Starting phenix.real_space_refine on Thu Jul 2 00:17:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8oof_17012/07_2026/8oof_17012.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oof_17012/07_2026/8oof_17012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8oof_17012/07_2026/8oof_17012.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8oof_17012/07_2026/8oof_17012.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oof_17012/07_2026/8oof_17012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oof_17012/07_2026/8oof_17012.map" model { file = "/net/cci-nas-00/data/ceres_data/8oof_17012/07_2026/8oof_17012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oof_17012/07_2026/8oof_17012.cif" } resolution = 2.9 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= 0.001 sd= 0.013 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-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: 1.40, per 1000 atoms: 0.31 Number of scatterers: 4479 At special positions: 0 Unit cell: (89.598, 87.132, 85.488, 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: 0.41 Conformation dependent library (CDL) restraints added in 211.5 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: 25 helices and 6 sheets defined 41.7% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'I' and resid 7 through 21 Processing helix chain 'I' and resid 43 through 52 Processing helix chain 'I' and resid 190 through 199 Processing helix chain 'I' and resid 203 through 211 removed outlier: 3.931A pdb=" N GLN I 207 " --> pdb=" O GLY I 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.743A 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 190 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 Processing helix chain 'J' and resid 276 through 283 removed outlier: 4.193A 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: 3.597A pdb=" N ALA J 611 " --> pdb=" O SER J 607 " (cutoff:3.500A) Processing helix chain 'J' and resid 634 through 639 Processing helix chain 'J' and resid 640 through 643 Processing helix chain 'J' and resid 645 through 650 Processing helix chain 'J' and resid 656 through 667 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 708 removed outlier: 3.648A pdb=" N ALA J 708 " --> pdb=" O GLN J 704 " (cutoff:3.500A) Processing helix chain 'J' and resid 726 through 736 Processing helix chain 'J' and resid 738 through 743 Processing helix chain 'J' and resid 748 through 755 removed outlier: 3.610A pdb=" N GLU J 753 " --> pdb=" O GLU J 749 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 179 through 180 removed outlier: 3.791A 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: 4.598A 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: 6.269A pdb=" N VAL J 686 " --> pdb=" O ARG J 719 " (cutoff:3.500A) 175 hydrogen bonds defined for protein. 486 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: 0.68 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1484 1.34 - 1.46: 727 1.46 - 1.57: 2346 1.57 - 1.69: 3 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 1.478 0.043 3.30e-02 9.18e+02 1.73e+00 bond pdb=" CB LEU J 683 " pdb=" CG LEU J 683 " ideal model delta sigma weight residual 1.530 1.508 0.022 2.00e-02 2.50e+03 1.19e+00 bond pdb=" N ALA I 160 " pdb=" CA ALA I 160 " ideal model delta sigma weight residual 1.455 1.477 -0.022 2.40e-02 1.74e+03 8.12e-01 bond pdb=" CG ARG J 636 " pdb=" CD ARG J 636 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.03e-01 bond pdb=" O3B ATP J 801 " pdb=" PB ATP J 801 " ideal model delta sigma weight residual 1.592 1.566 0.026 3.00e-02 1.11e+03 7.49e-01 ... (remaining 4589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 5833 1.35 - 2.70: 339 2.70 - 4.05: 49 4.05 - 5.39: 10 5.39 - 6.74: 2 Bond angle restraints: 6233 Sorted by residual: angle pdb=" CA GLU J 17 " pdb=" C GLU J 17 " pdb=" N PRO J 18 " ideal model delta sigma weight residual 116.90 121.49 -4.59 1.50e+00 4.44e-01 9.35e+00 angle pdb=" N THR J 627 " pdb=" CA THR J 627 " pdb=" C THR J 627 " ideal model delta sigma weight residual 110.19 107.25 2.94 1.24e+00 6.50e-01 5.61e+00 angle pdb=" N VAL J 634 " pdb=" CA VAL J 634 " pdb=" C VAL J 634 " ideal model delta sigma weight residual 111.05 113.96 -2.91 1.25e+00 6.40e-01 5.41e+00 angle pdb=" N ALA I 160 " pdb=" CA ALA I 160 " pdb=" C ALA I 160 " ideal model delta sigma weight residual 107.37 114.11 -6.74 2.96e+00 1.14e-01 5.19e+00 angle pdb=" CA ARG J 295 " pdb=" CB ARG J 295 " pdb=" CG ARG J 295 " ideal model delta sigma weight residual 114.10 109.68 4.42 2.00e+00 2.50e-01 