Starting phenix.real_space_refine on Thu Jun 5 00:59:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iqy_60798/06_2025/9iqy_60798.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iqy_60798/06_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_60798/06_2025/9iqy_60798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iqy_60798/06_2025/9iqy_60798.map" model { file = "/net/cci-nas-00/data/ceres_data/9iqy_60798/06_2025/9iqy_60798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iqy_60798/06_2025/9iqy_60798.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 3} 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: 3.79, per 1000 atoms: 0.81 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: 1.17 Conformation dependent library (CDL) restraints added in 542.4 milliseconds 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: 0.55 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: 1.13 Time building geometry restraints manager: 1.41 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: 2.200 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.770 Find NCS groups from input model: 0.050 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.320 ------------------------------------------------------------------------------- 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 : 9.12 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP B 409 HIS 0.002 0.001 HIS B 388 PHE 0.018 0.001 PHE B 386 TYR 0.015 0.001 TYR B 415 ARG 0.005 0.000 ARG B 320 Details of bonding type rmsd hydrogen bonds : bond 0.20287 ( 189) hydrogen bonds : angle 7.22413 ( 531) covalent geometry : bond 0.00369 ( 4780) covalent geometry : angle 0.75794 ( 6474) *********************** 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 : 0.582 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: 0.2035 time to fit residues: 22.9725 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 : 0.586 ------------------------------------------------------------------------------- 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 48 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 0.0570 chunk 27 optimal weight: 0.0470 chunk 33 optimal weight: 0.0870 chunk 52 optimal weight: 1.9990 overall best weight: 0.2974 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.186858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.154692 restraints weight = 5467.065| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.19 r_work: 0.3580 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1312 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= 0.117 Angle : 0.574 6.588 6474 Z= 0.288 Chirality : 0.042 0.178 724 Planarity : 0.004 0.037 834 Dihedral : 5.936 72.058 658 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.20 % Allowed : 7.20 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.35), residues: 583 helix: 0.62 (0.31), residues: 283 sheet: 0.97 (0.79), residues: 45 loop : -0.21 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 409 HIS 0.003 0.001 HIS B 388 PHE 0.026 0.001 PHE B 341 TYR 0.009 0.001 TYR B 253 ARG 0.003 0.000 ARG B 460 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 189) hydrogen bonds : angle 5.21179 ( 531) covalent geometry : bond 0.00274 ( 4780) covalent geometry : angle 0.57402 ( 6474) *********************** 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 88 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: B 331 ILE cc_start: 0.8867 (tp) cc_final: 0.8293 (tp) REVERT: J 93 GLU cc_start: 0.7946 (mp0) cc_final: 0.7645 (mp0) outliers start: 6 outliers final: 2 residues processed: 85 average time/residue: 0.1635 time to fit residues: 17.9802 Evaluate side-chains 76 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain C residue 403 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 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 = 0.4026 r_free = 0.4026 target = 0.179306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.146467 restraints weight = 5505.896| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.28 r_work: 0.3462 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1776 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= 0.166 Angle : 0.599 6.683 6474 Z= 0.299 Chirality : 0.044 0.190 724 Planarity : 0.004 0.036 834 Dihedral : 5.452 55.352 656 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.00 % Allowed : 9.80 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.35), residues: 583 helix: 0.77 (0.32), residues: 285 sheet: 0.85 (0.80), residues: 45 loop : -0.25 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 99 HIS 0.004 0.001 HIS B 388 PHE 0.015 0.001 PHE B 386 TYR 0.009 0.001 TYR B 346 ARG 0.009 0.001 ARG B 460 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 189) hydrogen bonds : angle 