Starting phenix.real_space_refine on Tue Aug 4 16:08:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rhc_53965/08_2026/9rhc_53965.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rhc_53965/08_2026/9rhc_53965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rhc_53965/08_2026/9rhc_53965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rhc_53965/08_2026/9rhc_53965.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rhc_53965/08_2026/9rhc_53965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rhc_53965/08_2026/9rhc_53965.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3024 2.51 5 N 758 2.21 5 O 838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4640 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2917 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 15, 'TRANS': 372} Chain: "B" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "C" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 816 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Time building chain proxies: 1.31, per 1000 atoms: 0.28 Number of scatterers: 4640 At special positions: 0 Unit cell: (68.634, 78.678, 100.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 838 8.00 N 758 7.00 C 3024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 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: 0.45 Conformation dependent library (CDL) restraints added in 214.7 milliseconds 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1112 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 8 sheets defined 54.6% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 Processing helix chain 'A' and resid 11 through 31 removed outlier: 4.176A pdb=" N GLY A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 43 removed outlier: 4.668A pdb=" N GLY A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N TRP A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 85 Processing helix chain 'A' and resid 86 through 89 removed outlier: 3.671A pdb=" N ALA A 89 " --> pdb=" O GLY A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 89' Processing helix chain 'A' and resid 90 through 117 removed outlier: 4.941A pdb=" N PHE A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) Proline residue: A 97 - end of helix Proline residue: A 108 - end of helix removed outlier: 3.834A pdb=" N PHE A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.586A pdb=" N GLU A 124 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP A 126 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 149 through 175 Processing helix chain 'A' and resid 180 through 200 Processing helix chain 'A' and resid 204 through 219 removed outlier: 3.633A pdb=" N TYR A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.802A pdb=" N GLY A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 262 Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 282 through 285 Processing helix chain 'A' and resid 286 through 298 Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 354 through 384 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.964A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50 Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.567A pdb=" N LYS B 3 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 25 " --> pdb=" O LYS B 3 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.551A pdb=" N ALA B 92 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LYS B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N TRP B 47 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR B 40 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU B 45 " --> pdb=" O THR B 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.551A pdb=" N ALA B 92 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N CYS B 96 " --> pdb=" O TRP B 108 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TRP B 108 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LYS B 98 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.415A pdb=" N GLN C 37 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ARG C 46 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.685A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) 304 hydrogen bonds defined for protein. 