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/9rhb_53964/08_2026/9rhb_53964.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rhb_53964/08_2026/9rhb_53964.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/9rhb_53964/08_2026/9rhb_53964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rhb_53964/08_2026/9rhb_53964.map" model { file = "/net/cci-nas-00/data/ceres_data/9rhb_53964/08_2026/9rhb_53964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rhb_53964/08_2026/9rhb_53964.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= 0.000 sd= 0.003 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 839 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s 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: 4641 Number of models: 1 Model: "" Number of chains: 4 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} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 0.78, per 1000 atoms: 0.17 Number of scatterers: 4641 At special positions: 0 Unit cell: (67.797, 80.352, 98.766, 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 839 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: 0.21 Conformation dependent library (CDL) restraints added in 98.3 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: 24 helices and 8 sheets defined 53.3% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 removed outlier: 3.757A pdb=" N SER A 10 " --> pdb=" O ARG A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 31 removed outlier: 4.503A pdb=" N GLY A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 59 through 66 Processing helix chain 'A' and resid 67 through 85 removed outlier: 3.964A pdb=" N PHE A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 89 removed outlier: 3.539A 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: 5.196A 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: 3.673A pdb=" N PHE A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 removed outlier: 4.489A pdb=" N GLU A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 145 removed outlier: 3.766A pdb=" N LEU A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 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 222 removed outlier: 3.714A pdb=" N TYR A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.806A 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 removed outlier: 3.583A pdb=" N ILE A 333 " --> pdb=" O MET A 329 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 351 Processing helix chain 'A' and resid 354 through 382 removed outlier: 3.931A pdb=" N ILE A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.699A pdb=" N ASP B 31 " --> pdb=" O THR B 28 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' 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: 3.564A pdb=" N LYS B 3 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.430A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.803A pdb=" N CYS B 96 " --> pdb=" O TRP B 108 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TRP B 108 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 6.893A 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 5 Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.468A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.614A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) 292 hydrogen bonds defined for protein. 813 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: 0.29 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: 1441 1.34 - 1.46: 1013 1.46 - 1.58: 2257 1.58 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 4744 Sorted by residual: bond pdb=" N GLN B 39 " pdb=" CA GLN B 39 " ideal model delta sigma weight residual 1.455 1.478 -0.023 1.25e-02 6.40e+03 3.43e+00 bond pdb=" CA TYR C 32 " pdb=" CB TYR C 32 " ideal model delta sigma weight residual 1.524 1.541 -0.018 1.33e-02 5.65e+03 1.79e+00 bond pdb=" N ILE A 337 " pdb=" CA ILE A 337 " ideal model delta sigma weight residual 1.474 1.457 0.018 1.57e-02 4.06e+03 1.27e+00 bond pdb=" C THR C 7 " pdb=" N PRO C 8 " ideal model delta sigma weight residual 1.334 1.357 -0.024 2.34e-02 1.83e+03 1.01e+00 bond pdb=" CG LEU C 54 " pdb=" CD1 LEU C 54 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.36e-01 ... (remaining 4739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 6087 1.39 - 2.78: 292 2.78 - 4.17: 48 4.17 - 5.55: 20 5.55 - 6.94: 4 Bond angle restraints: 6451 Sorted by residual: angle pdb=" N LEU B 45 " pdb=" CA LEU B 45 " pdb=" C LEU B 45 " ideal model delta sigma weight residual 109.46 114.22 -4.76 1.66e+00 3.63e-01 8.22e+00 angle pdb=" C ASP A 163 " pdb=" CA