Starting phenix.real_space_refine on Wed Sep 17 05:01:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iqy_60798/09_2025/9iqy_60798.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iqy_60798/09_2025/9iqy_60798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iqy_60798/09_2025/9iqy_60798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iqy_60798/09_2025/9iqy_60798.map" model { file = "/net/cci-nas-00/data/ceres_data/9iqy_60798/09_2025/9iqy_60798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iqy_60798/09_2025/9iqy_60798.cif" } resolution = 3.16 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= -0.002 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 24 5.16 5 C 2963 2.51 5 N 821 2.21 5 O 874 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4685 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2567 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 14, 'TRANS': 304} Chain: "C" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 729 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "J" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1360 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 11, 'TRANS': 168} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.12, per 1000 atoms: 0.24 Number of scatterers: 4685 At special positions: 0 Unit cell: (96.12, 109.08, 78.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 24 16.00 P 2 15.00 Mg 1 11.99 O 874 8.00 N 821 7.00 C 2963 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: 0.33 Conformation dependent library (CDL) restraints added in 169.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1114 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 3 sheets defined 56.0% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 162 through 167 removed outlier: 4.111A pdb=" N ASP B 167 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.878A pdb=" N LYS B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 221 removed outlier: 3.796A pdb=" N VAL B 212 " --> pdb=" O ASP B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 240 through 248 removed outlier: 3.747A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 323 through 331 removed outlier: 3.556A pdb=" N VAL B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 357 removed outlier: 4.087A pdb=" N THR B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 removed outlier: 3.989A pdb=" N VAL B 365 " --> pdb=" O LEU B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'B' and resid 382 through 391 removed outlier: 3.598A pdb=" N PHE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 403 removed outlier: 3.880A pdb=" N LEU B 402 " --> pdb=" O THR B 399 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 403 " --> pdb=" O ARG B 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 399 through 403' Processing helix chain 'B' and resid 432 through 440 Processing helix chain 'B' and resid 445 through 450 Processing helix chain 'B' and resid 452 through 466 removed outlier: 3.677A pdb=" N GLU B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 381 Processing helix chain 'C' and resid 382 through 391 Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 445 through 450 Processing helix chain 'C' and resid 452 through 462 Processing helix chain 'J' and resid 17 through 28 Processing helix chain 'J' and resid 65 through 70 Processing helix chain 'J' and resid 71 through 74 Processing helix chain 'J' and resid 89 through 107 Proline residue: J 96 - end of helix removed outlier: 4.759A pdb=" N THR J 100 " --> pdb=" O PRO J 96 " (cutoff:3.500A) Proline residue: J 101 - end of helix Processing helix chain 'J' and resid 118 through 123 removed outlier: 3.642A pdb=" N ASN J 123 " --> pdb=" O ASP J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 134 Processing helix chain 'J' and resid 140 through 152 Processing helix chain 'J' and resid 168 through 180 removed outlier: 3.537A pdb=" N GLN J 180 " --> pdb=" O ARG J 176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 405 through 411 removed outlier: 6.804A pdb=" N SER B 416 " --> pdb=" O ASP B 408 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ALA B 410 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL B 414 " --> pdb=" O ALA B 410 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 405 through 407 Processing sheet with id=AA3, first strand: chain 'J' and resid 42 through 47 removed outlier: 4.306A pdb=" N TYR J 42 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE J 4 " --> pdb=" O GLU J 54 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA J 56 " --> pdb=" O ILE J 4 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS J 6 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TRP J 58 " --> pdb=" O LYS J 6 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU