Starting phenix.real_space_refine on Thu Jul 2 07:55:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ynb_73168/07_2026/9ynb_73168.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ynb_73168/07_2026/9ynb_73168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ynb_73168/07_2026/9ynb_73168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ynb_73168/07_2026/9ynb_73168.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ynb_73168/07_2026/9ynb_73168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ynb_73168/07_2026/9ynb_73168.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 4861 2.51 5 N 1207 2.21 5 O 1368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7462 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7462 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 21, 'TRANS': 883} Chain breaks: 6 Time building chain proxies: 1.20, per 1000 atoms: 0.16 Number of scatterers: 7462 At special positions: 0 Unit cell: (88, 75.9, 141.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1368 8.00 N 1207 7.00 C 4861 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: 0.41 Conformation dependent library (CDL) restraints added in 325.2 milliseconds 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 60.9% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 35 through 39 removed outlier: 3.507A pdb=" N ASN A 38 " --> pdb=" O VAL A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 227 through 236 removed outlier: 3.779A pdb=" N SER A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 271 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 276 through 309 Processing helix chain 'A' and resid 314 through 321 Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 337 through 351 removed outlier: 3.543A pdb=" N ILE A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 368 removed outlier: 4.097A pdb=" N ASP A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 440 Processing helix chain 'A' and resid 456 through 463 removed outlier: 3.948A pdb=" N TYR A 460 " --> pdb=" O ASN A 456 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR A 461 " --> pdb=" O PRO A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 491 removed outlier: 3.836A pdb=" N TYR A 490 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 491 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 506 removed outlier: 4.149A pdb=" N ASP A 503 " --> pdb=" O ILE A 499 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASP A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 514 Processing helix chain 'A' and resid 516 through 519 Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'A' and resid 530 through 535 Processing helix chain 'A' and resid 539 through 549 removed outlier: 3.617A pdb=" N GLN A 548 " --> pdb=" O LYS A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 563 Processing helix chain 'A' and resid 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 570 through 575 Processing helix chain 'A' and resid 637 through 650 removed outlier: 3.846A pdb=" N VAL A 641 " --> pdb=" O GLY A 637 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET A 642 " --> pdb=" O LEU A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 671 Processing helix chain 'A' and resid 685 through 700 removed outlier: 3.723A pdb=" N MET A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 715 removed outlier: 3.567A pdb=" N ILE A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 719 removed outlier: 3.577A pdb=" N LEU A 719 " --> pdb=" O ASN A 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 716 through 719' Processing helix chain 'A' and resid 731 through 737 Processing helix chain 'A' and resid 746 through 760 Processing helix chain 'A' and resid 763 through 786 removed outlier: 4.780A pdb=" N GLU A 769 " --> pdb=" O LYS A 765 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN A 770 " --> pdb=" O ILE A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1066 removed outlier: 3.524A pdb=" N ALA A1050 " --> pdb=" O THR A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1108 Processing helix chain 'A' and resid 1110 through 1121 removed outlier: 3.784A pdb=" N ILE