Starting phenix.real_space_refine on Fri Aug 22 15:01:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oof_17012/08_2025/8oof_17012.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oof_17012/08_2025/8oof_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8oof_17012/08_2025/8oof_17012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oof_17012/08_2025/8oof_17012.map" model { file = "/net/cci-nas-00/data/ceres_data/8oof_17012/08_2025/8oof_17012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oof_17012/08_2025/8oof_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 1.07, per 1000 atoms: 0.24 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: 0.23 Conformation dependent library (CDL) restraints added in 114.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.12 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: 0.65 Time building geometry restraints manager: 0.31 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: 2518 16.44 - 32.88: 187 32.88 - 49.32: 51 49.32 - 65.76: 8 65.76 - 82.20: 6 Dihedral angle restraints: 2770 sinusoidal: 1160 harmonic: 1610 Sorted by residual: dihedral pdb=" CA GLU J 626 " pdb=" C GLU J 626 " pdb=" N THR J 627 " pdb=" CA THR J 627 " ideal model delta harmonic sigma weight residual 180.00 150.59 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 2767 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: 4.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.230 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:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 : 13.651 82.195 1734 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 aren 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 covalent geometry : bond 0.00421 ( 4594) covalent geometry : angle 0.70602 ( 6233) hydrogen bonds : bond 0.19711 ( 173) hydrogen bonds : angle 8.36313 ( 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 : 0.124 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: 0.6962 time to fit residues: 70.7980 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 : 0.161 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: I 199 ASN J 52 GLN J 654 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.092049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.074439 restraints weight = 7559.209| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.81 r_work: 0.3021 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2237 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= 0.143 Angle : 0.587 5.314 6233 Z= 0.312 Chirality : 0.044 0.145 654 Planarity : 0.005 0.041 811 Dihedral : 7.877 81.301 649 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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 aren not related in a simple way. whole: 0.39 (0.35), residues: 544 helix: 0.16 (0.35), residues: 217 sheet: 0.77 (0.88), residues: 41 loop : 0.45 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 35 TYR 0.012 0.002 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 J 197 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 4594) covalent geometry : angle 0.58719 ( 6233) hydrogen bonds : bond 0.04058 ( 173) hydrogen bonds : angle 5.52785 ( 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 : 0.182 Fit side-chains REVERT: I 48 LEU cc_start: 0.9123 (mt) cc_final: 0.8864 (mt) REVERT: I 158 GLU cc_start: 0.6780 (mt-10) cc_final: 0.6510 (mt-10) REVERT: I 191 LYS cc_start: 0.8306 (pttt) cc_final: 0.6889 (mmtt) REVERT: J 98 PHE cc_start: 0.8777 (m-80) cc_final: 0.8537 (m-10) REVERT: J 635 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6789 (pm20) REVERT: J 677 ASP cc_start: 0.8126 (t0) cc_final: 0.7920 (t0) outliers start: 10 outliers final: 2 residues processed: 80 average time/residue: 0.6597 time to fit residues: 54.3284 Evaluate side-chains 68 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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: 0.8980 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN ** 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 = 0.3413 r_free = 0.3413 target = 0.089388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.072172 restraints weight = 7518.354| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.77 r_work: 0.2978 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2606 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= 0.193 Angle : 0.603 5.942 6233 Z= 0.319 Chirality : 0.045 0.135 654 Planarity : 0.005 0.048 811 Dihedral : 7.886 80.657 649 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.36 % Allowed : 12.21 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.35), residues: 544 helix: 0.31 (0.35), residues: 217 sheet: 0.06 (0.77), residues: 45 loop : 0.42 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 602 TYR 0.014 0.002 TYR J 180 PHE 0.015 0.002 PHE J 612 TRP 0.015 0.002 TRP J 287 HIS 0.004 0.001 HIS I 189 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 