846 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: 0.48 Time building geometry restraints manager: 0.58 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: 1439 1.34 - 1.46: 846 1.46 - 1.58: 2426 1.58 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 4744 Sorted by residual: bond pdb=" CA ALA A 12 " pdb=" CB ALA A 12 " ideal model delta sigma weight residual 1.530 1.475 0.056 1.85e-02 2.92e+03 9.08e+00 bond pdb=" N GLU B 99 " pdb=" CA GLU B 99 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 7.05e+00 bond pdb=" C THR C 7 " pdb=" N PRO C 8 " ideal model delta sigma weight residual 1.335 1.357 -0.022 8.70e-03 1.32e+04 6.49e+00 bond pdb=" N ASP A 11 " pdb=" CA ASP A 11 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.43e+00 bond pdb=" N PHE A 8 " pdb=" CA PHE A 8 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.25e-02 6.40e+03 6.42e+00 ... (remaining 4739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 6139 1.65 - 3.30: 255 3.30 - 4.95: 45 4.95 - 6.60: 9 6.60 - 8.25: 3 Bond angle restraints: 6451 Sorted by residual: angle pdb=" CA ASP A 11 " pdb=" CB ASP A 11 " pdb=" CG ASP A 11 " ideal model delta sigma weight residual 112.60 116.23 -3.63 1.00e+00 1.00e+00 1.32e+01 angle pdb=" CA HIS A 3 " pdb=" CB HIS A 3 " pdb=" CG HIS A 3 " ideal model delta sigma weight residual 113.80 110.19 3.61 1.00e+00 1.00e+00 1.31e+01 angle pdb=" N LEU A 4 " pdb=" CA LEU A 4 " pdb=" C LEU A 4 " ideal model delta sigma weight residual 111.28 107.41 3.87 1.09e+00 8.42e-01 1.26e+01 angle pdb=" O LYS A 2 " pdb=" C LYS A 2 " pdb=" N HIS A 3 " ideal model delta sigma weight residual 122.07 125.69 -3.62 1.03e+00 9.43e-01 1.24e+01 angle pdb=" CA MET A 157 " pdb=" C MET A 157 " pdb=" O MET A 157 " ideal model delta sigma weight residual 120.82 117.19 3.63 1.05e+00 9.07e-01 1.20e+01 ... (remaining 6446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 2473 15.61 - 31.23: 222 31.23 - 46.84: 61 46.84 - 62.45: 17 62.45 - 78.06: 5 Dihedral angle restraints: 2778 sinusoidal: 1034 harmonic: 1744 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 56.83 36.17 1 1.00e+01 1.00e-02 1.85e+01 dihedral pdb=" CA ASN B 103 " pdb=" C ASN B 103 " pdb=" N ASP B 104 " pdb=" CA ASP B 104 " ideal model delta harmonic sigma weight residual 180.00 160.17 19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 88 " pdb=" CB CYS C 88 " ideal model delta sinusoidal sigma weight residual 93.00 61.04 31.96 1 1.00e+01 1.00e-02 1.46e+01 ... (remaining 2775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 466 0.033 - 0.066: 188 0.066 - 0.098: 64 0.098 - 0.131: 36 0.131 - 0.164: 8 Chirality restraints: 762 Sorted by residual: chirality pdb=" CA HIS A 3 " pdb=" N HIS A 3 " pdb=" C HIS A 3 " pdb=" CB HIS A 3 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA ILE C 48 " pdb=" N ILE C 48 " pdb=" C ILE C 48 " pdb=" CB ILE C 48 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA PHE A 7 " pdb=" N PHE A 7 " pdb=" C PHE A 7 " pdb=" CB PHE A 7 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.24e-01 ... (remaining 759 not shown) Planarity restraints: 794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 36 " 0.018 2.00e-02 2.50e+03 1.59e-02 6.32e+00 pdb=" CG TRP B 36 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 36 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B 36 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 36 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 36 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 36 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 36 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 36 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 35 " 0.017 2.00e-02 2.50e+03 1.56e-02 6.09e+00 pdb=" CG TRP C 35 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP C 35 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 35 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 35 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 35 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 35 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 35 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 35 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C 35 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 86 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.61e+00 pdb=" C GLY A 86 " -0.041 2.00e-02 2.50e+03 pdb=" O GLY A 86 " 0.016 2.00e-02 