J 8 " --> pdb=" O TRP J 58 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N VAL J 79 " --> pdb=" O ARG J 5 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS J 7 " --> pdb=" O VAL J 79 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU J 81 " --> pdb=" O LYS J 7 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL J 9 " --> pdb=" O LEU J 81 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N CYS J 83 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL J 11 " --> pdb=" O CYS J 83 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N SER J 85 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE J 80 " --> pdb=" O ILE J 113 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL J 115 " --> pdb=" O ILE J 80 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET J 82 " --> pdb=" O VAL J 115 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ASN J 117 " --> pdb=" O MET J 82 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE J 84 " --> pdb=" O ASN J 117 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY J 155 " --> pdb=" O ILE J 112 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET J 157 " --> pdb=" O LEU J 114 " (cutoff:3.500A) 189 hydrogen bonds defined for protein. 531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.62 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 785 1.32 - 1.44: 1224 1.44 - 1.56: 2731 1.56 - 1.69: 3 1.69 - 1.81: 37 Bond restraints: 4780 Sorted by residual: bond pdb=" C ILE J 10 " pdb=" O ILE J 10 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.08e-02 8.57e+03 1.66e+01 bond pdb=" N THR J 100 " pdb=" CA THR J 100 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.92e+00 bond pdb=" N ARG J 122 " pdb=" CA ARG J 122 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.23e-02 6.61e+03 7.95e+00 bond pdb=" N GLU J 102 " pdb=" CA GLU J 102 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.19e-02 7.06e+03 6.64e+00 bond pdb=" N ASP J 120 " pdb=" CA ASP J 120 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.25e-02 6.40e+03 6.44e+00 ... (remaining 4775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 6277 2.00 - 4.00: 168 4.00 - 6.00: 21 6.00 - 8.01: 5 8.01 - 10.01: 3 Bond angle restraints: 6474 Sorted by residual: angle pdb=" C ASP J 67 " pdb=" CA ASP J 67 " pdb=" CB ASP J 67 " ideal model delta sigma weight residual 110.79 102.69 8.10 1.66e+00 3.63e-01 2.38e+01 angle pdb=" N ILE J 86 " pdb=" CA ILE J 86 " pdb=" C ILE J 86 " ideal model delta sigma weight residual 110.62 106.29 4.33 1.02e+00 9.61e-01 1.80e+01 angle pdb=" N ASN B 204 " pdb=" CA ASN B 204 " pdb=" C ASN B 204 " ideal model delta sigma weight residual 113.23 108.18 5.05 1.22e+00 6.72e-01 1.71e+01 angle pdb=" CA ASN J 117 " pdb=" C ASN J 117 " pdb=" O ASN J 117 " ideal model delta sigma weight residual 121.87 117.50 4.37 1.16e+00 7.43e-01 1.42e+01 angle pdb=" C LYS B 340 " pdb=" N PHE B 341 " pdb=" CA PHE B 341 " ideal model delta sigma weight residual 122.09 115.74 6.35 1.79e+00 3.12e-01 1.26e+01 ... (remaining 6469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.87: 2740 22.87 - 45.74: 144 45.74 - 68.61: 19 68.61 - 91.49: 2 91.49 - 114.36: 2 Dihedral angle restraints: 2907 sinusoidal: 1187 harmonic: 1720 Sorted by residual: dihedral pdb=" O2B GDP J 201 " pdb=" O3A GDP J 201 " pdb=" PB GDP J 201 " pdb=" PA GDP J 201 " ideal model delta sinusoidal sigma weight residual -180.00 -65.64 -114.36 1 2.00e+01 2.50e-03 3.39e+01 dihedral pdb=" C5' GDP J 201 " pdb=" O5' GDP J 201 " pdb=" PA GDP J 201 " pdb=" O3A GDP J 201 " ideal model delta sinusoidal sigma weight residual 179.98 -69.34 -110.68 1 2.00e+01 2.50e-03 3.25e+01 dihedral pdb=" C ASP J 67 " pdb=" N ASP J 67 " pdb=" CA ASP J 67 " pdb=" CB ASP J 67 " ideal model delta harmonic sigma weight residual -122.60 -112.23 -10.37 0 2.50e+00 1.60e-01 1.72e+01 ... (remaining 2904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 715 0.122 - 0.245: 7 0.245 - 0.367: 1 0.367 - 0.490: 0 0.490 - 0.612: 1 Chirality restraints: 724 Sorted by residual: chirality pdb=" CB ILE J 10 " pdb=" CA ILE J 10 " pdb=" CG1 ILE J 10 " pdb=" CG2 ILE J 10 " both_signs ideal model delta sigma weight residual False 2.64 2.03 0.61 2.00e-01 2.50e+01 9.37e+00 chirality pdb=" CA ASP J 67 " pdb=" N ASP J 67 " pdb=" C ASP J 67 " pdb=" CB ASP J 67 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA ILE J 86 " pdb=" N ILE J 86 " pdb=" C ILE J 86 " pdb=" CB ILE J 86 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 721 not shown) Planarity restraints: 834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS J 107 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO J 108 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO J 108 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 108 