4594) covalent geometry : angle 0.60268 ( 6233) hydrogen bonds : bond 0.04233 ( 173) hydrogen bonds : angle 5.35362 ( 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 72 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9136 (mt) cc_final: 0.8871 (mt) REVERT: I 191 LYS cc_start: 0.8306 (pttt) cc_final: 0.6934 (mmtt) REVERT: J 98 PHE cc_start: 0.8826 (m-80) cc_final: 0.8613 (m-10) REVERT: J 174 GLU cc_start: 0.7693 (tt0) cc_final: 0.7471 (tt0) REVERT: J 196 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8560 (tpp-160) REVERT: J 626 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8254 (mt-10) outliers start: 11 outliers final: 5 residues processed: 69 average time/residue: 0.6169 time to fit residues: 43.9611 Evaluate side-chains 66 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 196 ARG Chi-restraints excluded: chain J residue 257 LYS 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: 0.2980 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 0.0980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3426 r_free = 0.3426 target = 0.090388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.073035 restraints weight = 7619.048| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.83 r_work: 0.2980 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4594 Z= 0.116 Angle : 0.526 6.161 6233 Z= 0.277 Chirality : 0.042 0.133 654 Planarity : 0.004 0.044 811 Dihedral : 7.269 83.789 649 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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 aren not related in a simple way. whole: 0.71 (0.36), residues: 544 helix: 0.69 (0.36), residues: 223 sheet: 0.05 (0.78), residues: 45 loop : 0.55 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 602 TYR 0.008 0.001 TYR J 180 PHE 0.009 0.001 PHE J 612 TRP 0.010 0.001 TRP J 129 HIS 0.005 0.001 HIS J 628 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 4594) covalent geometry : angle 0.52614 ( 6233) hydrogen bonds : bond 0.03238 ( 173) hydrogen bonds : angle 5.04864 ( 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 76 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9089 (mt) cc_final: 0.8827 (mt) REVERT: I 191 LYS cc_start: 0.8325 (pttt) cc_final: 0.6920 (mmtt) REVERT: J 174 GLU cc_start: 0.7755 (tt0) cc_final: 0.7539 (tt0) outliers start: 11 outliers final: 5 residues processed: 71 average time/residue: 0.6541 time to fit residues: 47.8258 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 : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 99 SER 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: 2.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 633 ASN J 697 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.088855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.071499 restraints weight = 7737.732| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.80 r_work: 0.2955 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4594 Z= 0.172 Angle : 0.563 5.521 6233 Z= 0.295 Chirality : 0.044 0.132 654 Planarity : 0.005 0.044 811 Dihedral : 7.521 81.440 649 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.57 % Allowed : 13.49 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.36), residues: 544 helix: 0.81 (0.36), residues: 217 sheet: -0.14 (0.75), residues: 45 loop : 0.45 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 40 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 covalent geometry : bond 0.00416 ( 4594) covalent geometry : angle 0.56339 ( 6233) hydrogen bonds : bond 0.03772 ( 173) hydrogen bonds : angle 5.13869 ( 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 71 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9117 (mt) cc_final: 0.8854 (mt) REVERT: I 191 LYS cc_start: 0.8338 (pttt) cc_final: 0.6985 (mmtt) outliers start: 12 outliers final: 8 residues processed: 65 average time/residue: 0.6776 time to fit residues: 45.3797 Evaluate side-chains 67 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 32 optimal weight: 0.9980 chunk 10 optimal weight: 0.0010 chunk 34 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 chunk 20 optimal weight: 0.1980 chunk 18 optimal weight: 0.2980 overall best weight: 0.