Starting phenix.real_space_refine on Thu Jul 2 00:00:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gcm_51234/07_2026/9gcm_51234.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gcm_51234/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9gcm_51234/07_2026/9gcm_51234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gcm_51234/07_2026/9gcm_51234.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gcm_51234/07_2026/9gcm_51234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gcm_51234/07_2026/9gcm_51234.map" } 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-dev-6108/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: 1.16, per 1000 atoms: 0.26 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: 0.45 Conformation dependent library (CDL) restraints added in 90.4 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: 0.54 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: 0.68 Time building geometry restraints manager: 0.50 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: 6460 1.77 - 3.54: 121 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=" CA PRO C 26 " pdb=" N PRO C 26 " pdb=" CD PRO C 26 " ideal model delta sigma weight residual 112.00 106.80 5.20 1.40e+00 5.10e-01 1.38e+01 angle pdb=" C1' G A 21 " pdb=" N9 G A 21 " pdb=" C8 G A 21 " ideal model delta sigma weight residual 127.00 122.56 4.44 1.30e+00 5.92e-01 1.17e+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 - 0.024: 514 0.024 - 0.048: 151 0.048 - 0.073: 65 0.073 - 0.097: 40 0.097 - 0.121: 13 Chirality restraints: 783 Sorted by residual: chirality pdb=" CA ILE C 97 " pdb=" N ILE C 97 " pdb=" C ILE C 97 " pdb=" CB ILE C 97 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA ILE C 136 " pdb=" N ILE C 136 " pdb=" C ILE C 136 " pdb=" CB ILE C 136 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA ILE B 126 " pdb=" N ILE B 126 " pdb=" C ILE B 126 " pdb=" CB ILE B 126 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-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: 5.400 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.240 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.020 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.000 ------------------------------------------------------------------------------- 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= 0.228 Angle : 0.651 8.859 6613 Z= 0.427 Chirality : 0.034 0.121 783 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 0.00386 / 0.23 ( 4677) covalent geometry : angle 0.65085 / 0.43 ( 6613) hydrogen bonds : bond 0.22820 / 23.16 ( 204) hydrogen bonds : angle 7.45579 / 8.09 ( 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 : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 73 average time/residue: 0.1057 time to fit residues: 9.0419 Evaluate side-chains 74 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.088 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 39 GLN C 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.106646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.082625 restraints weight = 13783.742| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.08 r_work: 0.3463 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4677 Z= 0.153 Angle : 0.619 8.055 6613 Z= 0.330 Chirality : 0.037 0.194 783 Planarity : 0.005 0.051 604 Dihedral : 20.240 111.949 1462 Min Nonbonded Distance : 2.236 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: -0.01 (0.44), residues: 371 helix: 0.54 (0.38), residues: 172 sheet: -1.15 (1.11), residues: 21 loop : -0.28 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 109 TYR 0.015 0.002 TYR C 109 PHE 0.013 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 0.00323 / 0.15 ( 4677) covalent geometry : angle 0.61889 / 0.33 ( 6613) hydrogen bonds : bond 0.06210 / 5.68 ( 204) hydrogen bonds : angle 4.79015 / 5.25 ( 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 87 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 MET cc_start: 0.8620 (mmm) cc_final: 0.8384 (mmm) REVERT: B 39 GLN cc_start: 0.7693 (tp-100) cc_final: 0.7461 (tp40) REVERT: C 29 ARG cc_start: 0.7822 (mtp85) cc_final: 0.7396 (ttm110) outliers start: 13 outliers final: 7 residues processed: 81 average time/residue: 0.1235 time to fit residues: 11.7615 Evaluate side-chains 71 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.134 ------------------------------------------------------------------------------- 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: 0.6980 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.105609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.080545 restraints weight = 13666.337| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.36 r_work: 0.3389 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4677 Z= 