Starting phenix.real_space_refine on Tue Aug 4 15:24:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gcm_51234/08_2026/9gcm_51234.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gcm_51234/08_2026/9gcm_51234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gcm_51234/08_2026/9gcm_51234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gcm_51234/08_2026/9gcm_51234.map" model { file = "/net/cci-nas-00/data/ceres_data/9gcm_51234/08_2026/9gcm_51234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gcm_51234/08_2026/9gcm_51234.cif" } resolution = 3.1 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= 0.006 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: 5 Type Number sf(0) Gaussians P 66 5.49 5 S 11 5.16 5 C 2553 2.51 5 N 811 2.21 5 O 1025 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: 4466 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1413 Classifications: {'RNA': 66} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 30, 'rna3p_pyr': 23} Link IDs: {'rna2p': 13, 'rna3p': 52} Chain breaks: 1 Chain: "B" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1032 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "C" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1261 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain: "D" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 760 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Time building chain proxies: 1.05, per 1000 atoms: 0.24 Number of scatterers: 4466 At special positions: 0 Unit cell: (86.87, 89.06, 84.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 P 66 15.00 O 1025 8.00 N 811 7.00 C 2553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 103.5 milliseconds 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 700 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 4 sheets defined 53.1% alpha, 12.5% beta 25 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'B' and resid 2 through 13 removed outlier: 4.288A pdb=" N GLU B 6 " --> pdb=" O ASP B 2 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY B 7 " --> pdb=" O VAL B 3 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B 13 " --> pdb=" O ALA B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.847A pdb=" N CYS B 18 " --> pdb=" O PRO B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 37 removed outlier: 3.618A pdb=" N VAL B 29 " --> pdb=" O THR B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 82 removed outlier: 3.609A pdb=" N ARG B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 95 Processing helix chain 'C' and resid 12 through 17 removed outlier: 3.920A pdb=" N GLY C 17 " --> pdb=" O PRO C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 63 through 72 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 101 through 113 removed outlier: 4.063A pdb=" N VAL C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 151 removed outlier: 3.802A pdb=" N GLY C 151 " --> pdb=" O LYS C 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 148 through 151' Processing helix chain 'D' and resid 292 through 332 removed outlier: 3.730A pdb=" N VAL D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU D 304 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL D 316 " --> pdb=" O THR D 312 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP D 317 " --> pdb=" O LYS D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 removed outlier: 4.116A pdb=" N LYS D 336 " --> pdb=" O ALA D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 384 removed outlier: 3.744A pdb=" N ALA D 344 " --> pdb=" O PRO D 340 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS D 351 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 352 " --> pdb=" O PHE D 348 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN D 353 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG D 354 " --> pdb=" O HIS D 350 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU D 383 " --> pdb=" O GLY D 379 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 52 through 58 removed outlier: 3.600A pdb=" N ASP B 121 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N CYS B 46 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N PHE B 125 " --> pdb=" O CYS B 46 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 126 " --> pdb=" O HIS B 