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 274 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO B 275 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 275 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 275 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR J 74 " 0.027 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO J 75 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO J 75 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 75 " 0.022 5.00e-02 4.00e+02 ... (remaining 831 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 59 2.64 - 3.20: 4271 3.20 - 3.77: 7124 3.77 - 4.33: 10060 4.33 - 4.90: 16297 Nonbonded interactions: 37811 Sorted by model distance: nonbonded pdb=" O1B GDP J 201 " pdb="MG MG J 202 " model vdw 2.074 2.170 nonbonded pdb=" O THR J 37 " pdb="MG MG J 202 " model vdw 2.218 2.170 nonbonded pdb=" OG1 THR J 19 " pdb="MG MG J 202 " model vdw 2.246 2.170 nonbonded pdb=" O PRO B 188 " pdb=" OG SER B 189 " model vdw 2.282 3.040 nonbonded pdb=" N ASN B 207 " pdb=" OH TYR B 253 " model vdw 2.300 3.120 ... (remaining 37806 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.510 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 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 0.044 4780 Z= 0.226 Angle : 0.758 10.008 6474 Z= 0.442 Chirality : 0.052 0.612 724 Planarity : 0.004 0.051 834 Dihedral : 13.927 114.356 1793 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.20 % Allowed : 0.80 % Favored : 99.00 % Cbeta Deviations : 0.18 % 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 aren not related in a simple way. whole: -0.07 (0.35), residues: 583 helix: 0.25 (0.31), residues: 287 sheet: 0.92 (0.78), residues: 45 loop : -0.45 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 320 TYR 0.015 0.001 TYR B 415 PHE 0.018 0.001 PHE B 386 TRP 0.010 0.001 TRP B 409 HIS 0.002 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 4780) covalent geometry : angle 0.75794 ( 6474) hydrogen bonds : bond 0.20287 ( 189) hydrogen bonds : angle 7.22413 ( 531) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.234 Fit side-chains REVERT: B 169 LEU cc_start: 0.8294 (tp) cc_final: 0.8087 (tp) REVERT: B 219 ARG cc_start: 0.7763 (mmt90) cc_final: 0.7401 (mmm-85) REVERT: J 27 LYS cc_start: 0.7016 (mtpt) cc_final: 0.6748 (mttm) outliers start: 1 outliers final: 1 residues processed: 91 average time/residue: 0.0851 time to fit residues: 9.6718 Evaluate side-chains 71 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 10 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 ASN B 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.182859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.150850 restraints weight = 5476.945| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.19 r_work: 0.3510 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4780 Z= 0.155 Angle : 0.606 6.581 6474 Z= 0.304 Chirality : 0.044 0.184 724 Planarity : 0.004 0.034 834 Dihedral : 6.141 74.409 658 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.60 % Allowed : 7.60 % Favored : 90.80 % 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 aren not related in a simple way. whole: 0.24 (0.35), residues: 583 helix: 0.51 (0.31), residues: 283 sheet: 0.95 (0.79), residues: 45 loop : -0.26 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 392 TYR 0.010 0.001 TYR B 253 PHE 0.026 0.001 PHE B 341 TRP 0.008 0.001 TRP B 409 HIS 0.004 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 4780) covalent geometry : angle 0.60602 ( 6474) hydrogen bonds : bond 0.03592 ( 189) hydrogen bonds : angle 5.30003 ( 531) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: B 331 ILE cc_start: 0.8889 (tp) cc_final: 0.8347 (tp) REVERT: J 93 GLU cc_start: 0.7905 (mp0) cc_final: 0.7621 (mp0) REVERT: J 157 MET cc_start: 0.4917 (OUTLIER) cc_final: 0.4653 (mtt) outliers start: 8 outliers final: 2 residues processed: 84 average time/residue: 0.0670 time to fit residues: 7.3711 Evaluate side-chains 77 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain J residue 157 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.178769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.146173 restraints weight = 5452.378| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.26 r_work: 0.3481 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4780 Z= 0.165 Angle : 0.597 6.634 6474 Z= 0.297 Chirality : 0.044 0.194 724 Planarity : 0.004 0.036 834 Dihedral : 5.574 56.610 656 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.80 % Allowed : 11.20 % Favored : 87.00 % 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 aren not related in a simple way. whole: 0.29 (0.35), residues: 583 helix: 0.64 (0.31), residues: 285 sheet: 0.81 (0.79), residues: 45 loop : -0.33 