0.157 Angle : 0.604 8.601 6613 Z= 0.321 Chirality : 0.037 0.184 783 Planarity : 0.005 0.040 604 Dihedral : 20.123 110.255 1456 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.77 % Favored : 95.69 % Rotamer: Outliers : 2.48 % Allowed : 24.46 % Favored : 73.07 % 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: -0.07 (0.44), residues: 371 helix: 0.53 (0.38), residues: 172 sheet: -2.41 (0.90), residues: 28 loop : -0.06 (0.51), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 109 TYR 0.013 0.002 TYR C 94 PHE 0.011 0.001 PHE C 123 TRP 0.011 0.002 TRP B 89 HIS 0.010 0.002 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 4677) covalent geometry : angle 0.60357 / 0.32 ( 6613) hydrogen bonds : bond 0.05297 / 4.89 ( 204) hydrogen bonds : angle 4.45719 / 5.16 ( 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 79 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 MET cc_start: 0.8668 (mmm) cc_final: 0.8402 (mmm) REVERT: B 41 MET cc_start: 0.7918 (ppp) cc_final: 0.7462 (ppp) REVERT: C 29 ARG cc_start: 0.7962 (mtp85) cc_final: 0.7433 (ttm110) outliers start: 8 outliers final: 7 residues processed: 75 average time/residue: 0.1069 time to fit residues: 9.3900 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 : 0.085 ------------------------------------------------------------------------------- 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: 0.9980 chunk 6 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 35 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.106091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.080903 restraints weight = 13689.060| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.37 r_work: 0.3398 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1567 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= 0.135 Angle : 0.582 9.535 6613 Z= 0.307 Chirality : 0.036 0.200 783 Planarity : 0.004 0.040 604 Dihedral : 20.054 110.396 1456 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.50 % Favored : 95.96 % Rotamer: Outliers : 3.10 % Allowed : 24.77 % 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: -2.44 (0.86), residues: 28 loop : 0.03 (0.52), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 109 TYR 0.011 0.001 TYR C 94 PHE 0.008 0.001 PHE C 123 TRP 0.010 0.002 TRP B 89 HIS 0.009 0.002 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 4677) covalent geometry : angle 0.58199 / 0.31 ( 6613) hydrogen bonds : bond 0.04609 / 4.22 ( 204) hydrogen bonds : angle 4.30893 / 4.95 ( 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 80 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 MET cc_start: 0.8723 (mmm) cc_final: 0.8449 (mmm) REVERT: B 41 MET cc_start: 0.8025 (ppp) cc_final: 0.7257 (ppp) REVERT: C 29 ARG cc_start: 0.7933 (mtp85) cc_final: 0.7393 (ttm110) outliers start: 10 outliers final: 6 residues processed: 75 average time/residue: 0.0897 time to fit residues: 8.1013 Evaluate side-chains 73 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.136 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 21 optimal weight: 0.0670 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 41 optimal weight: 0.8980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.106336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.081739 restraints weight = 13501.769| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.29 r_work: 0.3414 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1751 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= 0.125 Angle : 0.563 10.096 6613 Z= 0.298 Chirality : 0.035 0.196 783 Planarity : 0.004 0.038 604 Dihedral : 19.982 110.245 1456 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.50 % Favored : 95.96 % Rotamer: Outliers : 3.72 % Allowed : 22.60 % Favored : 73.68 % 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: 0.08 (0.44), residues: 371 helix: 0.61 (0.38), residues: 173 sheet: -2.33 (0.88), residues: 28 loop : 0.08 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 109 TYR 0.015 0.002 TYR C 39 PHE 0.007 0.001 PHE C 54 TRP 0.010 0.002 TRP C 32 HIS 0.009 0.002 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 4677) covalent geometry : angle 0.56304 / 0.30 ( 6613) hydrogen bonds : bond 0.04340 / 3.95 ( 204) hydrogen bonds : angle 4.22567 / 4.88 ( 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 87 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 MET cc_start: 0.8754 (mmm) cc_final: 0.8453 (mmm) REVERT: B 41 MET cc_start: 0.8039 (ppp) cc_final: 0.7675 (ppp) REVERT: B 68 LYS cc_start: 0.8909 (mtmt) cc_final: 0.8655 (mtpp) REVERT: C 29 ARG cc_start: 0.7837 (mtp85) cc_final: 0.7316 (ttm110) REVERT: D 362 ARG cc_start: 0.6624 (tpt170) cc_final: 0.5950 (mmp80) outliers start: 12 outliers final: 7 residues processed: 82 average time/residue: 