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 84 removed outlier: 5.272A pdb=" N ILE C 77 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLU C 98 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ARG C 79 " --> pdb=" O PHE C 96 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N PHE C 96 " --> pdb=" O ARG C 79 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ARG C 81 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N TYR C 94 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL C 83 " --> pdb=" O LYS C 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 116 through 117 Processing sheet with id=AA4, first strand: chain 'C' and resid 146 through 147 removed outlier: 4.078A pdb=" N LYS C 147 " --> pdb=" O GLN C 152 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN C 152 " --> pdb=" O LYS C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 142 hydrogen bonds defined for protein. 414 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 0.39 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1113 1.33 - 1.45: 1238 1.45 - 1.58: 2176 1.58 - 1.70: 131 1.70 - 1.82: 19 Bond restraints: 4677 Sorted by residual: bond pdb=" N9 G A 21 " pdb=" C4 G A 21 " ideal model delta sigma weight residual 1.375 1.389 -0.014 8.00e-03 1.56e+04 3.25e+00 bond pdb=" CB PRO C 26 " pdb=" CG PRO C 26 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.05e+00 bond pdb=" N9 A A 69 " pdb=" C4 A A 69 " ideal model delta sigma weight residual 1.374 1.365 0.009 6.00e-03 2.78e+04 2.22e+00 bond pdb=" N3 A A 69 " pdb=" C4 A A 69 " ideal model delta sigma weight residual 1.344 1.336 0.008 6.00e-03 2.78e+04 1.78e+00 bond pdb=" C6 G A 71 " pdb=" N1 G A 71 " ideal model delta sigma weight residual 1.391 1.382 0.009 7.00e-03 2.04e+04 1.78e+00 ... (remaining 4672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 6294 1.77 - 3.54: 287 3.54 - 5.32: 21 5.32 - 7.09: 9 7.09 - 8.86: 2 Bond angle restraints: 6613 Sorted by residual: angle pdb=" C5 G A 21 " pdb=" C4 G A 21 " pdb=" N3 G A 21 " ideal model delta sigma weight residual 128.60 126.31 2.29 5.00e-01 4.00e+00 2.10e+01 angle pdb=" C1' G A 21 " pdb=" N9 G A 21 " pdb=" C4 G A 21 " ideal model delta sigma weight residual 126.50 132.01 -5.51 1.30e+00 5.92e-01 1.80e+01 angle pdb=" N9 G A 21 " pdb=" C4 G A 21 " pdb=" N3 G A 21 " ideal model delta sigma weight residual 126.00 128.52 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" O5' U A 22 " pdb=" C5' U A 22 " pdb=" C4' U A 22 " ideal model delta sigma weight residual 109.40 112.61 -3.21 8.00e-01 1.56e+00 1.61e+01 angle pdb=" O4' C A 78 " pdb=" C1' C A 78 " pdb=" N1 C A 78 " ideal model delta sigma weight residual 108.20 111.21 -3.01 8.00e-01 1.56e+00 1.42e+01 ... (remaining 6608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.08: 2516 23.08 - 46.16: 301 46.16 - 69.23: 113 69.23 - 92.31: 19 92.31 - 115.39: 2 Dihedral angle restraints: 2951 sinusoidal: 1864 harmonic: 1087 Sorted by residual: dihedral pdb=" O4' U A 22 " pdb=" C1' U A 22 " pdb=" N1 U A 22 " pdb=" C2 U A 22 " ideal model delta sinusoidal sigma weight residual -128.00 -64.15 -63.85 1 1.70e+01 3.46e-03 1.86e+01 dihedral pdb=" O4' G A 55 " pdb=" C1' G A 55 " pdb=" N9 G A 55 " pdb=" C4 G A 55 " ideal model delta sinusoidal sigma weight residual -106.00 -159.65 53.65 1 1.70e+01 3.46e-03 1.35e+01 dihedral pdb=" O4' A A 20 " pdb=" C1' A A 20 " pdb=" N9 A A 20 " pdb=" C4 A A 20 " ideal model delta sinusoidal sigma weight residual -90.00 -29.93 -60.07 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 2948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 482 0.029 - 0.058: 150 0.058 - 0.086: 69 0.086 - 0.115: 24 0.115 - 0.144: 58 Chirality restraints: 783 Sorted by residual: chirality pdb=" C2' G A 21 " pdb=" C3' G A 21 " pdb=" O2' G A 21 " pdb=" C1' G A 21 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" C2' A A 66 " pdb=" C3' A A 66 " pdb=" O2' A A 66 " pdb=" C1' A A 66 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" C2' G A 23 " pdb=" C3' G A 23 " pdb=" O2' G A 23 " pdb=" C1' G A 23 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 780 not shown) Planarity restraints: 604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 25 " 0.058 5.00e-02 4.00e+02 8.61e-02 1.19e+01 pdb=" N PRO C 26 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 26 