2.50e+03 pdb=" N SER A 87 " 0.013 2.00e-02 2.50e+03 ... (remaining 791 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 126 2.70 - 3.25: 4617 3.25 - 3.80: 7449 3.80 - 4.35: 9596 4.35 - 4.90: 16265 Nonbonded interactions: 38053 Sorted by model distance: nonbonded pdb=" O SER C 30 " pdb=" OG SER C 30 " model vdw 2.154 3.040 nonbonded pdb=" NH2 ARG A 203 " pdb=" O LYS A 240 " model vdw 2.241 3.120 nonbonded pdb=" NH2 ARG C 66 " pdb=" OH TYR C 71 " model vdw 2.262 3.120 nonbonded pdb=" OH TYR A 38 " pdb=" O PHE A 269 " model vdw 2.278 3.040 nonbonded pdb=" NH2 ARG C 61 " pdb=" OD1 ASP C 82 " model vdw 2.304 3.120 ... (remaining 38048 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.000 Set scattering table: 0.000 Process input model: 6.120 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 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 : 0.005 0.056 4746 Z= 0.243 Angle : 0.781 8.245 6455 Z= 0.463 Chirality : 0.046 0.164 762 Planarity : 0.005 0.071 794 Dihedral : 13.668 78.063 1660 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.22 (0.34), residues: 606 helix: 1.37 (0.29), residues: 289 sheet: 1.50 (0.50), residues: 108 loop : -0.28 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 66 TYR 0.020 0.002 TYR C 49 PHE 0.013 0.002 PHE A 136 TRP 0.042 0.003 TRP B 36 HIS 0.011 0.002 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.24 ( 4744) covalent geometry : angle 0.78125 / 0.46 ( 6451) SS BOND : bond 0.00245 / 0.12 ( 2) SS BOND : angle 0.27971 / 0.13 ( 4) hydrogen bonds : bond 0.19583 / 13.11 ( 290) hydrogen bonds : angle 7.32542 / 5.45 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.167 Fit side-chains REVERT: A 19 ILE cc_start: 0.8858 (mm) cc_final: 0.8657 (mt) REVERT: A 26 MET cc_start: 0.8996 (tpp) cc_final: 0.8689 (mmm) REVERT: A 28 MET cc_start: 0.6782 (mmt) cc_final: 0.6528 (ttt) REVERT: A 44 THR cc_start: 0.8707 (m) cc_final: 0.8275 (p) REVERT: A 105 MET cc_start: 0.9003 (ttt) cc_final: 0.8638 (ttp) REVERT: A 221 LYS cc_start: 0.8931 (mtpt) cc_final: 0.8532 (mtmt) REVERT: A 313 ARG cc_start: 0.7525 (mmm160) cc_final: 0.7277 (ttp-170) REVERT: B 69 THR cc_start: 0.7454 (m) cc_final: 0.6915 (p) REVERT: C 97 THR cc_start: 0.8492 (m) cc_final: 0.8063 (p) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1030 time to fit residues: 11.2067 Evaluate side-chains 75 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.0020 chunk 48 optimal weight: 0.0870 chunk 56 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.5566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 56 ASN A 58 ASN A 271 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.186647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.131172 restraints weight = 5771.601| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.59 r_work: 0.3124 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4746 Z= 0.119 Angle : 0.576 6.870 6455 Z= 0.296 Chirality : 0.039 0.147 762 Planarity : 0.004 0.026 794 Dihedral : 4.277 19.373 652 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.03 % Allowed : 9.35 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.84 (0.34), residues: 606 helix: 2.03 (0.29), residues: 292 sheet: 1.66 (0.51), residues: 102 loop : -0.12 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 6 TYR 0.013 0.001 TYR C 49 PHE 0.013 0.001 PHE A 136 TRP 0.021 0.001 TRP B 36 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 4744) covalent geometry : angle 0.57600 / 0.30 ( 6451) SS BOND : bond 0.00416 / 0.20 ( 2) SS BOND : angle 0.60212 / 0.26 ( 4) hydrogen bonds : bond 0.04199 / 2.97 ( 290) hydrogen bonds : angle 5.02931 / 3.75 ( 846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.215 Fit side-chains REVERT: A 44 THR cc_start: 0.8928 (m) cc_final: 0.8552 (p) REVERT: A 313 ARG cc_start: 0.8017 (mmm160) cc_final: 0.7559 (ttp-170) REVERT: B 31 ASP cc_start: 0.8148 (m-30) cc_final: 0.7893 (m-30) REVERT: B 106 ASP cc_start: 0.5782 (t0) cc_final: 0.5499 (t0) REVERT: C 96 PHE cc_start: 0.8253 (m-10) cc_final: 0.7986 (m-10) outliers start: 10 outliers final: 4 residues processed: 94 average time/residue: 0.0735 time to fit residues: 8.8405 Evaluate side-chains 78 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 20 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 33 