0.1167 time to fit residues: 11.2866 Evaluate side-chains 76 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.0000 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 0.2980 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.106312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.081654 restraints weight = 13826.312| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.34 r_work: 0.3410 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4677 Z= 0.128 Angle : 0.582 11.311 6613 Z= 0.305 Chirality : 0.036 0.193 783 Planarity : 0.004 0.038 604 Dihedral : 19.940 109.965 1456 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.58 % Favored : 94.88 % Rotamer: Outliers : 4.33 % Allowed : 21.67 % 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: 0.11 (0.44), residues: 371 helix: 0.63 (0.38), residues: 173 sheet: -2.25 (0.88), residues: 28 loop : 0.10 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 109 TYR 0.016 0.002 TYR C 39 PHE 0.008 0.001 PHE C 54 TRP 0.011 0.002 TRP C 32 HIS 0.009 0.002 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 4677) covalent geometry : angle 0.58181 / 0.30 ( 6613) hydrogen bonds : bond 0.04300 / 3.94 ( 204) hydrogen bonds : angle 4.19997 / 4.85 ( 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 88 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 MET cc_start: 0.8766 (mmm) cc_final: 0.8458 (mmm) REVERT: B 41 MET cc_start: 0.8052 (ppp) cc_final: 0.7730 (ppp) REVERT: C 29 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7393 (ttm110) REVERT: D 362 ARG cc_start: 0.6647 (tpt170) cc_final: 0.5971 (mmp80) outliers start: 14 outliers final: 8 residues processed: 83 average time/residue: 0.1171 time to fit residues: 11.2857 Evaluate side-chains 78 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.086 ------------------------------------------------------------------------------- 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 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: 0.0570 chunk 32 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.106689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.082048 restraints weight = 13613.369| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.33 r_work: 0.3416 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4677 Z= 0.122 Angle : 0.581 11.024 6613 Z= 0.303 Chirality : 0.035 0.189 783 Planarity : 0.004 0.035 604 Dihedral : 19.905 109.881 1456 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.04 % Favored : 95.42 % Rotamer: Outliers : 3.10 % Allowed : 23.22 % Favored : 73.68 % 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: 0.24 (0.44), residues: 371 helix: 0.74 (0.39), residues: 173 sheet: -2.11 (0.89), residues: 28 loop : 0.13 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 109 TYR 0.018 0.002 TYR C 39 PHE 0.008 0.001 PHE C 54 TRP 0.014 0.002 TRP C 32 HIS 0.008 0.002 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 4677) covalent geometry : angle 0.58105 / 0.30 ( 6613) hydrogen bonds : bond 0.04210 / 3.84 ( 204) hydrogen bonds : angle 4.14690 / 4.74 ( 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 86 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 MET cc_start: 0.8780 (mmm) cc_final: 0.8461 (mmm) REVERT: B 41 MET cc_start: 0.8047 (ppp) cc_final: 0.7728 (ppp) REVERT: D 362 ARG cc_start: 0.6656 (tpt170) cc_final: 0.5943 (mmp80) outliers start: 10 outliers final: 8 residues processed: 82 average time/residue: 0.1089 time to fit residues: 10.5224 Evaluate side-chains 77 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 30 optimal weight: 0.0050 chunk 10 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 = 0.4031 r_free = 0.4031 target = 0.106324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.081616 restraints weight = 13790.256| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.35 r_work: 0.3404 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4677 Z= 0.133 Angle : 0.590 12.699 6613 Z= 0.305 Chirality : 0.036 0.184 783 Planarity : 0.004 0.035 604 Dihedral : 19.893 109.233 1456 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.04 % Favored : 95.42 % Rotamer: Outliers : 4.02 % Allowed : 23.22 % 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: 0.24 (0.44), residues: 371 helix: 0.74 (0.39), residues: 172 sheet: -1.97 (0.90), residues: 28 loop : 0.10 (0.51), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 329 TYR 0.019 0.002 TYR C 39 PHE 0.010 0.001 PHE C 123 TRP 0.016 0.003 TRP C 32 HIS 0.009 0.002 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 4677) covalent geometry : angle 0.59037 / 0.30 ( 6613) hydrogen bonds : bond 0.04164 / 3.81 ( 204) hydrogen bonds : angle 4.16091 / 4.76 ( 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 87 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 