A1114 " --> pdb=" O SER A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1139 Processing helix chain 'A' and resid 1147 through 1168 removed outlier: 3.759A pdb=" N LYS A1151 " --> pdb=" O TYR A1147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN A1168 " --> pdb=" O TYR A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1187 removed outlier: 4.428A pdb=" N TRP A1178 " --> pdb=" O ASN A1174 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN A1186 " --> pdb=" O ILE A1182 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN A1187 " --> pdb=" O PHE A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1197 Processing helix chain 'A' and resid 1198 through 1209 Processing helix chain 'A' and resid 1210 through 1212 No H-bonds generated for 'chain 'A' and resid 1210 through 1212' Processing helix chain 'A' and resid 1213 through 1228 Processing helix chain 'A' and resid 1232 through 1251 removed outlier: 3.600A pdb=" N ARG A1248 " --> pdb=" O SER A1244 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A1251 " --> pdb=" O HIS A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1267 Processing helix chain 'A' and resid 1268 through 1270 No H-bonds generated for 'chain 'A' and resid 1268 through 1270' Processing helix chain 'A' and resid 1271 through 1282 removed outlier: 4.174A pdb=" N ASN A1275 " --> pdb=" O PHE A1271 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A1276 " --> pdb=" O GLN A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1315 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 46 removed outlier: 5.174A pdb=" N LYS A 31 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR A 159 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TYR A 161 " --> pdb=" O HIS A 123 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N HIS A 123 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR A 163 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE A 121 " --> pdb=" O THR A 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 67 Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 131 Processing sheet with id=AA4, first strand: chain 'A' and resid 677 through 678 removed outlier: 3.512A pdb=" N LYS A 678 " --> pdb=" O ASP A 681 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1086 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: 1.25 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2300 1.35 - 1.46: 1804 1.46 - 1.58: 3468 1.58 - 1.70: 0 1.70 - 1.82: 42 Bond restraints: 7614 Sorted by residual: bond pdb=" C MET A 138 " pdb=" N PRO A 139 " ideal model delta sigma weight residual 1.328 1.368 -0.039 1.26e-02 6.30e+03 9.80e+00 bond pdb=" N ILE A 107 " pdb=" CA ILE A 107 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.14e-02 7.69e+03 9.55e+00 bond pdb=" N VAL A 106 " pdb=" CA VAL A 106 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.11e+00 bond pdb=" N PHE A 108 " pdb=" CA PHE A 108 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.21e-02 6.83e+03 6.29e+00 bond pdb=" C HIS A 63 " pdb=" N PRO A 64 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.38e-02 5.25e+03 5.87e+00 ... (remaining 7609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 10030 1.98 - 3.96: 203 3.96 - 5.94: 27 5.94 - 7.92: 8 7.92 - 9.90: 2 Bond angle restraints: 10270 Sorted by residual: angle pdb=" CA LYS A 95 " pdb=" CB LYS A 95 " pdb=" CG LYS A 95 " ideal model delta sigma weight residual 114.10 121.48 -7.38 2.00e+00 2.50e-01 1.36e+01 angle pdb=" CA LEU A 491 " pdb=" C LEU A 491 " pdb=" N PRO A 492 " ideal model delta sigma weight residual 118.44 123.98 -5.54 1.59e+00 3.96e-01 1.21e+01 angle pdb=" CB MET A 167 " pdb=" CG MET A 167 " pdb=" SD MET A 167 " ideal model delta sigma weight residual 112.70 122.60 -9.90 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N GLY A1196 " pdb=" CA GLY A1196 " pdb=" C GLY A1196 " ideal model delta sigma weight residual 112.50 116.05 -3.55 1.16e+00 7.43e-01 9.38e+00 angle pdb=" N LYS A1209 " pdb=" CA LYS A1209 " pdb=" C LYS A1209 " ideal model delta sigma weight residual 109.81 116.35 -6.54 2.21e+00 2.05e-01 8.75e+00 ... (remaining 10265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 