4.88e+00 ... (remaining 6228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 2509 16.44 - 32.88: 180 32.88 - 49.32: 38 49.32 - 65.76: 6 65.76 - 82.20: 6 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 180.00 150.59 29.41 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ASP J 104 " pdb=" C ASP J 104 " pdb=" N CYS J 105 " pdb=" CA CYS J 105 " ideal model delta harmonic sigma weight residual 180.00 151.04 28.96 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ARG J 90 " pdb=" C ARG J 90 " pdb=" N ASP J 91 " pdb=" CA ASP J 91 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 2736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 417 0.041 - 0.083: 170 0.083 - 0.124: 62 0.124 - 0.165: 2 0.165 - 0.206: 3 Chirality restraints: 654 Sorted by residual: 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 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 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 2.31 0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CA ARG I 185 " pdb=" N ARG I 185 " pdb=" C ARG I 185 " pdb=" CB ARG I 185 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 651 not shown) Planarity restraints: 811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 293 " -0.210 9.50e-02 1.11e+02 9.48e-02 6.86e+00 pdb=" NE ARG J 293 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG J 293 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG J 293 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG J 293 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 284 " -0.007 2.00e-02 2.50e+03 1.46e-02 4.28e+00 pdb=" CG TYR J 284 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR J 284 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR J 284 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR J 284 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR J 284 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR J 284 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR J 284 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 636 " 0.165 9.50e-02 1.11e+02 7.45e-02 4.03e+00 pdb=" NE ARG J 636 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG J 636 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG J 636 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG J 636 " 0.001 2.00e-02 2.50e+03 ... (remaining 808 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 35 2.61 - 3.19: 3966 3.19 - 3.76: 6776 3.76 - 4.33: 10095 4.33 - 4.90: 16176 Nonbonded interactions: 37048 Sorted by model distance: nonbonded pdb=" OD2 ASP J 190 " pdb="MG MG J 802 " model vdw 2.043 2.170 nonbonded pdb=" O1B ATP J 801 " pdb="MG MG J 802 " model vdw 2.087 2.170 nonbonded pdb=" O1G ATP J 801 " pdb="MG MG J 802 " model vdw 2.096 2.170 nonbonded pdb=" OE2 GLU J 264 " pdb=" NH2 ARG J 268 " model vdw 2.231 3.120 nonbonded pdb=" NZ LYS I 42 " pdb=" OE1 GLU I 50 " model vdw 2.305 3.120 ... (remaining 37043 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: 3.570 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.890 Find NCS groups from input model: 0.020 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:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 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 : 0.004 0.043 4594 Z= 0.179 Angle : 0.706 6.743 6233 Z= 0.407 Chirality : 0.049 0.206 654 Planarity : 0.009 0.095 811 Dihedral : 12.988 82.195 1703 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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 (0.34), residues: 544 helix: -1.27 (0.33), residues: 197 sheet: 0.92 (0.80), residues: 46 loop : -0.10 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.003 ARG J 293 TYR 0.023 0.004 TYR J 284 PHE 0.019 0.002 PHE J 612 TRP 0.021 0.002 TRP J 735 HIS 0.008 0.002 HIS J 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 4594) covalent geometry : angle 0.70602 / 0.41 ( 6233) hydrogen bonds : bond 0.19711 / 13.48 ( 173) hydrogen bonds : angle 8.36313 / 6.42 ( 486) *********************** 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 99 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: I 48 LEU cc_start: 0.8993 (mt) cc_final: 0.8675 (mt) REVERT: I 191 LYS cc_start: 0.8398 (pttt) cc_final: 0.7010 (mmtt) REVERT: J 677 ASP cc_start: 0.7923 (t0) cc_final: 0.7551 (t0) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.7344 time to fit residues: 74.6985 Evaluate side-chains 67 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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: 0.9990 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.0370 