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN J 128 ASN J 237 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.090597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.073038 restraints weight = 7786.944| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.88 r_work: 0.2983 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4594 Z= 0.110 Angle : 0.523 5.520 6233 Z= 0.274 Chirality : 0.041 0.131 654 Planarity : 0.004 0.040 811 Dihedral : 7.102 84.958 649 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.36 % Allowed : 13.28 % 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 aren not related in a simple way. whole: 0.77 (0.37), residues: 544 helix: 0.87 (0.36), residues: 223 sheet: -0.19 (0.74), residues: 45 loop : 0.50 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 21 TYR 0.007 0.001 TYR J 180 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 covalent geometry : bond 0.00255 ( 4594) covalent geometry : angle 0.52262 ( 6233) hydrogen bonds : bond 0.03075 ( 173) hydrogen bonds : angle 4.95989 ( 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 72 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9043 (mt) cc_final: 0.8784 (mt) REVERT: I 191 LYS cc_start: 0.8283 (pttt) cc_final: 0.6872 (mmtt) REVERT: J 174 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7576 (tt0) outliers start: 11 outliers final: 6 residues processed: 67 average time/residue: 0.6319 time to fit residues: 43.7250 Evaluate side-chains 65 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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 635 GLU Chi-restraints excluded: chain J residue 689 THR 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: 2.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 4 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN J 633 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.089197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.071687 restraints weight = 7752.736| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.84 r_work: 0.2961 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4594 Z= 0.157 Angle : 0.551 6.062 6233 Z= 0.288 Chirality : 0.043 0.134 654 Planarity : 0.004 0.044 811 Dihedral : 7.319 82.786 649 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.78 % Allowed : 14.35 % Favored : 82.87 % 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 aren not related in a simple way. whole: 0.57 (0.36), residues: 544 helix: 0.75 (0.36), residues: 223 sheet: -0.31 (0.73), residues: 45 loop : 0.36 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 21 TYR 0.010 0.001 TYR J 180 PHE 0.013 0.001 PHE J 612 TRP 0.013 0.001 TRP J 287 HIS 0.003 0.001 HIS I 189 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 4594) covalent geometry : angle 0.55115 ( 6233) hydrogen bonds : bond 0.03551 ( 173) hydrogen bonds : angle 5.04598 ( 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 73 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 16 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7303 (tt) REVERT: I 48 LEU cc_start: 0.9083 (mt) cc_final: 0.8824 (mt) REVERT: I 191 LYS cc_start: 0.8313 (pttt) cc_final: 0.6931 (mmtt) outliers start: 13 outliers final: 8 residues processed: 68 average time/residue: 0.6612 time to fit residues: 46.3921 Evaluate side-chains 67 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 155 THR 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 225 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 45 optimal weight: 0.0980 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.090034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.072534 restraints weight = 7733.028| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.84 r_work: 0.2978 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3356 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= 0.130 Angle : 0.545 6.826 6233 Z= 0.286 Chirality : 0.042 0.134 654 Planarity : 0.004 0.042 811 Dihedral : 7.163 84.337 649 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.78 % Allowed : 14.99 % Favored : 82.23 % 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 aren not related in a simple way. whole: 0.63 (0.37), residues: 544 helix: 0.81 (0.36), residues: 223 sheet: -0.32 (0.73), residues: 45 loop : 0.39 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 21 TYR 0.007 0.001 TYR J 180 PHE 0.010 0.001 PHE J 612 TRP 0.010 0.001 TRP J 287 HIS 0.004 0.001 HIS J 628 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4594) covalent geometry : angle 0.54510 ( 6233) hydrogen bonds : bond 0.03276 ( 173) hydrogen bonds : angle 4.99125 ( 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 72 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 48 LEU cc_start: 0.9070 (mt) cc_final: 0.8807 (mt) REVERT: I 191 LYS cc_start: 0.8301 (pttt) cc_final: 0.6920 (mmtt) REVERT: J 48 ARG cc_start: 0.7853 (mtt-85) cc_final: 0.7483 (mtp180) REVERT: J 722 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7320 (mt0) outliers start: 13 outliers final: 8 residues processed: 68 average time/residue: 0.5932 time to fit residues: 41.6519 Evaluate side-chains 67 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 99 SER Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Chi-restraints excluded: chain J residue 722 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 0.9980 chunk 9 optimal weight: 0.0970 chunk 12 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN J 633 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.089385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.072130 restraints weight = 7738.556| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.78 r_work: 0.2973 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4594 Z= 0.151 Angle : 0.556 7.271 6233 Z= 0.290 Chirality : 0.043 0.142 654 Planarity : 0.004 0.043 811 Dihedral : 7.267 83.745 649 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.71 % Allowed : 16.49 % Favored : 81.80 % 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 aren not related in a simple way. whole: 0.54 (0.36), residues: 544 helix: 0.72 (0.36), residues: 223 sheet: -0.37 (0.72), residues: 45 loop : 0.35 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 40 TYR 0.011 0.001 TYR J 167 PHE 0.012 0.001 PHE J 612 TRP 0.012 0.001 TRP J 287 HIS 0.003 0.001 HIS J 628 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 4594) covalent geometry : angle 0.55595 ( 6233) hydrogen bonds : bond 0.03500 ( 173) hydrogen bonds : angle 5.05431 ( 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 66 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 16 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7350 (tt) REVERT: I 48 LEU cc_start: 0.9101 (mt) cc_final: 0.8859 (mt) REVERT: I 191 LYS cc_start: 0.8318 (pttt) cc_final: 0.6970 (mmtt) REVERT: J 48 ARG cc_start: 0.7888 (mtt-85) cc_final: 0.7554 (mtp180) outliers start: 8 outliers final: 7 residues processed: 64 average time/residue: 0.6739 time to fit residues: 44.4129 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 : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 LEU 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 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: 0.9990 chunk 53 optimal weight: 0.0770 chunk 8 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.088704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.071402 restraints weight = 7725.770| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.87 r_work: 0.2950 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4594 Z= 0.135 Angle : 0.565 9.059 6233 Z= 0.294 Chirality : 0.042 0.141 654 Planarity : 0.004 0.042 811 Dihedral : 7.165 84.875 649 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.93 % Allowed : 16.92 % 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 aren not related in a simple way. whole: 0.61 (0.37), residues: 544 helix: 0.78 (0.36), residues: 223 sheet: -0.30 (0.72), residues: 45 loop : 0.38 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 21 TYR 0.010 0.001 TYR J 167 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 covalent geometry : bond 0.00323 ( 4594) covalent geometry : angle 0.56499 ( 6233) hydrogen bonds : bond 0.03325 ( 173) hydrogen bonds : angle 5.01608 ( 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 66 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 16 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7342 (tt) REVERT: I 48 LEU cc_start: 0.9028 (mt) cc_final: 0.8760 (mt) REVERT: I 191 LYS cc_start: 0.8317 (pttt) cc_final: 0.6931 (mmtt) REVERT: J 48 ARG cc_start: 0.7825 (mtt-85) cc_final: 0.7456 (mtp180) REVERT: J 722 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7270 (pt0) outliers start: 9 outliers final: 7 residues processed: 64 average time/residue: 0.6937 time to fit residues: 45.9037 Evaluate side-chains 65 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 16 LEU 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 635 GLU Chi-restraints excluded: chain J residue 689 THR Chi-restraints excluded: chain J residue 712 VAL Chi-restraints excluded: chain J residue 722 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.0670 chunk 22 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 46 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 199 ASN J 633 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.088619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.071327 restraints weight = 7696.153| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.87 r_work: 0.2948 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3475 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= 0.138 Angle : 0.556 10.398 6233 Z= 0.288 Chirality : 0.043 0.143 654 Planarity : 0.004 0.042 811 Dihedral : 7.161 84.889 649 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.14 % Allowed : 17.13 % Favored : 80.73 % 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 aren not related in a simple way. whole: 0.60 (0.37), residues: 544 helix: 0.74 (0.36), residues: 223 sheet: -0.23 (0.71), residues: 45 loop : 0.40 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 21 TYR 0.009 0.001 TYR J 167 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 covalent geometry : bond 0.00330 ( 4594) covalent geometry : angle 0.55584 ( 6233) hydrogen bonds : bond 0.03356 ( 173) hydrogen bonds : angle 5.00628 ( 486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2035.55 seconds wall clock time: 35 minutes 17.72 seconds (2117.72 seconds total)