 22 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8527 (mp) REVERT: I 191 LYS cc_start: 0.8957 (ptmm) cc_final: 0.8433 (tptt) REVERT: I 199 ASN cc_start: 0.8647 (t0) cc_final: 0.8433 (m110) REVERT: J 93 LYS cc_start: 0.8960 (tmmt) cc_final: 0.8723 (pptt) REVERT: J 154 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8265 (mtm) REVERT: J 279 ARG cc_start: 0.8623 (ttp80) cc_final: 0.8411 (ttp80) outliers start: 7 outliers final: 3 residues processed: 59 average time/residue: 0.6694 time to fit residues: 40.6909 Evaluate side-chains 60 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 24 SER 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: 3.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 13 optimal weight: 0.0010 chunk 46 optimal weight: 0.8980 chunk 6 optimal weight: 0.0470 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 overall best weight: 0.4284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.057410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.046135 restraints weight = 13262.130| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.75 r_work: 0.2698 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4594 Z= 0.124 Angle : 0.588 8.614 6233 Z= 0.307 Chirality : 0.042 0.136 654 Planarity : 0.004 0.039 811 Dihedral : 5.419 71.907 618 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.28 % Allowed : 13.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.37), residues: 544 helix: 0.94 (0.36), residues: 221 sheet: 0.04 (0.64), residues: 55 loop : 0.53 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 35 TYR 0.010 0.001 TYR I 188 PHE 0.006 0.001 PHE J 35 TRP 0.012 0.001 TRP J 129 HIS 0.003 0.001 HIS J 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 ( 4594) covalent geometry : angle 0.58797 / 0.31 ( 6233) hydrogen bonds : bond 0.03056 / 2.12 ( 178) hydrogen bonds : angle 5.26432 / 3.82 ( 498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1664.59 seconds wall clock time: 29 minutes 5.31 seconds (1745.31 seconds total)