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 6 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 ASN A 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.184021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.116747 restraints weight = 5692.854| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.45 r_work: 0.3065 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4746 Z= 0.144 Angle : 0.577 8.915 6455 Z= 0.290 Chirality : 0.040 0.152 762 Planarity : 0.003 0.028 794 Dihedral : 4.213 19.839 652 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.83 % Allowed : 10.77 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.94 (0.34), residues: 606 helix: 2.07 (0.29), residues: 292 sheet: 1.61 (0.51), residues: 96 loop : 0.11 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 92 TYR 0.011 0.001 TYR A 38 PHE 0.009 0.001 PHE A 72 TRP 0.027 0.002 TRP C 35 HIS 0.003 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 4744) covalent geometry : angle 0.57607 / 0.29 ( 6451) SS BOND : bond 0.00159 / 0.08 ( 2) SS BOND : angle 1.17267 / 0.58 ( 4) hydrogen bonds : bond 0.03887 / 2.78 ( 290) hydrogen bonds : angle 4.79445 / 3.59 ( 846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.099 Fit side-chains REVERT: A 1 MET cc_start: 0.1514 (mmt) cc_final: 0.0469 (ptt) REVERT: A 19 ILE cc_start: 0.8947 (mm) cc_final: 0.8684 (mt) REVERT: A 28 MET cc_start: 0.7230 (mmp) cc_final: 0.6833 (mtp) REVERT: A 44 THR cc_start: 0.8914 (m) cc_final: 0.8512 (p) REVERT: A 82 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8095 (mm-30) REVERT: A 199 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8124 (mp) REVERT: A 313 ARG cc_start: 0.8041 (mmm160) cc_final: 0.7553 (ttp-170) REVERT: B 31 ASP cc_start: 0.7936 (m-30) cc_final: 0.7687 (m-30) REVERT: B 106 ASP cc_start: 0.6173 (t0) cc_final: 0.5906 (t0) outliers start: 9 outliers final: 6 residues processed: 82 average time/residue: 0.0664 time to fit residues: 7.0974 Evaluate side-chains 80 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 71 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 30 optimal weight: 0.6980 chunk 49 optimal weight: 8.9990 chunk 36 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 33 optimal weight: 0.0770 chunk 14 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.184546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.130818 restraints weight = 5672.642| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.04 r_work: 0.3080 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4746 Z= 0.102 Angle : 0.537 8.079 6455 Z= 0.266 Chirality : 0.038 0.147 762 Planarity : 0.004 0.051 794 Dihedral : 4.069 19.538 652 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.63 % Allowed : 11.99 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.11 (0.34), residues: 606 helix: 2.24 (0.29), residues: 292 sheet: 1.75 (0.52), residues: 96 loop : 0.11 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 92 TYR 0.013 0.001 TYR C 49 PHE 0.006 0.001 PHE A 72 TRP 0.025 0.001 TRP C 35 HIS 0.002 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 4744) covalent geometry : angle 0.53743 / 0.27 ( 6451) SS BOND : bond 0.00321 / 0.15 ( 2) SS BOND : angle 0.39790 / 0.20 ( 4) hydrogen bonds : bond 0.03378 / 2.46 ( 290) hydrogen bonds : angle 4.61989 / 3.45 ( 846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.162 Fit side-chains REVERT: A 1 MET cc_start: 0.1136 (mmt) cc_final: 0.0191 (ptt) REVERT: A 19 ILE cc_start: 0.8987 (mm) cc_final: 0.8721 (mt) REVERT: A 28 MET cc_start: 0.7311 (mmp) cc_final: 0.6867 (mtp) REVERT: A 44 THR cc_start: 0.8942 (m) cc_final: 0.8547 (p) REVERT: A 56 ASN cc_start: 0.8617 (t0) cc_final: 0.7400 (p0) REVERT: A 82 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8118 (mm-30) REVERT: A 105 MET cc_start: 0.8861 (ttp) cc_final: 0.8524 (ttp) REVERT: A 313 ARG cc_start: 0.8099 (mmm160) cc_final: 0.7628 (ttp-170) outliers start: 8 outliers final: 5 residues processed: 81 average time/residue: 0.0453 time to fit residues: 4.9863 Evaluate side-chains 79 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 103 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 34 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.184192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.118215 restraints weight = 