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 26 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C A 78 " -0.030 2.00e-02 2.50e+03 1.51e-02 5.13e+00 pdb=" N1 C A 78 " 0.031 2.00e-02 2.50e+03 pdb=" C2 C A 78 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C A 78 " 0.005 2.00e-02 2.50e+03 pdb=" N3 C A 78 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C A 78 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C A 78 " -0.008 2.00e-02 2.50e+03 pdb=" C5 C A 78 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C A 78 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 12 " 0.030 5.00e-02 4.00e+02 4.63e-02 3.42e+00 pdb=" N PRO C 13 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 13 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 13 " 0.026 5.00e-02 4.00e+02 ... (remaining 601 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 215 2.69 - 3.24: 4546 3.24 - 3.80: 7861 3.80 - 4.35: 10332 4.35 - 4.90: 14833 Nonbonded interactions: 37787 Sorted by model distance: nonbonded pdb=" O2' G A 63 " pdb=" OG SER C 150 " model vdw 2.142 3.040 nonbonded pdb=" O LYS D 308 " pdb=" OG1 THR D 312 " model vdw 2.232 3.040 nonbonded pdb=" N GLU C 102 " pdb=" OE1 GLU C 102 " model vdw 2.237 3.120 nonbonded pdb=" O2' C A 62 " pdb=" OE2 GLU C 149 " model vdw 2.255 3.040 nonbonded pdb=" O LYS C 68 " pdb=" OG SER C 72 " model vdw 2.260 3.040 ... (remaining 37782 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: 6.380 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.290 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 0.087 4677 Z= 0.243 Angle : 0.759 8.859 6613 Z= 0.526 Chirality : 0.049 0.144 783 Planarity : 0.006 0.086 604 Dihedral : 20.804 115.389 2251 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.23 % Favored : 96.23 % Rotamer: Outliers : 0.93 % Allowed : 25.08 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.45), residues: 371 helix: 0.74 (0.41), residues: 162 sheet: -1.76 (1.03), residues: 21 loop : -0.43 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 109 TYR 0.023 0.003 TYR C 39 PHE 0.010 0.002 PHE C 54 TRP 0.021 0.003 TRP C 32 HIS 0.006 0.002 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.24 ( 4677) covalent geometry : angle 0.75907 / 0.53 ( 6613) hydrogen bonds : bond 0.22820 / 25.20 ( 204) hydrogen bonds : angle 7.45579 / 8.55 ( 522) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 73 average time/residue: 0.1154 time to fit residues: 9.7213 Evaluate side-chains 73 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.106590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.082593 restraints weight = 13784.699| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.09 r_work: 0.3460 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4677 Z= 0.152 Angle : 0.629 7.719 6613 Z= 0.331 Chirality : 0.037 0.134 783 Planarity : 0.005 0.049 604 Dihedral : 20.187 111.621 1462 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.23 % Favored : 96.23 % Rotamer: Outliers : 4.02 % Allowed : 20.12 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.00 (0.44), residues: 371 helix: 0.53 (0.38), residues: 172 sheet: -1.14 (1.11), residues: 21 loop : -0.27 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 109 TYR 0.015 0.002 TYR C 109 PHE 0.012 0.002 PHE C 123 TRP 0.013 0.002 TRP B 89 HIS 0.008 0.003 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 4677) covalent geometry : angle 0.62920 / 0.33 ( 6613) hydrogen bonds : bond 0.06091 / 6.42 ( 204) hydrogen bonds : angle 4.82053 / 5.58 ( 522) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 MET cc_start: 0.8617 (mmm) cc_final: 0.8376 (mmm) REVERT: D 314 ARG cc_start: 0.8430 (tpp80) cc_final: 0.7986 (tpt90) outliers start: 13 outliers final: 7 residues processed: 80 average time/residue: 0.0988 time to fit residues: 9.2779 Evaluate side-chains 69 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 366 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.1980 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4031 r_free = 0.4031 target = 0.106115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.081224 restraints weight = 13702.228| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.29 r_work: 0.3399 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4677 Z= 0.148 Angle : 0.613 8.713 6613 Z= 0.322 