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 199 ASN J 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.091838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.074178 restraints weight = 7572.515| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.81 r_work: 0.3014 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4594 Z= 0.149 Angle : 0.595 5.384 6233 Z= 0.317 Chirality : 0.044 0.151 654 Planarity : 0.005 0.041 811 Dihedral : 6.608 81.671 618 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.14 % Allowed : 11.13 % 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 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: 0.37 (0.35), residues: 544 helix: 0.07 (0.35), residues: 217 sheet: 0.79 (0.84), residues: 46 loop : 0.49 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 748 TYR 0.012 0.001 TYR J 180 PHE 0.012 0.002 PHE J 612 TRP 0.015 0.002 TRP J 129 HIS 0.004 0.001 HIS I 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 4594) covalent geometry : angle 0.59506 / 0.32 ( 6233) hydrogen bonds : bond 0.04214 / 2.93 ( 173) hydrogen bonds : angle 5.60690 / 4.33 ( 486) *********************** 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 86 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.175 Fit side-chains REVERT: I 48 LEU cc_start: 0.9123 (mt) cc_final: 0.8845 (mt) REVERT: I 158 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6447 (mt-10) REVERT: I 191 LYS cc_start: 0.8317 (pttt) cc_final: 0.6888 (mmtt) REVERT: J 242 MET cc_start: 0.8771 (tpp) cc_final: 0.8489 (tpp) REVERT: J 635 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6834 (pm20) outliers start: 10 outliers final: 2 residues processed: 80 average time/residue: 0.7080 time to fit residues: 58.2963 Evaluate side-chains 66 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 1 optimal weight: 0.0040 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 199 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN J 628 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.090397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.073268 restraints weight = 7520.506| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.77 r_work: 0.2999 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4594 Z= 0.157 Angle : 0.573 5.545 6233 Z= 0.302 Chirality : 0.044 0.135 654 Planarity : 0.005 0.044 811 Dihedral : 6.331 82.880 618 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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: 0.47 (0.36), residues: 544 helix: 0.40 (0.35), residues: 223 sheet: 0.06 (0.77), residues: 45 loop : 0.48 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 602 TYR 0.012 0.001 TYR J 180 PHE 0.014 0.002 PHE J 612 TRP 0.013 0.001 TRP J 287 HIS 0.004 0.001 HIS I 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 4594) covalent geometry : angle 0.57307 / 0.30 ( 6233) hydrogen bonds : bond 0.03864 / 2.69 ( 173) hydrogen bonds : angle 5.24976 / 4.06 ( 486) *********************** 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 74 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9143 (mt) cc_final: 0.8869 (mt) REVERT: I 191 LYS cc_start: 0.8327 (pttt) cc_final: 0.6943 (mmtt) REVERT: J 174 GLU cc_start: 0.7695 (tt0) cc_final: 0.7470 (tt0) REVERT: J 626 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8225 (mt-10) outliers start: 13 outliers final: 4 residues processed: 69 average time/residue: 0.6480 time to fit residues: 46.1567 Evaluate side-chains 65 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 626 GLU Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 17 optimal weight: 0.4980 chunk 2 optimal weight: 0.0050 chunk 8 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 199 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.089706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.072322 restraints weight = 7650.448| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.82 r_work: 0.2971 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4594 Z= 0.137 Angle : 0.548 6.589 6233 Z= 0.286 Chirality : 0.043 0.134 654 Planarity : 0.004 0.043 811 Dihedral : 6.075 84.060 618 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.36 % Allowed : 12.85 % 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: 0.63 (0.36), residues: 544 helix: 0.61 (0.35), residues: 223 sheet: -0.03 (0.77), residues: 45 loop : 0.53 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 602 TYR 0.011 0.001 TYR J 180 PHE 0.012 0.001 PHE J 612 TRP 0.012 0.001 TRP J 129 HIS 0.004 0.001 HIS J 