MET cc_start: 0.8820 (mmm) cc_final: 0.8502 (mmm) REVERT: B 41 MET cc_start: 0.8103 (ppp) cc_final: 0.7768 (ppp) REVERT: D 362 ARG cc_start: 0.6766 (tpt170) cc_final: 0.6026 (mmp80) outliers start: 13 outliers final: 10 residues processed: 79 average time/residue: 0.1044 time to fit residues: 9.7173 Evaluate side-chains 82 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 28 ASP 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 322 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: 0.9990 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.105336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.081021 restraints weight = 13611.115| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 3.09 r_work: 0.3436 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4677 Z= 0.196 Angle : 0.642 12.312 6613 Z= 0.333 Chirality : 0.038 0.172 783 Planarity : 0.004 0.034 604 Dihedral : 19.984 107.687 1456 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.85 % Favored : 94.61 % Rotamer: Outliers : 3.72 % Allowed : 23.84 % 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: 0.05 (0.43), residues: 371 helix: 0.56 (0.38), residues: 172 sheet: -1.93 (0.92), residues: 28 loop : 0.01 (0.50), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 109 TYR 0.021 0.003 TYR C 74 PHE 0.011 0.002 PHE C 54 TRP 0.025 0.004 TRP B 93 HIS 0.010 0.002 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 ( 4677) covalent geometry : angle 0.64241 / 0.33 ( 6613) hydrogen bonds : bond 0.04556 / 4.10 ( 204) hydrogen bonds : angle 4.28921 / 4.90 ( 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 89 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 MET cc_start: 0.8865 (mmm) cc_final: 0.8551 (mmm) REVERT: B 41 MET cc_start: 0.8055 (ppp) cc_final: 0.7838 (ppp) REVERT: D 358 LEU cc_start: 0.8606 (tp) cc_final: 0.8268 (tp) REVERT: D 362 ARG cc_start: 0.6746 (tpt170) cc_final: 0.5940 (mmp80) outliers start: 12 outliers final: 7 residues processed: 82 average time/residue: 0.1100 time to fit residues: 10.6183 Evaluate side-chains 80 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.105565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.081335 restraints weight = 13848.408| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.15 r_work: 0.3438 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4677 Z= 0.157 Angle : 0.645 12.869 6613 Z= 0.331 Chirality : 0.037 0.172 783 Planarity : 0.004 0.034 604 Dihedral : 19.997 108.468 1456 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.85 % Favored : 94.61 % Rotamer: Outliers : 1.86 % Allowed : 26.32 % Favored : 71.83 % 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 (0.43), residues: 371 helix: 0.57 (0.38), residues: 172 sheet: -2.05 (0.91), residues: 28 loop : 0.03 (0.50), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 329 TYR 0.022 0.002 TYR C 39 PHE 0.009 0.002 PHE B 4 TRP 0.025 0.004 TRP B 93 HIS 0.010 0.002 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 4677) covalent geometry : angle 0.64508 / 0.33 ( 6613) hydrogen bonds : bond 0.04409 / 3.97 ( 204) hydrogen bonds : angle 4.21645 / 4.83 ( 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 80 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 MET cc_start: 0.8879 (mmm) cc_final: 0.8561 (mmm) REVERT: D 362 ARG cc_start: 0.6844 (tpt170) cc_final: 0.6135 (mmp80) outliers start: 6 outliers final: 6 residues processed: 77 average time/residue: 0.1235 time to fit residues: 11.0764 Evaluate side-chains 79 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.136 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.105930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.081292 restraints weight = 13782.396| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 3.23 r_work: 0.3443 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4677 Z= 0.155 Angle : 0.650 12.742 6613 Z= 0.332 Chirality : 0.037 0.171 783 Planarity : 0.004 0.034 604 Dihedral : 19.996 108.551 1456 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.39 % Favored : 94.07 % Rotamer: Outliers : 2.17 % Allowed : 26.32 % Favored : 71.52 % 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 (0.43), residues: 371 helix: 0.61 (0.38), residues: 172 sheet: -2.01 (0.90), residues: 28 loop : -0.04 (0.50), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 329 TYR 0.025 0.002 TYR B 115 PHE 0.009 0.002 PHE B 4 TRP 0.025 0.004 TRP B 93 HIS 0.010 0.002 HIS D 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 4677) covalent geometry : angle 0.65037 / 0.33 ( 6613) hydrogen bonds : bond 0.04339 / 3.94 ( 204) hydrogen bonds : angle 4.21265 / 4.90 ( 522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1626.04 seconds wall clock time: 28 minutes 33.41 seconds (1713.41 seconds total)