Chirality : 0.037 0.160 783 Planarity : 0.005 0.040 604 Dihedral : 20.027 109.277 1456 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.77 % Favored : 95.69 % Rotamer: Outliers : 3.10 % Allowed : 22.91 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.02 (0.44), residues: 371 helix: 0.56 (0.38), residues: 173 sheet: -2.39 (0.91), residues: 28 loop : -0.02 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 109 TYR 0.012 0.002 TYR C 94 PHE 0.011 0.001 PHE C 123 TRP 0.010 0.002 TRP B 89 HIS 0.010 0.002 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 4677) covalent geometry : angle 0.61309 / 0.32 ( 6613) hydrogen bonds : bond 0.05194 / 5.46 ( 204) hydrogen bonds : angle 4.48298 / 5.47 ( 522) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: B 10 MET cc_start: 0.8685 (mmm) cc_final: 0.8424 (mmm) REVERT: B 41 MET cc_start: 0.7953 (ppp) cc_final: 0.7440 (ppp) outliers start: 10 outliers final: 7 residues processed: 81 average time/residue: 0.1020 time to fit residues: 9.7058 Evaluate side-chains 70 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain D residue 366 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 0.0470 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.106335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.081768 restraints weight = 13603.399| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.31 r_work: 0.3410 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4677 Z= 0.128 Angle : 0.592 9.769 6613 Z= 0.308 Chirality : 0.035 0.135 783 Planarity : 0.005 0.040 604 Dihedral : 19.978 109.632 1456 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.50 % Favored : 95.96 % Rotamer: Outliers : 3.41 % Allowed : 24.46 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.44), residues: 371 helix: 0.48 (0.38), residues: 173 sheet: -2.40 (0.87), residues: 28 loop : 0.02 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 109 TYR 0.015 0.002 TYR C 39 PHE 0.008 0.001 PHE C 123 TRP 0.010 0.002 TRP B 93 HIS 0.009 0.002 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 4677) covalent geometry : angle 0.59201 / 0.31 ( 6613) hydrogen bonds : bond 0.04629 / 4.84 ( 204) hydrogen bonds : angle 4.32976 / 5.29 ( 522) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 MET cc_start: 0.8702 (mmm) cc_final: 0.8424 (mmm) REVERT: B 41 MET cc_start: 0.7945 (ppp) cc_final: 0.7054 (ppp) outliers start: 11 outliers final: 8 residues processed: 75 average time/residue: 0.1020 time to fit residues: 9.1026 Evaluate side-chains 74 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain D residue 366 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 10.9990 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.104901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.080499 restraints weight = 13673.018| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.16 r_work: 0.3425 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4677 Z= 0.193 Angle : 0.624 10.090 6613 Z= 0.326 Chirality : 0.038 0.151 783 Planarity : 0.005 0.039 604 Dihedral : 19.985 107.673 1456 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.04 % Favored : 95.42 % Rotamer: Outliers : 5.57 % Allowed : 21.98 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.44), residues: 371 helix: 0.45 (0.38), residues: 172 sheet: -2.27 (0.89), residues: 28 loop : -0.04 (0.51), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 109 TYR 0.018 0.002 TYR C 94 PHE 0.010 0.002 PHE C 54 TRP 0.013 0.003 TRP B 93 HIS 0.009 0.002 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 ( 4677) covalent geometry : angle 0.62449 / 0.33 ( 6613) hydrogen bonds : bond 0.04807 / 4.95 ( 204) hydrogen bonds : angle 4.35396 / 5.33 ( 522) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: B 10 MET cc_start: 0.8766 (mmm) cc_final: 0.8477 (mmm) REVERT: B 41 MET cc_start: 0.8054 (ppp) cc_final: 0.7437 (ppp) outliers start: 18 outliers final: 9 residues processed: 79 average time/residue: 0.0875 time to fit residues: 8.3345 Evaluate side-chains 77 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 366 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 26 optimal weight: 0.0870 chunk 33 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.105684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.081302 restraints weight = 