ASP A 163 " pdb=" CB ASP A 163 " ideal model delta sigma weight residual 110.01 105.07 4.94 1.80e+00 3.09e-01 7.54e+00 angle pdb=" N GLY B 44 " pdb=" CA GLY B 44 " pdb=" C GLY B 44 " ideal model delta sigma weight residual 111.47 115.99 -4.52 1.72e+00 3.38e-01 6.91e+00 angle pdb=" C LEU B 4 " pdb=" N HIS B 5 " pdb=" CA HIS B 5 " ideal model delta sigma weight residual 120.94 124.89 -3.95 1.57e+00 4.06e-01 6.33e+00 angle pdb=" CA THR C 7 " pdb=" C THR C 7 " pdb=" N PRO C 8 " ideal model delta sigma weight residual 118.44 122.44 -4.00 1.59e+00 3.96e-01 6.32e+00 ... (remaining 6446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 2533 17.64 - 35.28: 192 35.28 - 52.92: 41 52.92 - 70.56: 6 70.56 - 88.20: 6 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 50.13 42.87 1 1.00e+01 1.00e-02 2.56e+01 dihedral pdb=" CA ASP A 163 " pdb=" C ASP A 163 " pdb=" N ASP A 164 " pdb=" CA ASP A 164 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA GLU B 99 " pdb=" C GLU B 99 " pdb=" N GLU B 100 " pdb=" CA GLU B 100 " ideal model delta harmonic sigma weight residual 180.00 160.92 19.08 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 2775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 446 0.031 - 0.062: 197 0.062 - 0.092: 79 0.092 - 0.123: 31 0.123 - 0.154: 9 Chirality restraints: 762 Sorted by residual: chirality pdb=" CA THR C 7 " pdb=" N THR C 7 " pdb=" C THR C 7 " pdb=" CB THR C 7 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA VAL A 353 " pdb=" N VAL A 353 " pdb=" C VAL A 353 " pdb=" CB VAL A 353 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA MET A 341 " pdb=" N MET A 341 " pdb=" C MET A 341 " pdb=" CB MET A 341 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 759 not shown) Planarity restraints: 794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 29 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" C ILE C 29 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE C 29 " -0.013 2.00e-02 2.50e+03 pdb=" N SER C 30 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 71 " -0.011 2.00e-02 2.50e+03 9.95e-03 1.98e+00 pdb=" CG TYR C 71 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR C 71 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR C 71 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 71 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 71 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 71 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 71 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 124 " 0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" CD GLU A 124 " -0.020 2.00e-02 2.50e+03 pdb=" OE1 GLU A 124 " 0.007 2.00e-02 2.50e+03 pdb=" OE2 GLU A 124 " 0.007 2.00e-02 2.50e+03 ... (remaining 791 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 906 2.77 - 3.31: 4502 3.31 - 3.84: 7699 3.84 - 4.37: 9109 4.37 - 4.90: 15931 Nonbonded interactions: 38147 Sorted by model distance: nonbonded pdb=" O PRO C 8 " pdb=" OG1 THR C 102 " model vdw 2.242 3.040 nonbonded pdb=" NZ LYS C 39 " pdb=" OE2 GLU C 81 " model vdw 2.261 3.120 nonbonded pdb=" NE2 GLN A 327 " pdb=" OH TYR C 32 " model vdw 2.295 3.120 nonbonded pdb=" O HIS B 35 " pdb=" OG1 THR B 97 " model vdw 2.310 3.040 nonbonded pdb=" O ALA A 172 " pdb=" OG1 THR A 176 " model vdw 2.332 3.040 ... (remaining 38142 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.290 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:5.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 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 0.036 4746 Z= 0.166 Angle : 0.742 6.942 6455 Z= 0.421 Chirality : 0.044 0.154 762 Planarity : 0.003 0.024 794 Dihedral : 13.688 88.203 1660 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.20 % Allowed : 11.59 % Favored : 88.21 % 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: 0.49 (0.34), residues: 606 helix: 0.90 (0.31), residues: 289 sheet: 0.32 (0.48), residues: 120 loop : -0.35 (0.45), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 92 TYR 0.024 0.002 TYR C 71 PHE 0.014 0.002 PHE C 83 TRP 0.011 0.001 TRP C 35 HIS 0.006 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 4744) covalent geometry : angle 0.74122 / 0.42 ( 6451) SS BOND : bond 0.00259 / 0.13 ( 2) SS BOND : angle 1.29565 / 0.63 ( 4) hydrogen bonds : bond 0.20460 / 13.52 ( 277) hydrogen bonds : angle 8.17248 / 6.14 ( 813) *********************** 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 57 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.130 Fit side-chains REVERT: A 82 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7743 (mm-30) REVERT: A 84 MET cc_start: 0.7960 (mtt) cc_final: 0.7682 (mmt) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.4140 time to fit residues: 24.6648 Evaluate side-chains 52 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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: 9.