4117 17.78 - 35.56: 404 35.56 - 53.33: 75 53.33 - 71.11: 17 71.11 - 88.89: 6 Dihedral angle restraints: 4619 sinusoidal: 1899 harmonic: 2720 Sorted by residual: dihedral pdb=" CA SER A 81 " pdb=" C SER A 81 " pdb=" N PHE A 82 " pdb=" CA PHE A 82 " ideal model delta harmonic sigma weight residual 180.00 -149.15 -30.85 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" CA THR A 128 " pdb=" C THR A 128 " pdb=" N TRP A 129 " pdb=" CA TRP A 129 " ideal model delta harmonic sigma weight residual 180.00 155.48 24.52 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA CYS A 144 " pdb=" C CYS A 144 " pdb=" N ASN A 145 " pdb=" CA ASN A 145 " ideal model delta harmonic sigma weight residual -180.00 -159.77 -20.23 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 4616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 911 0.051 - 0.102: 202 0.102 - 0.153: 41 0.153 - 0.205: 9 0.205 - 0.256: 1 Chirality restraints: 1164 Sorted by residual: chirality pdb=" CB ILE A 330 " pdb=" CA ILE A 330 " pdb=" CG1 ILE A 330 " pdb=" CG2 ILE A 330 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB ILE A 72 " pdb=" CA ILE A 72 " pdb=" CG1 ILE A 72 " pdb=" CG2 ILE A 72 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE A 75 " pdb=" CA ILE A 75 " pdb=" CG1 ILE A 75 " pdb=" CG2 ILE A 75 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.05e-01 ... (remaining 1161 not shown) Planarity restraints: 1270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 163 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO A 164 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 490 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.18e+00 pdb=" C TYR A 490 " -0.035 2.00e-02 2.50e+03 pdb=" O TYR A 490 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 491 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A1207 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" CD GLU A1207 " -0.029 2.00e-02 2.50e+03 pdb=" OE1 GLU A1207 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU A1207 " 0.010 2.00e-02 2.50e+03 ... (remaining 1267 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 960 2.76 - 3.29: 7351 3.29 - 3.83: 12291 3.83 - 4.36: 14182 4.36 - 4.90: 24564 Nonbonded interactions: 59348 Sorted by model distance: nonbonded pdb=" OE1 GLU A 32 " pdb=" NE2 HIS A 44 " model vdw 2.221 3.120 nonbonded pdb=" OH TYR A1308 " pdb=" OD1 ASP A1318 " model vdw 2.241 3.040 nonbonded pdb=" O ASN A1221 " pdb=" OG1 THR A1225 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR A 317 " pdb=" O ASP A 370 " model vdw 2.265 3.040 nonbonded pdb=" NH1 ARG A1061 " pdb=" O ILE A1120 " model vdw 2.297 3.120 ... (remaining 59343 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.520 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 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 : 0.003 0.039 7614 Z= 0.167 Angle : 0.690 9.901 10270 Z= 0.377 Chirality : 0.046 0.256 1164 Planarity : 0.004 0.060 1270 Dihedral : 14.791 88.889 2851 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.24 % Allowed : 0.60 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.27), residues: 891 helix: 1.28 (0.23), residues: 464 sheet: 0.07 (0.98), residues: 33 loop : -1.95 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 563 TYR 0.022 0.001 TYR A 55 PHE 0.012 0.001 PHE A 653 TRP 0.020 0.002 TRP A 129 HIS 0.007 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.17 ( 7614) covalent geometry : angle 0.68951 / 0.38 (10270) hydrogen bonds : bond 0.13605 / 9.26 ( 372) hydrogen bonds : angle 5.17692 / 3.52 ( 1086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.195 Fit side-chains REVERT: A 69 MET cc_start: 0.3551 (tmm) cc_final: 0.3207 (tmm) REVERT: A 114 TRP cc_start: 0.5912 (t60) cc_final: 0.5401 (t60) REVERT: A 785 TYR cc_start: 0.4714 (m-10) cc_final: 0.3807 (m-10) REVERT: A 1063 MET cc_start: 0.6752 (mtp) cc_final: 0.6242 (mtp) outliers start: 2 outliers final: 1 residues processed: 120 average time/residue: 0.0741 time to fit residues: 11.9556 Evaluate side-chains 87 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 HIS ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 HIS A 721 ASN ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.208606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.197981 restraints weight = 8062.955| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 0.52 r_work: 0.3954 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7614 Z= 0.210 Angle : 0.708 9.959 10270 Z= 0.373 Chirality : 0.046 0.169 1164 Planarity : 0.005 0.066 1270 Dihedral : 5.766 38.046 976 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.19 % Allowed : 8.95 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.28), residues: 891 helix: 1.13 (0.23), residues: 471 sheet: -0.32 (0.98), residues: 33 loop : -1.99 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 76 TYR 0.028 0.002 TYR A 696 PHE 0.018 0.002 PHE A 730 TRP 0.015 0.003 TRP A 507 HIS 0.007 0.002 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 ( 7614) covalent geometry : angle 0.70773 / 0.37 (10270) hydrogen bonds : bond 0.06010 / 3.99 ( 372) hydrogen bonds : angle 4.71590 / 3.26 ( 1086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.198 Fit side-chains REVERT: A 69 MET cc_start: 0.4058 (tmm) cc_final: 0.2965 (tmm) REVERT: A 1276 LYS cc_start: 0.7332 (mtpt) cc_final: 0.6869 (mttp) outliers start: 10 outliers final: 7 residues processed: 105 average time/residue: 0.0796 time to fit residues: 11.1152 Evaluate side-chains 99 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 1070 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 73 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 0.0270 chunk 49 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 HIS A 47 GLN ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN A1184 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.213991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.204065 restraints weight = 7965.934| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 0.49 r_work: 0.4028 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7614 Z= 0.123 Angle : 0.564 7.776 10270 Z= 0.304 Chirality : 0.041 0.161 1164 Planarity : 0.004 0.057 1270 Dihedral : 5.173 28.434 976 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.67 % Allowed : 11.69 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.28), residues: 891 helix: 1.51 (0.24), residues: 471 sheet: -0.43 (0.92), residues: 33 loop : -1.91 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 76 TYR 0.017 0.001 TYR A 696 PHE 0.011 0.001 PHE A 249 TRP 0.018 0.002 TRP A 507 HIS 0.004 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 7614) covalent geometry : angle 0.56379 / 0.30 (10270) hydrogen bonds : bond 0.04570 / 3.02 ( 372) hydrogen bonds : angle 4.33178 / 3.01 ( 1086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.263 Fit side-chains REVERT: A 38 ASN cc_start: 0.6480 (m110) cc_final: 0.6182 (m110) REVERT: A 162 HIS cc_start: 0.7567 (OUTLIER) cc_final: 0.7003 (m-70) REVERT: A 632 ASN cc_start: 0.5843 (t0) cc_final: 0.5525 (m-40) REVERT: A 1129 ASP cc_start: 0.5698 (t0) cc_final: 0.5452 (t70) outliers start: 14 outliers final: 8 residues processed: 102 average time/residue: 0.0764 time to fit residues: 10.5195 Evaluate side-chains 94 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 1070 THR Chi-restraints excluded: chain A residue 1240 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 11 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 0.3980 chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 HIS ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN A1051 ASN A1131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.206511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.191086 restraints weight = 8045.809| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 1.08 r_work: 0.3833 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7614 Z= 0.184 Angle : 0.654 9.429 10270 Z= 0.345 Chirality : 0.045 0.278 1164 Planarity : 0.005 0.059 1270 Dihedral : 5.404 28.946 974 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.27 % Allowed : 13.84 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.28), residues: 891 helix: 1.31 (0.24), residues: 472 sheet: -0.27 (0.73), residues: 48 loop : -2.04 