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 4594) covalent geometry : angle 0.54756 / 0.29 ( 6233) hydrogen bonds : bond 0.03462 / 2.40 ( 173) hydrogen bonds : angle 5.08125 / 3.94 ( 486) *********************** 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 73 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9086 (mt) cc_final: 0.8823 (mt) REVERT: I 191 LYS cc_start: 0.8300 (pttt) cc_final: 0.6903 (mmtt) REVERT: J 48 ARG cc_start: 0.7881 (mtt-85) cc_final: 0.7510 (mtp180) REVERT: J 174 GLU cc_start: 0.7756 (tt0) cc_final: 0.7555 (tt0) REVERT: J 196 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8496 (tpp-160) outliers start: 11 outliers final: 6 residues processed: 68 average time/residue: 0.6528 time to fit residues: 45.7657 Evaluate side-chains 64 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 196 ARG Chi-restraints excluded: chain J residue 257 LYS Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 19 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 199 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 237 HIS J 697 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.088458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.071296 restraints weight = 7780.639| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.76 r_work: 0.2949 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4594 Z= 0.186 Angle : 0.580 5.927 6233 Z= 0.303 Chirality : 0.044 0.132 654 Planarity : 0.005 0.044 811 Dihedral : 6.154 82.815 618 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.78 % Allowed : 13.49 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.62 (0.36), residues: 544 helix: 0.71 (0.36), residues: 217 sheet: -0.27 (0.73), residues: 45 loop : 0.46 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 212 TYR 0.012 0.002 TYR J 180 PHE 0.015 0.002 PHE J 612 TRP 0.014 0.002 TRP J 287 HIS 0.004 0.001 HIS I 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 ( 4594) covalent geometry : angle 0.57960 / 0.30 ( 6233) hydrogen bonds : bond 0.03902 / 2.70 ( 173) hydrogen bonds : angle 5.17828 / 4.02 ( 486) *********************** 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 69 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9124 (mt) cc_final: 0.8868 (mt) REVERT: I 191 LYS cc_start: 0.8336 (pttt) cc_final: 0.6982 (mmtt) REVERT: J 48 ARG cc_start: 0.7912 (mtt-85) cc_final: 0.7600 (mtp180) REVERT: J 196 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8437 (tpp-160) outliers start: 13 outliers final: 9 residues processed: 64 average time/residue: 0.7165 time to fit residues: 47.2431 Evaluate side-chains 67 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 196 ARG Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 257 LYS Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 700 GLU Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 34 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 199 ASN J 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.089331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.072154 restraints weight = 7827.342| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.79 r_work: 0.2971 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3198 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= 0.141 Angle : 0.548 5.795 6233 Z= 0.287 Chirality : 0.043 0.131 654 Planarity : 0.004 0.043 811 Dihedral : 6.020 84.258 618 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.43 % Allowed : 12.85 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.71 (0.36), residues: 544 helix: 0.85 (0.36), residues: 217 sheet: -0.35 (0.72), residues: 45 loop : 0.47 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 21 TYR 0.009 0.001 TYR J 180 PHE 0.012 0.001 PHE J 612 TRP 0.012 0.001 TRP J 287 HIS 0.004 0.001 HIS J 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 4594) covalent geometry : angle 0.54818 / 0.29 ( 6233) hydrogen bonds : bond 0.03448 / 2.38 ( 173) hydrogen bonds : angle 5.07225 / 3.94 ( 486) *********************** 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 77 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9118 (mt) cc_final: 0.8865 (mt) REVERT: I 191 LYS cc_start: 0.8309 (pttt) cc_final: 0.6968 (mmtt) REVERT: J 174 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7507 (tt0) REVERT: J 196 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8518 (tpp-160) outliers start: 16 outliers final: 10 residues processed: 72 average time/residue: 0.6615 time to fit residues: 49.2422 Evaluate side-chains 71 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 196 