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.187149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.107833 restraints weight = 5181.459| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.19 r_work: 0.2851 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1298 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= 0.124 Angle : 0.574 6.083 6455 Z= 0.298 Chirality : 0.041 0.162 762 Planarity : 0.004 0.030 794 Dihedral : 4.565 20.304 652 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.02 % Allowed : 10.98 % Favored : 88.01 % 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: 0.83 (0.34), residues: 606 helix: 1.19 (0.30), residues: 299 sheet: 0.45 (0.47), residues: 117 loop : -0.24 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 381 TYR 0.013 0.001 TYR C 49 PHE 0.011 0.001 PHE A 96 TRP 0.006 0.001 TRP A 37 HIS 0.005 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 4744) covalent geometry : angle 0.57357 / 0.30 ( 6451) SS BOND : bond 0.00325 / 0.16 ( 2) SS BOND : angle 0.49046 / 0.26 ( 4) hydrogen bonds : bond 0.03892 / 2.71 ( 277) hydrogen bonds : angle 5.37854 / 4.03 ( 813) *********************** 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 61 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.217 Fit side-chains REVERT: A 91 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7867 (mp) REVERT: A 119 ASP cc_start: 0.7585 (t0) cc_final: 0.7115 (t0) REVERT: A 241 GLU cc_start: 0.7491 (mp0) cc_final: 0.7245 (mp0) REVERT: A 381 ARG cc_start: 0.7547 (mtt-85) cc_final: 0.7079 (mtp180) REVERT: B 81 MET cc_start: 0.3805 (ttp) cc_final: 0.3456 (ttp) outliers start: 5 outliers final: 0 residues processed: 59 average time/residue: 0.5596 time to fit residues: 34.1932 Evaluate side-chains 53 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 57 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 45 optimal weight: 20.0000 chunk 6 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 24 optimal weight: 0.2980 chunk 47 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.187154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.108768 restraints weight = 5073.122| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.17 r_work: 0.2869 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1729 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= 0.106 Angle : 0.522 5.912 6455 Z= 0.268 Chirality : 0.040 0.157 762 Planarity : 0.004 0.040 794 Dihedral : 4.299 19.433 652 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.22 % Allowed : 10.77 % Favored : 88.01 % 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: 0.96 (0.34), residues: 606 helix: 1.31 (0.30), residues: 300 sheet: 0.60 (0.46), residues: 117 loop : -0.28 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 381 TYR 0.011 0.001 TYR A 175 PHE 0.009 0.001 PHE A 96 TRP 0.007 0.001 TRP B 47 HIS 0.004 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 4744) covalent geometry : angle 0.52248 / 0.27 ( 6451) SS BOND : bond 0.00328 / 0.16 ( 2) SS BOND : angle 0.47275 / 0.17 ( 4) hydrogen bonds : bond 0.03425 / 2.37 ( 277) hydrogen bonds : angle 4.96812 / 3.72 ( 813) *********************** 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 64 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.179 Fit side-chains REVERT: A 91 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7925 (mp) REVERT: A 119 ASP cc_start: 0.7633 (t0) cc_final: 0.7117 (t0) REVERT: A 150 LEU cc_start: 0.7859 (mp) cc_final: 0.7654 (mt) REVERT: A 381 ARG cc_start: 0.7579 (mtt-85) cc_final: 0.7164 (mtp180) outliers start: 6 outliers final: 3 residues processed: 62 average time/residue: 0.5484 time to fit residues: 35.4322 Evaluate side-chains 56 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 183 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 5 optimal weight: 1.9990 chunk 55 optimal weight: 30.0000 chunk 51 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 30.