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 76 TYR 0.029 0.002 TYR A 696 PHE 0.015 0.002 PHE A 249 TRP 0.015 0.002 TRP A 507 HIS 0.006 0.002 HIS A1184 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 7614) covalent geometry : angle 0.65415 / 0.35 (10270) hydrogen bonds : bond 0.05599 / 3.69 ( 372) hydrogen bonds : angle 4.63657 / 3.23 ( 1086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.237 Fit side-chains REVERT: A 69 MET cc_start: 0.5886 (tmm) cc_final: 0.4659 (ttt) REVERT: A 145 ASN cc_start: 0.6369 (m110) cc_final: 0.6065 (m-40) REVERT: A 162 HIS cc_start: 0.7836 (OUTLIER) cc_final: 0.7275 (m-70) REVERT: A 489 CYS cc_start: 0.5974 (m) cc_final: 0.5676 (m) REVERT: A 1301 LEU cc_start: 0.6891 (mp) cc_final: 0.6645 (mp) outliers start: 19 outliers final: 12 residues processed: 116 average time/residue: 0.0687 time to fit residues: 10.9405 Evaluate side-chains 112 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 1070 THR Chi-restraints excluded: chain A residue 1240 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 33 optimal weight: 0.0470 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 HIS ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.208766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.191029 restraints weight = 8092.491| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 1.28 r_work: 0.3833 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7614 Z= 0.143 Angle : 0.593 7.707 10270 Z= 0.317 Chirality : 0.042 0.192 1164 Planarity : 0.004 0.057 1270 Dihedral : 5.204 27.270 974 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.51 % Allowed : 15.63 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.28), residues: 891 helix: 1.47 (0.24), residues: 469 sheet: -0.73 (0.85), residues: 39 loop : -1.95 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 76 TYR 0.019 0.001 TYR A 696 PHE 0.015 0.001 PHE A 87 TRP 0.017 0.002 TRP A 507 HIS 0.005 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 7614) covalent geometry : angle 0.59287 / 0.32 (10270) hydrogen bonds : bond 0.04869 / 3.21 ( 372) hydrogen bonds : angle 4.47023 / 3.11 ( 1086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.202 Fit side-chains REVERT: A 69 MET cc_start: 0.5562 (tmm) cc_final: 0.4490 (ttt) REVERT: A 145 ASN cc_start: 0.6132 (m110) cc_final: 0.5850 (m-40) REVERT: A 162 HIS cc_start: 0.7729 (OUTLIER) cc_final: 0.7111 (m-70) REVERT: A 333 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6680 (tm130) REVERT: A 470 ARG cc_start: 0.7461 (ttt-90) cc_final: 0.7220 (ptm-80) REVERT: A 632 ASN cc_start: 0.5914 (t0) cc_final: 0.5490 (m-40) outliers start: 21 outliers final: 12 residues processed: 116 average time/residue: 0.0608 time to fit residues: 9.9214 Evaluate side-chains 107 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 1070 THR Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1256 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 66 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 HIS ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.209417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.192800 restraints weight = 7962.104| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 1.29 r_work: 0.3853 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7614 Z= 0.142 Angle : 0.594 8.074 10270 Z= 0.319 Chirality : 0.042 0.203 1164 Planarity : 0.004 0.059 1270 Dihedral : 5.165 26.836 974 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.74 % Allowed : 16.23 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.28), residues: 891 helix: 1.51 (0.24), residues: 469 sheet: -0.83 (0.84), residues: 39 loop : -1.92 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 76 TYR 0.019 0.001 TYR A 696 PHE 0.013 0.001 PHE A 87 TRP 0.017 0.002 TRP A 507 HIS 0.005 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 7614) covalent geometry : angle 0.59440 / 0.32 (10270) hydrogen bonds : bond 0.04818 / 3.18 ( 372) hydrogen bonds : angle 4.45008 / 3.09 ( 1086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.167 Fit side-chains REVERT: A 69 MET cc_start: 0.5275 (tmm) cc_final: 0.4311 (ttt) REVERT: A 145 ASN cc_start: 0.6135 (m110) cc_final: 