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 460 TYR 0.009 0.001 TYR B 346 PHE 0.014 0.001 PHE B 341 TRP 0.007 0.001 TRP J 99 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 4780) covalent geometry : angle 0.59732 ( 6474) hydrogen bonds : bond 0.03330 ( 189) hydrogen bonds : angle 4.92473 ( 531) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: B 331 ILE cc_start: 0.8968 (tp) cc_final: 0.8475 (tp) REVERT: J 51 LYS cc_start: 0.7815 (ptmt) cc_final: 0.7532 (ptmm) REVERT: J 93 GLU cc_start: 0.7959 (mp0) cc_final: 0.6985 (mp0) REVERT: J 157 MET cc_start: 0.4948 (OUTLIER) cc_final: 0.4684 (mtt) outliers start: 9 outliers final: 2 residues processed: 87 average time/residue: 0.0724 time to fit residues: 8.1958 Evaluate side-chains 79 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain J residue 157 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 35 optimal weight: 0.5980 chunk 53 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.183238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.150798 restraints weight = 5482.650| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.20 r_work: 0.3508 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4780 Z= 0.125 Angle : 0.557 6.599 6474 Z= 0.275 Chirality : 0.042 0.188 724 Planarity : 0.004 0.038 834 Dihedral : 5.183 52.629 656 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.80 % Allowed : 11.60 % Favored : 85.60 % 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 aren not related in a simple way. whole: 0.47 (0.35), residues: 583 helix: 0.85 (0.31), residues: 286 sheet: 0.86 (0.79), residues: 45 loop : -0.32 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 460 TYR 0.010 0.001 TYR B 439 PHE 0.013 0.001 PHE B 341 TRP 0.006 0.001 TRP B 409 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4780) covalent geometry : angle 0.55669 ( 6474) hydrogen bonds : bond 0.02834 ( 189) hydrogen bonds : angle 4.66955 ( 531) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: B 331 ILE cc_start: 0.9018 (tp) cc_final: 0.8485 (tp) REVERT: J 51 LYS cc_start: 0.7815 (ptmt) cc_final: 0.7529 (ptmm) REVERT: J 93 GLU cc_start: 0.7908 (mp0) cc_final: 0.7509 (mp0) REVERT: J 157 MET cc_start: 0.5300 (OUTLIER) cc_final: 0.4998 (mtt) outliers start: 14 outliers final: 7 residues processed: 87 average time/residue: 0.0678 time to fit residues: 7.6555 Evaluate side-chains 87 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 157 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 36 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 16 optimal weight: 0.0570 chunk 6 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.179621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.147040 restraints weight = 5494.788| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.32 r_work: 0.3491 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4780 Z= 0.139 Angle : 0.574 6.600 6474 Z= 0.285 Chirality : 0.043 0.182 724 Planarity : 0.004 0.039 834 Dihedral : 5.150 51.410 656 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.40 % Allowed : 14.20 % Favored : 83.40 % 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 aren not related in a simple way. whole: 0.54 (0.35), residues: 583 helix: 0.94 (0.31), residues: 286 sheet: 0.92 (0.79), residues: 45 loop : -0.32 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 460 TYR 0.011 0.001 TYR B 439 PHE 0.016 0.001 PHE B 341 TRP 0.006 0.001 TRP J 99 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 4780) covalent geometry : angle 0.57373 ( 6474) hydrogen bonds : bond 0.02859 ( 189) hydrogen bonds : angle 4.61161 ( 531) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: B 331 ILE cc_start: 0.8979 (tp) cc_final: 0.8468 (tp) REVERT: C 389 ILE cc_start: 0.7730 (mt) cc_final: 0.7398 (mt) REVERT: J 93 GLU cc_start: 0.7900 (mp0) cc_final: 0.7075 (mp0) REVERT: J 157 MET cc_start: 0.5132 (OUTLIER) cc_final: 0.4793 (mtt) outliers start: 12 outliers final: 6 residues processed: 84 average time/residue: 0.0713 time to fit residues: 7.8176 Evaluate side-chains 85 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain J residue 80 ILE Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 157 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 51 optimal weight: 0.0570 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 28 optimal weight: 0.0980 chunk 37 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.182555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.150566 restraints weight = 5542.173| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.23 r_work: 0.3497 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4780 Z= 0.136 Angle : 0.570 6.546 6474 Z= 0.283 Chirality : 0.043 0.182 724 Planarity : 0.004 0.039 834 Dihedral : 5.105 51.115 656 