ARG Chi-restraints excluded: chain J residue 225 LEU Chi-restraints excluded: chain J residue 257 LYS Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 700 GLU Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 52 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 45 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.088828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.071381 restraints weight = 7773.158| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.83 r_work: 0.2953 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4594 Z= 0.163 Angle : 0.561 5.950 6233 Z= 0.293 Chirality : 0.043 0.137 654 Planarity : 0.004 0.044 811 Dihedral : 6.015 83.052 618 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.21 % Allowed : 14.35 % Favored : 82.44 % 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: 0.46 (0.36), residues: 544 helix: 0.61 (0.36), residues: 223 sheet: -0.45 (0.72), residues: 45 loop : 0.35 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 21 TYR 0.009 0.001 TYR J 180 PHE 0.013 0.002 PHE J 612 TRP 0.013 0.001 TRP J 287 HIS 0.004 0.001 HIS I 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 ( 4594) covalent geometry : angle 0.56096 / 0.29 ( 6233) hydrogen bonds : bond 0.03653 / 2.54 ( 173) hydrogen bonds : angle 5.13379 / 3.98 ( 486) *********************** 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 75 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9096 (mt) cc_final: 0.8841 (mt) REVERT: I 191 LYS cc_start: 0.8318 (pttt) cc_final: 0.6937 (mmtt) REVERT: J 196 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8423 (tpp-160) outliers start: 15 outliers final: 10 residues processed: 69 average time/residue: 0.7249 time to fit residues: 51.5159 Evaluate side-chains 68 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 196 ARG Chi-restraints excluded: chain J residue 225 LEU Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 700 GLU Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 0.0980 chunk 36 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 6 optimal weight: 0.0000 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.089668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.072265 restraints weight = 7758.368| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.83 r_work: 0.2973 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3421 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= 0.134 Angle : 0.551 6.507 6233 Z= 0.288 Chirality : 0.042 0.130 654 Planarity : 0.004 0.042 811 Dihedral : 5.894 84.314 618 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.57 % Allowed : 16.27 % Favored : 81.16 % 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: 0.55 (0.36), residues: 544 helix: 0.70 (0.36), residues: 223 sheet: -0.27 (0.72), residues: 45 loop : 0.37 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 112 TYR 0.022 0.001 TYR J 167 PHE 0.011 0.001 PHE J 612 TRP 0.011 0.001 TRP J 287 HIS 0.004 0.001 HIS J 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 ( 4594) covalent geometry : angle 0.55055 / 0.29 ( 6233) hydrogen bonds : bond 0.03335 / 2.31 ( 173) hydrogen bonds : angle 5.04622 / 3.92 ( 486) *********************** 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 70 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9072 (mt) cc_final: 0.8818 (mt) REVERT: I 191 LYS cc_start: 0.8297 (pttt) cc_final: 0.6917 (mmtt) REVERT: J 196 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8501 (tpp-160) outliers start: 12 outliers final: 9 residues processed: 67 average time/residue: 0.6875 time to fit residues: 47.4997 Evaluate side-chains 67 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 196 ARG Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 700 GLU Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.0980 chunk 53 optimal weight: 0.0670 chunk 46 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 overall best weight: 0.3118 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.090609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.073478 restraints weight = 7740.568| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.80 r_work: 0.2998 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3594 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= 0.112 Angle : 0.520 6.593 6233 Z= 0.270 Chirality : 0.041 0.135 654 Planarity : 0.004 0.039 811 Dihedral : 5.716 85.279 618 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.14 % Allowed : 17.34 % Favored : 80.51 % 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 (0.37), residues: 