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.185088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.104311 restraints weight = 5150.826| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.27 r_work: 0.2797 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4746 Z= 0.163 Angle : 0.579 6.732 6455 Z= 0.292 Chirality : 0.042 0.158 762 Planarity : 0.004 0.046 794 Dihedral : 4.504 20.471 652 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.03 % Allowed : 11.59 % 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: 0.76 (0.34), residues: 606 helix: 1.07 (0.30), residues: 299 sheet: 0.54 (0.46), residues: 117 loop : -0.25 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 381 TYR 0.022 0.002 TYR A 175 PHE 0.010 0.002 PHE A 96 TRP 0.008 0.001 TRP B 47 HIS 0.007 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 ( 4744) covalent geometry : angle 0.57918 / 0.29 ( 6451) SS BOND : bond 0.00311 / 0.15 ( 2) SS BOND : angle 0.52910 / 0.21 ( 4) hydrogen bonds : bond 0.03810 / 2.62 ( 277) hydrogen bonds : angle 5.06591 / 3.78 ( 813) *********************** 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 67 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.169 Fit side-chains REVERT: A 91 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7796 (mp) REVERT: A 119 ASP cc_start: 0.7591 (t0) cc_final: 0.7177 (t0) REVERT: A 381 ARG cc_start: 0.7631 (mtt-85) cc_final: 0.7174 (mtp180) outliers start: 10 outliers final: 4 residues processed: 62 average time/residue: 0.5380 time to fit residues: 34.7463 Evaluate side-chains 59 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain C residue 7 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.4980 chunk 51 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 38 optimal weight: 30.0000 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.186861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.106033 restraints weight = 5112.255| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.23 r_work: 0.2822 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4746 Z= 0.129 Angle : 0.528 5.647 6455 Z= 0.267 Chirality : 0.041 0.163 762 Planarity : 0.004 0.047 794 Dihedral : 4.352 19.591 652 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.63 % Allowed : 13.01 % Favored : 85.37 % 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: 0.90 (0.34), residues: 606 helix: 1.24 (0.30), residues: 295 sheet: 0.60 (0.46), residues: 117 loop : -0.26 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 381 TYR 0.013 0.001 TYR A 175 PHE 0.008 0.001 PHE A 339 TRP 0.007 0.001 TRP B 47 HIS 0.005 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 4744) covalent geometry : angle 0.52765 / 0.27 ( 6451) SS BOND : bond 0.00311 / 0.15 ( 2) SS BOND : angle 0.51503 / 0.19 ( 4) hydrogen bonds : bond 0.03396 / 2.34 ( 277) hydrogen bonds : angle 4.87911 / 3.64 ( 813) *********************** 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 66 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.158 Fit side-chains REVERT: A 91 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7858 (mp) REVERT: A 119 ASP cc_start: 0.7606 (t0) cc_final: 0.7168 (t0) REVERT: A 163 ASP cc_start: 0.8129 (p0) cc_final: 0.7911 (p0) REVERT: A 381 ARG cc_start: 0.7732 (mtt-85) cc_final: 0.7329 (mtp180) outliers start: 8 outliers final: 3 residues processed: 61 average time/residue: 0.5725 time to fit residues: 36.2691 Evaluate side-chains 63 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 183 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 57 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 23 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.185566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.104841 restraints weight = 5187.739| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.26 r_work: 0.2803 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4746 Z= 0.156 Angle : 0.549 6.379 6455 Z= 0.277 Chirality : 0.041 0.137 762 Planarity : 0.004 0.043 794 Dihedral : 4.438 20.049 652 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: 0.81 (0.33), residues: 606 helix: 1.14 (0.30), residues: 295 sheet: 0.60 (0.46), residues: 117 loop : -0.30 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 381 TYR 0.017 0.001 TYR A 175 PHE 0.010 0.001 PHE A 339 TRP 0.007 0.001 TRP B 47 HIS 0.006 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 4744) covalent geometry : angle 0.54905 / 0.28 ( 6451) SS BOND : bond 0.00284 / 0.14 ( 2) SS BOND : angle 0.50429 / 0.20 ( 4) hydrogen bonds : bond 0.03633 / 2.49 ( 277) hydrogen bonds : angle 4.94421 / 3.69 ( 813) *********************** 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 69 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.201 Fit side-chains REVERT: A 91 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7741 (mp) REVERT: A 163 ASP cc_start: 0.8079 (p0) cc_final: 0.7829 (p0) REVERT: A 381 ARG cc_start: 0.7715 (mtt-85) cc_final: 0.7273 (mtp180) REVERT: B 58 THR cc_start: 0.8214 (p) cc_final: 0.7860 (m) outliers start: 10 outliers final: 5 residues processed: 63 average time/residue: 0.5803 time to fit residues: 38.0769 Evaluate side-chains 62 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 184 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 57 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 14 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 55 optimal weight: 50.0000 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.185805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.105212 restraints weight = 5115.063| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.22 r_work: 0.2811 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4746 Z= 0.156 Angle : 0.549 6.291 6455 Z= 0.277 Chirality : 0.041 0.138 762 Planarity : 0.004 0.040 794 Dihedral : 4.448 19.482 652 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: 0.78 (0.33), residues: 606 helix: 1.13 (0.30), residues: 295 sheet: 0.69 (0.46), residues: 115 loop : -0.38 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 381 TYR 0.015 0.001 TYR A 175 PHE 0.009 0.001 PHE A 339 TRP 0.008 0.001 TRP C 35 HIS 0.006 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 4744) covalent geometry : angle 0.54895 / 0.28 ( 6451) SS BOND : bond 0.00271 / 0.13 ( 2) SS BOND : angle 0.44323 / 0.16 ( 4) hydrogen bonds : bond 0.03612 / 2.49 ( 277) hydrogen bonds : angle 4.92024 / 3.67 ( 813) *********************** 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 72 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.201 Fit side-chains REVERT: A 91 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7745 (mp) REVERT: A 163 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7693 (p0) REVERT: A 240 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8414 (ptmm) REVERT: A 381 ARG cc_start: 0.7730 (mtt-85) cc_final: 0.7306 (mtp180) REVERT: B 58 THR cc_start: 0.8211 (p) cc_final: 0.7939 (m) outliers start: 11 outliers final: 3 residues processed: 64 average time/residue: 0.5460 time to fit residues: 36.4220 Evaluate side-chains 66 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 240 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 9 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 chunk 21 optimal weight: 0.6980 chunk 49 optimal weight: 0.0980 chunk 38 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.189375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.107854 restraints weight = 5181.697| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.29 r_work: 0.2946 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4746 Z= 0.101 Angle : 0.497 6.581 6455 Z= 0.251 Chirality : 0.039 0.134 762 Planarity : 0.003 0.039 794 Dihedral : 4.203 18.953 652 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.63 % Allowed : 15.45 % Favored : 82.93 % 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: 1.00 (0.34), residues: 606 helix: 1.42 (0.30), residues: 294 sheet: 0.81 (0.47), residues: 115 loop : -0.50 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 381 TYR 0.011 0.001 TYR C 49 PHE 0.007 0.001 PHE A 72 TRP 0.012 0.001 TRP B 36 HIS 0.004 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 4744) covalent geometry : angle 0.49747 / 0.25 ( 6451) SS BOND : bond 0.00262 / 0.12 ( 2) SS BOND : angle 0.51915 / 0.23 ( 4) hydrogen bonds : bond 0.03090 / 2.15 ( 277) hydrogen bonds : angle 4.69371 / 3.50 ( 813) *********************** 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 66 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.170 Fit side-chains REVERT: A 91 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7924 (mp) REVERT: A 163 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7814 (p0) REVERT: A 381 ARG cc_start: 0.7813 (mtt-85) cc_final: 0.7455 (mtp180) REVERT: B 58 THR cc_start: 0.8206 (p) cc_final: 0.7972 (m) outliers start: 8 outliers final: 4 residues processed: 61 average time/residue: 0.5792 time to fit residues: 36.7083 Evaluate side-chains 64 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 382 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.188359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.107778 restraints weight = 5117.522| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.23 r_work: 0.2845 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4746 Z= 0.116 Angle : 0.513 7.008 6455 Z= 0.258 Chirality : 0.040 0.135 762 Planarity : 0.003 0.037 794 Dihedral : 4.218 18.596 