13793.382| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 3.20 r_work: 0.3402 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4677 Z= 0.128 Angle : 0.587 10.905 6613 Z= 0.307 Chirality : 0.035 0.157 783 Planarity : 0.004 0.037 604 Dihedral : 19.962 109.416 1456 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.50 % Favored : 95.96 % Rotamer: Outliers : 3.10 % Allowed : 24.46 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.02 (0.44), residues: 371 helix: 0.57 (0.38), residues: 173 sheet: -2.34 (0.88), residues: 28 loop : 0.03 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 109 TYR 0.017 0.002 TYR C 39 PHE 0.008 0.001 PHE C 54 TRP 0.012 0.002 TRP B 93 HIS 0.009 0.002 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 4677) covalent geometry : angle 0.58724 / 0.31 ( 6613) hydrogen bonds : bond 0.04426 / 4.60 ( 204) hydrogen bonds : angle 4.21777 / 5.11 ( 522) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: B 10 MET cc_start: 0.8789 (mmm) cc_final: 0.8487 (mmm) REVERT: B 41 MET cc_start: 0.8133 (ppp) cc_final: 0.7517 (ppp) REVERT: D 362 ARG cc_start: 0.6687 (tpt170) cc_final: 0.5960 (mmp80) outliers start: 10 outliers final: 6 residues processed: 78 average time/residue: 0.0944 time to fit residues: 8.5562 Evaluate side-chains 74 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 366 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.106059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.082360 restraints weight = 13830.642| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.09 r_work: 0.3458 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4677 Z= 0.139 Angle : 0.601 11.607 6613 Z= 0.312 Chirality : 0.036 0.155 783 Planarity : 0.004 0.036 604 Dihedral : 19.929 108.941 1456 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.31 % Favored : 95.15 % Rotamer: Outliers : 3.72 % Allowed : 23.53 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.44), residues: 371 helix: 0.50 (0.38), residues: 173 sheet: -2.25 (0.90), residues: 28 loop : 0.01 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 109 TYR 0.018 0.002 TYR C 39 PHE 0.008 0.001 PHE B 4 TRP 0.016 0.003 TRP B 93 HIS 0.009 0.002 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 4677) covalent geometry : angle 0.60081 / 0.31 ( 6613) hydrogen bonds : bond 0.04381 / 4.56 ( 204) hydrogen bonds : angle 4.21595 / 5.16 ( 522) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: B 10 MET cc_start: 0.8808 (mmm) cc_final: 0.8501 (mmm) REVERT: B 41 MET cc_start: 0.7948 (ppp) cc_final: 0.7517 (ppp) REVERT: D 362 ARG cc_start: 0.6705 (tpt170) cc_final: 0.5988 (mmp80) outliers start: 12 outliers final: 8 residues processed: 81 average time/residue: 0.0913 time to fit residues: 8.7237 Evaluate side-chains 76 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 366 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.105890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.082344 restraints weight = 13636.980| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.05 r_work: 0.3453 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4677 Z= 0.149 Angle : 0.618 11.709 6613 Z= 0.320 Chirality : 0.036 0.151 783 Planarity : 0.004 0.036 604 Dihedral : 19.936 108.586 1456 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.58 % Favored : 94.88 % Rotamer: Outliers : 3.41 % Allowed : 25.39 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.01 (0.43), residues: 371 helix: 0.52 (0.38), residues: 172 sheet: -2.17 (0.91), residues: 28 loop : 0.00 (0.50), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 120 TYR 0.016 0.002 TYR C 39 PHE 0.009 0.002 PHE C 123 TRP 0.019 0.003 TRP B 93 HIS 0.009 0.002 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 4677) covalent geometry : angle 0.61809 / 0.32 ( 6613) hydrogen bonds : bond 0.04355 / 4.52 ( 204) hydrogen bonds : angle 4.19393 / 5.17 ( 522) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: B 10 MET cc_start: 0.8816 (mmm) cc_final: 0.8504 (mmm) REVERT: B 41 MET cc_start: 0.7778 (ppp) cc_final: 0.7503 (ppp) REVERT: D 362 ARG cc_start: 0.6840 (tpt170) cc_final: 0.6088 (mmp80) outliers start: 11 outliers final: 9 residues processed: 77 average time/residue: 0.0924 time to fit residues: 8.1806 Evaluate side-chains 75 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 366 