4.89600 ( 531) covalent geometry : bond 0.00414 ( 4780) covalent geometry : angle 0.59861 ( 6474) *********************** 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: 10 poor density : 81 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: B 331 ILE cc_start: 0.8962 (tp) cc_final: 0.8438 (tp) REVERT: J 51 LYS cc_start: 0.7807 (ptmt) cc_final: 0.7567 (ptmm) REVERT: J 93 GLU cc_start: 0.7950 (mp0) cc_final: 0.6986 (mp0) outliers start: 10 outliers final: 3 residues processed: 88 average time/residue: 0.1644 time to fit residues: 19.5530 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 : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 402 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 49 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 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 = 0.4021 r_free = 0.4021 target = 0.178492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.145861 restraints weight = 5520.809| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.30 r_work: 0.3478 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1964 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= 0.164 Angle : 0.583 6.802 6474 Z= 0.290 Chirality : 0.044 0.192 724 Planarity : 0.004 0.038 834 Dihedral : 5.305 54.080 656 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.40 % Allowed : 11.60 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.35), residues: 583 helix: 0.81 (0.31), residues: 285 sheet: 0.85 (0.79), residues: 45 loop : -0.27 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 99 HIS 0.004 0.001 HIS B 326 PHE 0.019 0.001 PHE B 341 TYR 0.009 0.001 TYR B 346 ARG 0.010 0.001 ARG B 460 Details of bonding type rmsd hydrogen bonds : bond 0.03065 ( 189) hydrogen bonds : angle 4.76949 ( 531) covalent geometry : bond 0.00407 ( 4780) covalent geometry : angle 0.58252 ( 6474) *********************** 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 88 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: B 331 ILE cc_start: 0.8997 (tp) cc_final: 0.8489 (tp) REVERT: J 51 LYS cc_start: 0.7881 (ptmt) cc_final: 0.7600 (ptmm) REVERT: J 93 GLU cc_start: 0.7894 (mp0) cc_final: 0.7534 (mp0) outliers start: 12 outliers final: 6 residues processed: 82 average time/residue: 0.1740 time to fit residues: 18.5604 Evaluate side-chains 83 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 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 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 16 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 0.0470 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.180392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.148776 restraints weight = 5479.024| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.16 r_work: 0.3491 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2084 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= 0.135 Angle : 0.566 6.685 6474 Z= 0.281 Chirality : 0.043 0.186 724 Planarity : 0.004 0.038 834 Dihedral : 5.178 52.583 656 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.40 % Allowed : 12.80 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.35), residues: 583 helix: 0.94 (0.31), residues: 286 sheet: 0.92 (0.79), residues: 45 loop : -0.26 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 99 HIS 0.003 0.001 HIS B 326 PHE 0.014 0.001 PHE B 341 TYR 0.010 0.001 TYR B 439 ARG 0.010 0.001 ARG B 460 Details of bonding type rmsd hydrogen bonds : bond 0.02840 ( 189) hydrogen bonds : angle 4.61794 ( 531) covalent geometry : bond 0.00332 ( 4780) covalent geometry : angle 0.56627 ( 6474) *********************** 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 85 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: B 331 ILE cc_start: 0.8977 (tp) cc_final: 0.8473 (tp) REVERT: J 93 GLU cc_start: 0.7880 (mp0) cc_final: 0.7068 (mp0) outliers start: 12 outliers final: 9 residues processed: 78 average time/residue: 0.1932 time to fit residues: 20.1081 Evaluate side-chains 80 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Chi-restraints excluded: chain J residue 159 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 57 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 30 optimal weight: 0.0870 chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.178682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.146000 restraints weight = 5556.423| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.31 r_work: 0.3478 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4780 Z= 0.148 Angle : 0.575 6.693 6474 Z= 0.286 Chirality : 0.043 0.186 724 Planarity : 0.004 0.038 834 Dihedral : 5.189 51.943 656 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.40 % Allowed : 13.40 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.35), residues: 