652 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.63 % Allowed : 15.24 % Favored : 83.13 % 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: 0.99 (0.34), residues: 606 helix: 1.40 (0.30), residues: 295 sheet: 0.83 (0.48), residues: 114 loop : -0.51 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 381 TYR 0.011 0.001 TYR A 175 PHE 0.007 0.001 PHE A 339 TRP 0.011 0.001 TRP C 35 HIS 0.005 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 4744) covalent geometry : angle 0.51299 / 0.26 ( 6451) SS BOND : bond 0.00274 / 0.13 ( 2) SS BOND : angle 0.54620 / 0.24 ( 4) hydrogen bonds : bond 0.03226 / 2.24 ( 277) hydrogen bonds : angle 4.69366 / 3.51 ( 813) *********************** 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 71 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.176 Fit side-chains REVERT: A 91 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7835 (mp) REVERT: A 163 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7710 (p0) REVERT: A 381 ARG cc_start: 0.7741 (mtt-85) cc_final: 0.7363 (mtp180) REVERT: B 58 THR cc_start: 0.8168 (p) cc_final: 0.7935 (m) outliers start: 8 outliers final: 4 residues processed: 66 average time/residue: 0.5386 time to fit residues: 37.0829 Evaluate side-chains 66 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 382 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 17 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 44 optimal weight: 30.0000 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.188920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.109167 restraints weight = 5113.066| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.22 r_work: 0.2865 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4746 Z= 0.102 Angle : 0.495 7.025 6455 Z= 0.249 Chirality : 0.039 0.134 762 Planarity : 0.003 0.037 794 Dihedral : 4.127 17.897 652 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.42 % Allowed : 15.65 % Favored : 82.93 % 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: 1.08 (0.34), residues: 606 helix: 1.54 (0.30), residues: 292 sheet: 0.98 (0.51), residues: 103 loop : -0.55 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 381 TYR 0.011 0.001 TYR C 49 PHE 0.007 0.001 PHE A 96 TRP 0.011 0.001 TRP C 35 HIS 0.004 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 4744) covalent geometry : angle 0.49530 / 0.25 ( 6451) SS BOND : bond 0.00257 / 0.12 ( 2) SS BOND : angle 0.57220 / 0.27 ( 4) hydrogen bonds : bond 0.03051 / 2.12 ( 277) hydrogen bonds : angle 4.58352 / 3.43 ( 813) ********************** 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 67 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.174 Fit side-chains REVERT: A 91 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7881 (mp) REVERT: A 119 ASP cc_start: 0.7436 (t0) cc_final: 0.6964 (t0) REVERT: A 163 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7662 (p0) REVERT: A 381 ARG cc_start: 0.7715 (mtt-85) cc_final: 0.7347 (mtp180) REVERT: B 58 THR cc_start: 0.8178 (p) cc_final: 0.7970 (m) outliers start: 7 outliers final: 3 residues processed: 63 average time/residue: 0.5668 time to fit residues: 37.1913 Evaluate side-chains 63 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 382 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 28 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 58 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.189346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.109823 restraints weight = 5139.695| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.24 r_work: 0.2872 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4746 Z= 0.100 Angle : 0.487 7.017 6455 Z= 0.245 Chirality : 0.039 0.134 762 Planarity : 0.003 0.037 794 Dihedral : 4.072 17.659 652 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.83 % Allowed : 15.24 % Favored : 82.93 % 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: 1.14 (0.34), residues: 606 helix: 1.59 (0.30), residues: 292 sheet: 1.03 (0.51), residues: 103 loop : -0.52 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 381 TYR 0.011 0.001 TYR C 49 PHE 0.006 0.001 PHE A 96 TRP 0.015 0.001 TRP C 35 HIS 0.004 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 4744) covalent geometry : angle 0.48741 / 0.25 ( 6451) SS BOND : bond 0.00261 / 0.12 ( 2) SS BOND : angle 0.55358 / 0.26 ( 4) hydrogen bonds : bond 0.02994 / 2.08 ( 277) hydrogen bonds : angle 4.53424 / 3.40 ( 813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2055.45 seconds wall clock time: 35 minutes 47.74 seconds (2147.74 seconds total)