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.105877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.081401 restraints weight = 13766.652| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.21 r_work: 0.3448 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4677 Z= 0.149 Angle : 0.637 11.986 6613 Z= 0.330 Chirality : 0.036 0.155 783 Planarity : 0.004 0.033 604 Dihedral : 19.940 108.431 1456 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.58 % Favored : 94.88 % Rotamer: Outliers : 4.02 % Allowed : 25.39 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.44), residues: 371 helix: 0.39 (0.38), residues: 173 sheet: -2.09 (0.92), residues: 28 loop : -0.02 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 329 TYR 0.021 0.002 TYR C 39 PHE 0.009 0.001 PHE C 54 TRP 0.022 0.004 TRP B 93 HIS 0.010 0.002 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 4677) covalent geometry : angle 0.63706 / 0.33 ( 6613) hydrogen bonds : bond 0.04455 / 4.63 ( 204) hydrogen bonds : angle 4.21989 / 5.17 ( 522) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: B 10 MET cc_start: 0.8815 (mmm) cc_final: 0.8496 (mmm) REVERT: B 41 MET cc_start: 0.7915 (ppp) cc_final: 0.7649 (ppp) REVERT: D 358 LEU cc_start: 0.8626 (tp) cc_final: 0.8295 (tp) REVERT: D 362 ARG cc_start: 0.6827 (tpt170) cc_final: 0.6021 (mmp80) outliers start: 13 outliers final: 8 residues processed: 79 average time/residue: 0.0785 time to fit residues: 7.3772 Evaluate side-chains 75 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 377 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.106168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.081804 restraints weight = 13774.119| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.20 r_work: 0.3456 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4677 Z= 0.146 Angle : 0.655 12.648 6613 Z= 0.334 Chirality : 0.036 0.159 783 Planarity : 0.004 0.033 604 Dihedral : 19.933 108.527 1456 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.58 % Favored : 94.88 % Rotamer: Outliers : 2.79 % Allowed : 26.32 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.44), residues: 371 helix: 0.36 (0.38), residues: 173 sheet: -2.06 (0.92), residues: 28 loop : -0.05 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 72 TYR 0.019 0.002 TYR C 39 PHE 0.008 0.001 PHE C 54 TRP 0.023 0.003 TRP B 93 HIS 0.010 0.002 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 4677) covalent geometry : angle 0.65517 / 0.33 ( 6613) hydrogen bonds : bond 0.04419 / 4.58 ( 204) hydrogen bonds : angle 4.20427 / 5.10 ( 522) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: B 10 MET cc_start: 0.8867 (mmm) cc_final: 0.8547 (mmm) REVERT: B 41 MET cc_start: 0.7974 (ppp) cc_final: 0.7604 (ppp) REVERT: D 358 LEU cc_start: 0.8605 (tp) cc_final: 0.8252 (tp) REVERT: D 362 ARG cc_start: 0.6888 (tpt170) cc_final: 0.6121 (mmp80) outliers start: 9 outliers final: 7 residues processed: 78 average time/residue: 0.0839 time to fit residues: 7.7837 Evaluate side-chains 77 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 377 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 71 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.106180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.082157 restraints weight = 13719.916| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.11 r_work: 0.3454 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4677 Z= 0.145 Angle : 0.647 12.501 6613 Z= 0.331 Chirality : 0.036 0.161 783 Planarity : 0.004 0.033 604 Dihedral : 19.923 108.320 1456 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.58 % Favored : 94.88 % Rotamer: Outliers : 2.48 % Allowed : 26.32 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.09 (0.44), residues: 371 helix: 0.46 (0.39), residues: 173 sheet: -1.96 (0.91), residues: 28 loop : -0.09 (0.50), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 329 TYR 0.019 0.002 TYR C 39 PHE 0.008 0.001 PHE C 54 TRP 0.024 0.004 TRP C 32 HIS 0.010 0.002 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 4677) covalent geometry : angle 0.64664 / 0.33 ( 6613) hydrogen bonds : bond 0.04425 / 4.57 ( 204) hydrogen bonds : angle 4.15301 / 5.08 ( 522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1392.64 seconds wall clock time: 24 minutes 25.91 seconds (1465.91 seconds total)