583 helix: 1.03 (0.31), residues: 280 sheet: 0.96 (0.79), residues: 45 loop : -0.18 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 99 HIS 0.004 0.001 HIS B 326 PHE 0.017 0.001 PHE B 341 TYR 0.011 0.001 TYR B 439 ARG 0.010 0.001 ARG B 460 Details of bonding type rmsd hydrogen bonds : bond 0.02877 ( 189) hydrogen bonds : angle 4.61382 ( 531) covalent geometry : bond 0.00366 ( 4780) covalent geometry : angle 0.57461 ( 6474) *********************** 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 85 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: B 331 ILE cc_start: 0.8965 (tp) cc_final: 0.8447 (tp) REVERT: C 389 ILE cc_start: 0.7799 (mt) cc_final: 0.7474 (mt) REVERT: J 65 ASP cc_start: 0.7592 (p0) cc_final: 0.7299 (p0) REVERT: J 93 GLU cc_start: 0.7856 (mp0) cc_final: 0.6992 (mp0) outliers start: 12 outliers final: 9 residues processed: 79 average time/residue: 0.1721 time to fit residues: 17.6642 Evaluate side-chains 82 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 33 optimal weight: 0.0050 chunk 15 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.180968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148813 restraints weight = 5484.143| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.29 r_work: 0.3497 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2282 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= 0.141 Angle : 0.579 6.621 6474 Z= 0.288 Chirality : 0.043 0.181 724 Planarity : 0.004 0.038 834 Dihedral : 5.145 51.887 656 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.80 % Allowed : 14.60 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.35), residues: 583 helix: 1.11 (0.32), residues: 280 sheet: 0.95 (0.79), residues: 45 loop : -0.19 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 409 HIS 0.003 0.001 HIS B 326 PHE 0.017 0.001 PHE B 341 TYR 0.012 0.001 TYR B 439 ARG 0.010 0.001 ARG B 460 Details of bonding type rmsd hydrogen bonds : bond 0.02859 ( 189) hydrogen bonds : angle 4.56844 ( 531) covalent geometry : bond 0.00346 ( 4780) covalent geometry : angle 0.57939 ( 6474) *********************** 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 89 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 331 ILE cc_start: 0.9040 (tp) cc_final: 0.8508 (tp) REVERT: C 389 ILE cc_start: 0.7997 (mt) cc_final: 0.7670 (mt) REVERT: J 93 GLU cc_start: 0.7882 (mp0) cc_final: 0.6931 (mp0) outliers start: 9 outliers final: 8 residues processed: 84 average time/residue: 0.1568 time to fit residues: 17.3438 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 : 0.551 ------------------------------------------------------------------------------- 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 95 ILE Chi-restraints excluded: chain J residue 157 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 32 optimal weight: 0.4980 chunk 21 optimal weight: 0.3980 chunk 41 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 14 optimal weight: 0.0970 chunk 55 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.180740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.148346 restraints weight = 5489.434| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.29 r_work: 0.3506 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2367 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= 0.124 Angle : 0.569 6.552 6474 Z= 0.282 Chirality : 0.042 0.179 724 Planarity : 0.004 0.038 834 Dihedral : 5.020 50.522 656 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.40 % Allowed : 14.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.35), residues: 583 helix: 1.23 (0.32), residues: 280 sheet: 1.13 (0.90), residues: 38 loop : -0.15 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 409 HIS 0.003 0.001 HIS B 326 PHE 0.013 0.001 PHE B 341 TYR 0.012 0.001 TYR B 439 ARG 0.006 0.000 ARG B 460 Details of bonding type rmsd hydrogen bonds : bond 0.02710 ( 189) hydrogen bonds : angle 4.52131 ( 531) covalent geometry : bond 0.00299 ( 4780) covalent geometry : angle 0.56892 ( 6474) *********************** 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 89 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: B 331 ILE cc_start: 0.8986 (tp) cc_final: 0.8470 (tp) REVERT: C 389 ILE cc_start: 0.7980 (mt) cc_final: 0.7642 (mt) REVERT: J 93 GLU cc_start: 0.7840 (mp0) cc_final: 0.6882 (mp0) outliers start: 12 outliers final: 10 residues processed: 83 average time/residue: 0.1522 time to fit residues: 16.6403 Evaluate side-chains 85 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 46 optimal weight: 4.9990 chunk 4 optimal weight: 0.2980 chunk 50 optimal weight: 0.0570 chunk 57 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 0.0470 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 overall best weight: 0.3196 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.184480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.152406 restraints weight = 5566.347| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.33 r_work: 0.3522 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2401 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= 0.114 Angle : 0.564 6.723 6474 Z= 0.281 Chirality : 0.042 0.175 724 Planarity : 0.004 0.038 834 Dihedral : 4.855 48.646 656 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.20 % Allowed : 15.