5745.958| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.41 r_work: 0.3085 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4746 Z= 0.107 Angle : 0.513 6.692 6455 Z= 0.256 Chirality : 0.038 0.139 762 Planarity : 0.003 0.042 794 Dihedral : 3.951 18.010 652 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.42 % Allowed : 13.41 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.20 (0.34), residues: 606 helix: 2.30 (0.29), residues: 293 sheet: 1.79 (0.52), residues: 96 loop : 0.16 (0.43), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.011 0.001 TYR C 49 PHE 0.006 0.001 PHE A 72 TRP 0.029 0.002 TRP C 35 HIS 0.002 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 4744) covalent geometry : angle 0.51291 / 0.26 ( 6451) SS BOND : bond 0.00116 / 0.06 ( 2) SS BOND : angle 0.77585 / 0.39 ( 4) hydrogen bonds : bond 0.03262 / 2.40 ( 290) hydrogen bonds : angle 4.51294 / 3.37 ( 846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.104 Fit side-chains REVERT: A 1 MET cc_start: 0.0970 (mmt) cc_final: -0.0028 (ptt) REVERT: A 19 ILE cc_start: 0.8938 (mm) cc_final: 0.8640 (mt) REVERT: A 28 MET cc_start: 0.7235 (mmp) cc_final: 0.6851 (mtp) REVERT: A 44 THR cc_start: 0.8950 (m) cc_final: 0.8519 (p) REVERT: A 82 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8023 (mm-30) REVERT: A 105 MET cc_start: 0.8852 (ttp) cc_final: 0.8494 (ttp) REVERT: A 119 ASP cc_start: 0.7683 (t0) cc_final: 0.7422 (t0) REVERT: A 313 ARG cc_start: 0.8073 (mmm160) cc_final: 0.7613 (ttp-170) outliers start: 7 outliers final: 6 residues processed: 84 average time/residue: 0.0489 time to fit residues: 5.5999 Evaluate side-chains 83 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 51 optimal weight: 0.0070 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 58 ASN C 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.183077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.117033 restraints weight = 5743.801| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.42 r_work: 0.2971 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4746 Z= 0.121 Angle : 0.522 6.319 6455 Z= 0.260 Chirality : 0.038 0.132 762 Planarity : 0.003 0.040 794 Dihedral : 3.963 18.715 652 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.83 % Allowed : 13.01 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.20 (0.34), residues: 606 helix: 2.32 (0.29), residues: 292 sheet: 1.79 (0.51), residues: 96 loop : 0.15 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.011 0.001 TYR C 49 PHE 0.008 0.001 PHE A 72 TRP 0.032 0.002 TRP C 35 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 4744) covalent geometry : angle 0.52185 / 0.26 ( 6451) SS BOND : bond 0.00140 / 0.07 ( 2) SS BOND : angle 0.49799 / 0.25 ( 4) hydrogen bonds : bond 0.03332 / 2.44 ( 290) hydrogen bonds : angle 4.50109 / 3.36 ( 846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.162 Fit side-chains REVERT: A 1 MET cc_start: 0.1142 (mmt) cc_final: 0.0075 (ptt) REVERT: A 19 ILE cc_start: 0.8860 (mm) cc_final: 0.8548 (mt) REVERT: A 28 MET cc_start: 0.7225 (mmp) cc_final: 0.6809 (mtp) REVERT: A 44 THR cc_start: 0.8902 (m) cc_final: 0.8420 (p) REVERT: A 105 MET cc_start: 0.8842 (ttp) cc_final: 0.8487 (ttp) REVERT: A 119 ASP cc_start: 0.7648 (t0) cc_final: 0.7308 (t0) REVERT: A 313 ARG cc_start: 0.8041 (mmm160) cc_final: 0.7580 (ttp-170) outliers start: 9 outliers final: 8 residues processed: 82 average time/residue: 0.0481 time to fit residues: 5.2816 Evaluate side-chains 83 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 0.0870 chunk 57 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.183875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.123889 restraints weight = 5725.366| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.72 r_work: 0.3061 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4746 Z= 0.113 Angle : 0.514 6.532 6455 Z= 0.256 Chirality : 0.038 0.136 762 Planarity : 0.003 0.038 794 Dihedral : 3.891 17.178 652 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.44 % Allowed : 13.21 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.23 (0.34), residues: 606 helix: 2.33 (0.29), residues: 293 sheet: 1.84 (0.52), residues: 96 loop : 0.15 (0.43), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.011 0.001 TYR C 49 PHE 0.007 