544 helix: 0.82 (0.36), residues: 223 sheet: -0.11 (0.73), residues: 45 loop : 0.47 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 40 TYR 0.010 0.001 TYR J 167 PHE 0.008 0.001 PHE J 612 TRP 0.009 0.001 TRP J 287 HIS 0.004 0.001 HIS J 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 4594) covalent geometry : angle 0.51965 / 0.27 ( 6233) hydrogen bonds : bond 0.03046 / 2.10 ( 173) hydrogen bonds : angle 4.90324 / 3.82 ( 486) *********************** 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 67 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9097 (mt) cc_final: 0.8850 (mt) REVERT: I 191 LYS cc_start: 0.8285 (pttt) cc_final: 0.6948 (mmtt) REVERT: J 48 ARG cc_start: 0.7899 (mtt-85) cc_final: 0.7601 (mtp180) REVERT: J 196 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8469 (tpp-160) REVERT: J 722 GLN cc_start: 0.7491 (mt0) cc_final: 0.7212 (pt0) outliers start: 10 outliers final: 7 residues processed: 64 average time/residue: 0.6846 time to fit residues: 45.1741 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 : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 196 ARG Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 49 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 chunk 10 optimal weight: 0.0270 overall best weight: 0.4038 ------------------------------------------------------------------------------- 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 = 0.3426 r_free = 0.3426 target = 0.090258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.073110 restraints weight = 7679.192| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.79 r_work: 0.2989 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3618 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= 0.129 Angle : 0.576 14.062 6233 Z= 0.292 Chirality : 0.042 0.132 654 Planarity : 0.004 0.041 811 Dihedral : 5.726 84.876 618 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.71 % Allowed : 17.77 % Favored : 80.51 % 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: 0.68 (0.37), residues: 544 helix: 0.80 (0.36), residues: 223 sheet: -0.15 (0.73), residues: 45 loop : 0.44 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 617 TYR 0.008 0.001 TYR J 167 PHE 0.009 0.001 PHE J 612 TRP 0.011 0.001 TRP J 287 HIS 0.004 0.001 HIS J 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 4594) covalent geometry : angle 0.57606 / 0.29 ( 6233) hydrogen bonds : bond 0.03191 / 2.20 ( 173) hydrogen bonds : angle 4.93933 / 3.86 ( 486) ********************** 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: 8 poor density : 54 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9092 (mt) cc_final: 0.8838 (mt) REVERT: I 191 LYS cc_start: 0.8289 (pttt) cc_final: 0.6949 (mmtt) REVERT: J 48 ARG cc_start: 0.7902 (mtt-85) cc_final: 0.7607 (mtp180) REVERT: J 196 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8493 (tpp-160) REVERT: J 225 LEU cc_start: 0.8697 (mm) cc_final: 0.8434 (mt) REVERT: J 722 GLN cc_start: 0.7517 (mt0) cc_final: 0.7249 (pt0) outliers start: 8 outliers final: 7 residues processed: 61 average time/residue: 0.6595 time to fit residues: 41.6236 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 : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 196 ARG Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 6 optimal weight: 0.0870 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.089933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.072535 restraints weight = 7669.818| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.83 r_work: 0.2974 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3634 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= 0.134 Angle : 0.563 13.226 6233 Z= 0.286 Chirality : 0.042 0.131 654 Planarity : 0.004 0.042 811 Dihedral : 5.760 84.554 618 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.93 % Allowed : 17.77 % Favored : 80.30 % 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: 0.64 (0.37), residues: 544 helix: 0.75 (0.36), residues: 223 sheet: -0.16 (0.73), residues: 45 loop : 0.43 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 617 TYR 0.014 0.001 TYR J 251 PHE 0.010 0.001 PHE J 612 TRP 0.011 0.001 TRP J 287 HIS 0.004 0.001 HIS J 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 4594) covalent geometry : angle 0.56262 / 0.29 ( 6233) hydrogen bonds : bond 0.03276 / 2.26 ( 173) hydrogen bonds : angle 4.97112 / 3.89 ( 486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2232.50 seconds wall clock time: 38 minutes 47.42 seconds (2327.42 seconds total)