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.36), residues: 583 helix: 1.34 (0.32), residues: 280 sheet: 1.43 (1.15), residues: 24 loop : -0.10 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 409 HIS 0.002 0.001 HIS B 326 PHE 0.012 0.001 PHE B 341 TYR 0.008 0.001 TYR B 346 ARG 0.010 0.001 ARG B 460 Details of bonding type rmsd hydrogen bonds : bond 0.02594 ( 189) hydrogen bonds : angle 4.44200 ( 531) covalent geometry : bond 0.00268 ( 4780) covalent geometry : angle 0.56373 ( 6474) *********************** 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 86 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 331 ILE cc_start: 0.8884 (tp) cc_final: 0.8365 (tp) REVERT: B 457 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6568 (tm-30) REVERT: C 389 ILE cc_start: 0.7688 (mt) cc_final: 0.7346 (mt) REVERT: J 158 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7680 (mt-10) outliers start: 11 outliers final: 9 residues processed: 80 average time/residue: 0.1577 time to fit residues: 16.6201 Evaluate side-chains 82 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 222 ASN Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 396 ASP 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 Chi-restraints excluded: chain J residue 157 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 44 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.178106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.145877 restraints weight = 5451.157| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.35 r_work: 0.3440 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4780 Z= 0.182 Angle : 0.620 6.689 6474 Z= 0.310 Chirality : 0.045 0.189 724 Planarity : 0.004 0.039 834 Dihedral : 5.167 49.560 656 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.60 % Allowed : 15.20 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.35), residues: 583 helix: 1.01 (0.31), residues: 281 sheet: 1.47 (1.16), residues: 24 loop : -0.18 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 99 HIS 0.004 0.001 HIS B 326 PHE 0.021 0.001 PHE B 341 TYR 0.015 0.001 TYR B 439 ARG 0.008 0.001 ARG B 460 Details of bonding type rmsd hydrogen bonds : bond 0.03104 ( 189) hydrogen bonds : angle 4.67674 ( 531) covalent geometry : bond 0.00449 ( 4780) covalent geometry : angle 0.61987 ( 6474) ********************** 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 85 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 331 ILE cc_start: 0.8985 (tp) cc_final: 0.8483 (tp) REVERT: B 457 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.6669 (tm-30) REVERT: J 158 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7871 (mt-10) outliers start: 13 outliers final: 9 residues processed: 80 average time/residue: 0.1634 time to fit residues: 17.2139 Evaluate side-chains 81 residues out of total 517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 396 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain C residue 383 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 chunk 28 optimal weight: 0.0470 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.181477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.149530 restraints weight = 5488.223| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.25 r_work: 0.3469 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2444 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= 0.142 Angle : 0.595 6.819 6474 Z= 0.298 Chirality : 0.044 0.173 724 Planarity : 0.004 0.039 834 Dihedral : 5.068 51.268 656 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.80 % Allowed : 16.00 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.35), residues: 583 helix: 1.10 (0.32), residues: 281 sheet: 1.43 (1.16), residues: 24 loop : -0.15 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 409 HIS 0.003 0.001 HIS B 326 PHE 0.015 0.001 PHE B 341 TYR 0.009 0.001 TYR B 346 ARG 0.009 0.001 ARG B 460 Details of bonding type rmsd hydrogen bonds : bond 0.02823 ( 189) hydrogen bonds : angle 4.58827 ( 531) covalent geometry : bond 0.00347 ( 4780) covalent geometry : angle 0.59495 ( 6474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3046.83 seconds wall clock time: 53 minutes 31.80 seconds (3211.80 seconds total)