0.001 PHE A 72 TRP 0.039 0.002 TRP C 35 HIS 0.002 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 4744) covalent geometry : angle 0.51391 / 0.26 ( 6451) SS BOND : bond 0.00098 / 0.05 ( 2) SS BOND : angle 0.44982 / 0.23 ( 4) hydrogen bonds : bond 0.03211 / 2.37 ( 290) hydrogen bonds : angle 4.44597 / 3.32 ( 846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.172 Fit side-chains REVERT: A 1 MET cc_start: 0.1136 (mmt) cc_final: -0.0113 (ptt) REVERT: A 4 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6486 (tt) REVERT: A 19 ILE cc_start: 0.8934 (mm) cc_final: 0.8634 (mt) REVERT: A 28 MET cc_start: 0.7297 (mmp) cc_final: 0.6931 (mtp) REVERT: A 44 THR cc_start: 0.8917 (m) cc_final: 0.8453 (p) REVERT: A 105 MET cc_start: 0.8873 (ttp) cc_final: 0.8512 (ttp) REVERT: A 119 ASP cc_start: 0.7513 (t0) cc_final: 0.7154 (t0) REVERT: A 313 ARG cc_start: 0.8062 (mmm160) cc_final: 0.7606 (ttp-170) outliers start: 12 outliers final: 9 residues processed: 84 average time/residue: 0.0471 time to fit residues: 5.4084 Evaluate side-chains 84 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 9 optimal weight: 0.0770 chunk 41 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.184080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.118238 restraints weight = 5837.110| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.44 r_work: 0.3098 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4746 Z= 0.103 Angle : 0.517 6.882 6455 Z= 0.256 Chirality : 0.037 0.132 762 Planarity : 0.003 0.037 794 Dihedral : 3.834 16.887 652 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.03 % Allowed : 13.62 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.26 (0.34), residues: 606 helix: 2.39 (0.29), residues: 293 sheet: 1.80 (0.51), residues: 96 loop : 0.13 (0.43), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.009 0.001 TYR C 49 PHE 0.006 0.001 PHE A 72 TRP 0.043 0.002 TRP C 35 HIS 0.002 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 ( 4744) covalent geometry : angle 0.51688 / 0.26 ( 6451) SS BOND : bond 0.00159 / 0.08 ( 2) SS BOND : angle 0.18010 / 0.10 ( 4) hydrogen bonds : bond 0.03119 / 2.30 ( 290) hydrogen bonds : angle 4.41246 / 3.30 ( 846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.104 Fit side-chains REVERT: A 1 MET cc_start: 0.1285 (mmt) cc_final: 0.0001 (ptt) REVERT: A 4 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6538 (tt) REVERT: A 19 ILE cc_start: 0.8987 (mm) cc_final: 0.8696 (mt) REVERT: A 28 MET cc_start: 0.7352 (mmp) cc_final: 0.7007 (mtp) REVERT: A 44 THR cc_start: 0.8959 (m) cc_final: 0.8517 (p) REVERT: A 105 MET cc_start: 0.8875 (ttp) cc_final: 0.8512 (ttp) REVERT: A 119 ASP cc_start: 0.7476 (t0) cc_final: 0.7124 (t0) REVERT: A 313 ARG cc_start: 0.8040 (mmm160) cc_final: 0.7585 (ttp-170) REVERT: B 106 ASP cc_start: 0.6606 (t0) cc_final: 0.6374 (m-30) REVERT: C 47 LEU cc_start: 0.7730 (mp) cc_final: 0.7509 (mt) outliers start: 10 outliers final: 9 residues processed: 81 average time/residue: 0.0444 time to fit residues: 4.9283 Evaluate side-chains 84 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 0.0670 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 28 optimal weight: 0.0980 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.185232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.119699 restraints weight = 5736.461| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.43 r_work: 0.3092 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4746 Z= 0.094 Angle : 0.504 7.578 6455 Z= 0.248 Chirality : 0.037 0.130 762 Planarity : 0.003 0.037 794 Dihedral : 3.745 16.556 652 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.03 % Allowed : 14.23 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.31 (0.34), residues: 606 helix: 2.44 (0.29), residues: 294 sheet: 1.81 (0.51), residues: 96 loop : 0.15 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.009 0.001 TYR C 49 PHE 0.004 0.001 PHE C 98 TRP 0.053 0.002 TRP C 35 HIS 0.002 0.000 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.09 ( 4744) covalent geometry : angle 0.50368 / 0.25 ( 6451) SS BOND : bond 0.00212 / 0.10 ( 2) SS BOND : angle 0.17544 / 0.10 ( 4) hydrogen bonds : bond 0.02988 / 2.21 ( 290) hydrogen bonds : angle 4.36618 / 3.26 ( 846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.142 