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.60 % Allowed : 14.40 % Favored : 83.00 % 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 aren not related in a simple way. whole: 0.73 (0.35), residues: 583 helix: 1.12 (0.32), residues: 280 sheet: 0.95 (0.79), residues: 45 loop : -0.22 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 460 TYR 0.011 0.001 TYR B 439 PHE 0.015 0.001 PHE B 341 TRP 0.006 0.001 TRP J 99 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 4780) covalent geometry : angle 0.57018 ( 6474) hydrogen bonds : bond 0.02786 ( 189) hydrogen bonds : angle 4.56827 ( 531) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: B 331 ILE cc_start: 0.8979 (tp) cc_final: 0.8461 (tp) REVERT: C 389 ILE cc_start: 0.7736 (mt) cc_final: 0.7401 (mt) REVERT: J 93 GLU cc_start: 0.7893 (mp0) cc_final: 0.6998 (mp0) outliers start: 13 outliers final: 9 residues processed: 85 average time/residue: 0.0723 time to fit residues: 8.0460 Evaluate side-chains 83 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain J residue 80 ILE Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 157 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 8 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 39 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 30 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.179485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.148453 restraints weight = 5475.057| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.04 r_work: 0.3537 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4780 Z= 0.126 Angle : 0.576 6.478 6474 Z= 0.285 Chirality : 0.043 0.176 724 Planarity : 0.004 0.039 834 Dihedral : 5.039 49.982 656 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.60 % Allowed : 15.60 % Favored : 82.80 % 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 aren not related in a simple way. whole: 0.83 (0.35), residues: 583 helix: 1.22 (0.32), residues: 280 sheet: 0.96 (0.79), residues: 45 loop : -0.19 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 460 TYR 0.012 0.001 TYR B 439 PHE 0.013 0.001 PHE B 341 TRP 0.006 0.001 TRP C 409 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4780) covalent geometry : angle 0.57565 ( 6474) hydrogen bonds : bond 0.02678 ( 189) hydrogen bonds : angle 4.52284 ( 531) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 331 ILE cc_start: 0.8981 (tp) cc_final: 0.8453 (tp) REVERT: B 337 GLU cc_start: 0.7613 (mp0) cc_final: 0.7372 (mm-30) REVERT: C 389 ILE cc_start: 0.7889 (mt) cc_final: 0.7568 (mt) REVERT: J 93 GLU cc_start: 0.7816 (mp0) cc_final: 0.6836 (mp0) outliers start: 8 outliers final: 6 residues processed: 81 average time/residue: 0.0690 time to fit residues: 7.3879 Evaluate side-chains 81 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain J residue 95 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 23 optimal weight: 0.8980 chunk 55 optimal weight: 0.0670 chunk 36 optimal weight: 0.0970 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 20 optimal weight: 0.0570 chunk 32 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.2032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.183316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.152249 restraints weight = 5494.233| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.14 r_work: 0.3544 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4780 Z= 0.102 Angle : 0.549 6.381 6474 Z= 0.272 Chirality : 0.041 0.173 724 Planarity : 0.004 0.039 834 Dihedral : 4.802 47.640 656 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.60 % Allowed : 15.40 % Favored : 83.00 % 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 aren not related in a simple way. whole: 1.02 (0.36), residues: 583 helix: 1.40 (0.32), residues: 280 sheet: 0.94 (0.79), residues: 45 loop : -0.09 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 460 TYR 0.013 0.001 TYR B 439 PHE 0.009 0.001 PHE B 386 TRP 0.006 0.001 TRP C 409 HIS 0.002 0.000 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 4780) covalent geometry : angle 0.54947 ( 6474) hydrogen bonds : bond 0.02426 ( 189) hydrogen bonds : angle 4.31080 ( 531) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 331 ILE cc_start: 0.8864 (tp) cc_final: 0.8377 (tp) REVERT: B 457 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6568 (tm-30) REVERT: C 374 LEU cc_start: 0.6663 (tt) cc_final: 0.6374 (tt) REVERT: C 389 ILE cc_start: 0.7647 (mt) cc_final: 0.7288 (mt) REVERT: J 147 MET cc_start: 0.7891 (tpp) cc_final: 0.7658 (tpp) outliers start: 8 outliers final: 4 residues processed: 80 average time/residue: 0.0691 time to fit residues: 7.0479 Evaluate side-chains 81 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 402 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 0.1980 chunk 5 optimal