Fit side-chains REVERT: A 1 MET cc_start: 0.1163 (mmt) cc_final: -0.0027 (ptt) REVERT: A 4 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6502 (tt) REVERT: A 19 ILE cc_start: 0.8933 (mm) cc_final: 0.8634 (mt) REVERT: A 26 MET cc_start: 0.8937 (tpp) cc_final: 0.8679 (mmm) REVERT: A 28 MET cc_start: 0.7259 (mmp) cc_final: 0.6936 (mtp) REVERT: A 44 THR cc_start: 0.8957 (m) cc_final: 0.8517 (p) REVERT: A 105 MET cc_start: 0.8822 (ttp) cc_final: 0.8421 (ttp) REVERT: A 119 ASP cc_start: 0.7413 (t0) cc_final: 0.7050 (t0) REVERT: A 313 ARG cc_start: 0.8001 (mmm160) cc_final: 0.7545 (ttp-170) REVERT: B 106 ASP cc_start: 0.6533 (t0) cc_final: 0.6312 (m-30) REVERT: C 47 LEU cc_start: 0.7681 (mp) cc_final: 0.7348 (mt) outliers start: 10 outliers final: 9 residues processed: 84 average time/residue: 0.0440 time to fit residues: 4.9687 Evaluate side-chains 83 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 33 optimal weight: 0.0870 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.184289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.118311 restraints weight = 5761.339| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.44 r_work: 0.3077 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4746 Z= 0.103 Angle : 0.511 7.213 6455 Z= 0.252 Chirality : 0.037 0.133 762 Planarity : 0.003 0.036 794 Dihedral : 3.753 16.382 652 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.24 % Allowed : 14.02 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.33 (0.34), residues: 606 helix: 2.45 (0.29), residues: 293 sheet: 1.84 (0.51), residues: 96 loop : 0.18 (0.43), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.009 0.001 TYR C 49 PHE 0.007 0.001 PHE C 62 TRP 0.069 0.002 TRP C 35 HIS 0.002 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 ( 4744) covalent geometry : angle 0.51097 / 0.25 ( 6451) SS BOND : bond 0.00246 / 0.12 ( 2) SS BOND : angle 0.17369 / 0.10 ( 4) hydrogen bonds : bond 0.03064 / 2.26 ( 290) hydrogen bonds : angle 4.39006 / 3.28 ( 846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.121 Fit side-chains REVERT: A 1 MET cc_start: 0.1151 (mmt) cc_final: -0.0014 (ptt) REVERT: A 4 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6542 (tt) REVERT: A 19 ILE cc_start: 0.8921 (mm) cc_final: 0.8619 (mt) REVERT: A 26 MET cc_start: 0.8931 (tpp) cc_final: 0.8676 (mmm) REVERT: A 28 MET cc_start: 0.7309 (mmp) cc_final: 0.6960 (mtp) REVERT: A 44 THR cc_start: 0.8965 (m) cc_final: 0.8534 (p) REVERT: A 105 MET cc_start: 0.8822 (ttp) cc_final: 0.8446 (ttp) REVERT: A 119 ASP cc_start: 0.7430 (t0) cc_final: 0.7089 (t0) REVERT: A 313 ARG cc_start: 0.8003 (mmm160) cc_final: 0.7541 (ttp-170) outliers start: 11 outliers final: 10 residues processed: 81 average time/residue: 0.0467 time to fit residues: 5.0735 Evaluate side-chains 84 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 41 optimal weight: 7.9990 chunk 12 optimal weight: 0.0010 chunk 36 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 9 optimal weight: 0.0000 chunk 20 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 51 optimal weight: 20.0000 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.185450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.119897 restraints weight = 5809.397| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.43 r_work: 0.3112 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4746 Z= 0.090 Angle : 0.497 7.473 6455 Z= 0.246 Chirality : 0.037 0.130 762 Planarity : 0.003 0.036 794 Dihedral : 3.711 16.051 652 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.24 % Allowed : 14.23 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.37 (0.34), residues: 606 helix: 2.48 (0.29), residues: 294 sheet: 1.85 (0.51), residues: 96 loop : 0.19 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.008 0.001 TYR C 49 PHE 0.005 0.001 PHE C 62 TRP 0.059 0.002 TRP C 35 HIS 0.002 0.000 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 ( 4744) covalent geometry : angle 0.49725 / 0.25 ( 6451) SS BOND : bond 0.00265 / 0.13 ( 2) SS BOND : angle 0.26875 / 0.14 ( 4) hydrogen bonds : bond 0.02912 / 2.17 ( 290) hydrogen bonds : angle 4.33943 / 3.24 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1389.06 seconds wall clock time: 24 minutes 19.96 seconds (1459.96 seconds total)