weight: 0.0170 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.0060 chunk 20 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 33 optimal weight: 0.3980 overall best weight: 0.2034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.184570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.152728 restraints weight = 5455.510| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.23 r_work: 0.3560 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4780 Z= 0.099 Angle : 0.542 6.382 6474 Z= 0.267 Chirality : 0.042 0.173 724 Planarity : 0.004 0.039 834 Dihedral : 4.660 45.409 656 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.00 % Allowed : 15.20 % Favored : 82.80 % 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 aren not related in a simple way. whole: 1.09 (0.36), residues: 583 helix: 1.50 (0.32), residues: 280 sheet: 0.94 (0.77), residues: 45 loop : -0.10 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 460 TYR 0.009 0.001 TYR B 346 PHE 0.009 0.001 PHE B 386 TRP 0.006 0.001 TRP B 409 HIS 0.002 0.000 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 4780) covalent geometry : angle 0.54232 ( 6474) hydrogen bonds : bond 0.02404 ( 189) hydrogen bonds : angle 4.24910 ( 531) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 179 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7987 (mtm180) REVERT: B 331 ILE cc_start: 0.8858 (tp) cc_final: 0.8356 (tp) REVERT: B 457 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6455 (tm-30) REVERT: C 374 LEU cc_start: 0.6652 (tt) cc_final: 0.6374 (tt) REVERT: C 389 ILE cc_start: 0.7595 (mt) cc_final: 0.7225 (mt) REVERT: J 147 MET cc_start: 0.7904 (tpp) cc_final: 0.7695 (tpp) outliers start: 10 outliers final: 5 residues processed: 87 average time/residue: 0.0711 time to fit residues: 8.0277 Evaluate side-chains 82 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 402 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 23 optimal weight: 0.1980 chunk 47 optimal weight: 0.1980 chunk 54 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.186339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.153799 restraints weight = 5568.313| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.33 r_work: 0.3532 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4780 Z= 0.119 Angle : 0.571 6.608 6474 Z= 0.284 Chirality : 0.043 0.169 724 Planarity : 0.004 0.039 834 Dihedral : 4.703 45.104 656 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.60 % Allowed : 15.60 % Favored : 82.80 % 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 aren not related in a simple way. whole: 1.04 (0.36), residues: 583 helix: 1.45 (0.32), residues: 280 sheet: 0.92 (0.77), residues: 45 loop : -0.11 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 460 TYR 0.015 0.001 TYR B 439 PHE 0.014 0.001 PHE B 341 TRP 0.005 0.001 TRP B 409 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 4780) covalent geometry : angle 0.57054 ( 6474) hydrogen bonds : bond 0.02530 ( 189) hydrogen bonds : angle 4.32060 ( 531) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 331 ILE cc_start: 0.8979 (tp) cc_final: 0.8435 (tp) REVERT: B 457 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6623 (tm-30) REVERT: C 389 ILE cc_start: 0.7935 (mt) cc_final: 0.7611 (mt) outliers start: 8 outliers final: 5 residues processed: 79 average time/residue: 0.0760 time to fit residues: 7.6062 Evaluate side-chains 82 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain J residue 95 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 39 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 0.2980 chunk 42 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.184138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.152510 restraints weight = 5586.873| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.27 r_work: 0.3535 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4780 Z= 0.111 Angle : 0.551 6.435 6474 Z= 0.275 Chirality : 0.042 0.167 724 Planarity : 0.004 0.039 834 Dihedral : 4.677 45.199 656 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.20 % Allowed : 16.40 % Favored : 82.40 % 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 aren not related in a simple way. whole: 1.02 (0.35), residues: 583 helix: 1.45 (0.32), residues: 282 sheet: 0.91 (0.77), residues: 45 loop : -0.16 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 460 TYR 0.009 0.001 TYR B 346 PHE 0.010 0.001 PHE B 341 TRP 0.005 0.001 TRP B 409 HIS 0.002 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 4780) covalent geometry : angle 0.55104 ( 6474) hydrogen bonds : bond 0.02438 ( 189) hydrogen bonds : angle 4.30488 ( 531) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1390.62 seconds wall clock time: 24 minutes 30.60 seconds (1470.60 seconds total)