0.5900 (m-40) REVERT: A 162 HIS cc_start: 0.7657 (OUTLIER) cc_final: 0.7011 (m-70) REVERT: A 333 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6672 (tm130) REVERT: A 470 ARG cc_start: 0.7453 (ttt-90) cc_final: 0.7241 (ptm-80) REVERT: A 490 TYR cc_start: 0.7122 (m-80) cc_final: 0.6568 (m-80) REVERT: A 632 ASN cc_start: 0.5813 (t0) cc_final: 0.5458 (m-40) REVERT: A 1129 ASP cc_start: 0.5844 (t0) cc_final: 0.5543 (t70) REVERT: A 1208 LEU cc_start: 0.5214 (OUTLIER) cc_final: 0.4337 (mm) outliers start: 23 outliers final: 15 residues processed: 114 average time/residue: 0.0676 time to fit residues: 10.5721 Evaluate side-chains 117 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 1070 THR Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1256 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 HIS ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.210154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.193313 restraints weight = 8082.460| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 1.53 r_work: 0.3877 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7614 Z= 0.134 Angle : 0.581 8.130 10270 Z= 0.313 Chirality : 0.042 0.218 1164 Planarity : 0.004 0.058 1270 Dihedral : 5.084 26.065 974 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.74 % Allowed : 16.59 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.28), residues: 891 helix: 1.55 (0.24), residues: 470 sheet: -1.03 (0.80), residues: 39 loop : -1.91 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 76 TYR 0.017 0.001 TYR A 696 PHE 0.014 0.001 PHE A 87 TRP 0.017 0.002 TRP A 507 HIS 0.005 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 7614) covalent geometry : angle 0.58073 / 0.31 (10270) hydrogen bonds : bond 0.04650 / 3.07 ( 372) hydrogen bonds : angle 4.41688 / 3.07 ( 1086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.312 Fit side-chains REVERT: A 69 MET cc_start: 0.5073 (tmm) cc_final: 0.4300 (ttt) REVERT: A 162 HIS cc_start: 0.7652 (OUTLIER) cc_final: 0.6980 (m-70) REVERT: A 259 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7392 (mttp) REVERT: A 333 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.6649 (tm130) REVERT: A 489 CYS cc_start: 0.6276 (m) cc_final: 0.6001 (m) REVERT: A 490 TYR cc_start: 0.7144 (m-80) cc_final: 0.6562 (m-80) REVERT: A 632 ASN cc_start: 0.5622 (t0) cc_final: 0.5344 (m-40) REVERT: A 1129 ASP cc_start: 0.5747 (t0) cc_final: 0.5446 (t70) REVERT: A 1208 LEU cc_start: 0.5105 (OUTLIER) cc_final: 0.4262 (mm) outliers start: 23 outliers final: 16 residues processed: 116 average time/residue: 0.0847 time to fit residues: 13.7361 Evaluate side-chains 120 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 1070 THR Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1256 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 56 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 HIS ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 ASN A 660 ASN A1131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.203220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.192304 restraints weight = 8188.935| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 0.55 r_work: 0.3907 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 7614 Z= 0.243 Angle : 0.734 9.399 10270 Z= 0.388 Chirality : 0.048 0.229 1164 Planarity : 0.005 0.060 1270 Dihedral : 5.677 30.112 974 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.58 % Allowed : 16.95 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.27), residues: 891 helix: 1.07 (0.23), residues: 470 sheet: -1.08 (0.67), residues: 48 loop : -2.15 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 76 TYR 0.033 0.002 TYR A 696 PHE 0.019 0.002 PHE A 87 TRP 0.014 0.003 TRP A1027 HIS 0.007 0.002 HIS A1184 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.24 ( 7614) covalent geometry : angle 0.73376 / 0.39 (10270) hydrogen bonds : bond 0.06214 / 4.11 ( 372) hydrogen bonds : angle 4.94054 / 3.43 ( 1086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.305 Fit side-chains REVERT: A 69 MET cc_start: 0.4367 (tmm) cc_final: 0.3987 (ttt) REVERT: A 78 LYS cc_start: 0.6542 (mptt) cc_final: 0.5764 (tppt) REVERT: A 162 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.6877 (m90) REVERT: A 333 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6825 (tm130) REVERT: A 490 TYR cc_start: 0.7033 (m-80) cc_final: 0.6660 (m-80) REVERT: A 1129 ASP cc_start: 0.5661 (t0) cc_final: 0.5404 (t70) REVERT: A 1208 LEU cc_start: 0.5314 (OUTLIER) cc_final: 0.4481 (mm) REVERT: A 1246 TYR cc_start: 0.4843 (m-10) cc_final: 0.4557 (m-10) REVERT: A 1301 LEU cc_start: 0.7097 (mp) cc_final: 0.6869 (mp) outliers start: 30 outliers final: 21 residues processed: 129 average time/residue: 0.0960 time to fit residues: 16.9409 Evaluate side-chains 129 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 632 ASN Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1070 THR Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1256 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.5980 chunk 3 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 54 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 HIS ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 HIS ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.207523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.190058 restraints weight = 8085.265| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 1.23 r_work: 0.3815 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7614 Z= 0.145 Angle : 0.625 8.380 10270 Z= 0.335 Chirality : 0.044 0.234 1164 Planarity : 0.004 0.060 1270 Dihedral : 5.317 27.130 974 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.74 % Allowed : 17.54 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.28), residues: 891 helix: 1.36 (0.24), residues: 470 sheet: -1.23 (0.77), residues: 39 loop : -2.08 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 76 TYR 0.018 0.001 TYR A 696 PHE 0.015 0.001 PHE A 87 TRP 0.018 0.002 TRP A 507 HIS 0.010 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 7614) covalent geometry : angle 0.62483 / 0.34 (10270) hydrogen bonds : bond 0.04983 / 3.30 ( 372) hydrogen bonds : angle 4.64966 / 3.23 ( 1086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.297 Fit side-chains REVERT: A 28 HIS cc_start: 0.6454 (m-70) cc_final: 0.6040 (m170) REVERT: A 69 MET cc_start: 0.4979 (tmm) cc_final: 0.4216 (ttt) REVERT: A 162 HIS cc_start: 0.7332 (OUTLIER) cc_final: 0.6241 (m90) REVERT: A 490 TYR cc_start: 0.7251 (m-80) cc_final: 0.6727 (m-80) REVERT: A 632 ASN cc_start: 0.5799 (t0) cc_final: 0.5277 (m-40) REVERT: A 1208 LEU cc_start: 0.5348 (OUTLIER) cc_final: 0.4432 (mm) REVERT: A 1246 TYR cc_start: 0.4804 (m-10) cc_final: 0.4561 (m-10) REVERT: A 1301 LEU cc_start: 0.6918 (mp) cc_final: 0.6716 (mp) outliers start: 23 outliers final: 16 residues processed: 123 average time/residue: 0.0836 time to fit residues: 14.2604 Evaluate side-chains 123 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1070 THR Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1256 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 HIS ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.207465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.189867 restraints weight = 8107.998| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 1.18 r_work: 0.3815 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7614 Z= 0.160 Angle : 0.640 8.227 10270 Z= 0.343 Chirality : 0.045 0.257 1164 Planarity : 0.004 0.061 1270 Dihedral : 5.297 27.255 974 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.86 % Allowed : 17.42 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.28), residues: 891 helix: 1.36 (0.24), residues: 470 sheet: -1.28 (0.75), residues: 39 loop : -2.07 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 76 TYR 0.020 0.001 TYR A 696 PHE 0.016 0.002 PHE A 87 TRP 0.016 0.002 TRP A 507 HIS 0.006 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 7614) covalent geometry : angle 0.63955 / 0.34 (10270) hydrogen bonds : bond 0.05054 / 3.35 ( 372) hydrogen bonds : angle 4.67652 / 3.24 ( 1086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.174 Fit side-chains REVERT: A 28 HIS cc_start: 0.6519 (m-70) cc_final: 0.6117 (m170) REVERT: A 69 MET cc_start: 0.4979 (tmm) cc_final: 0.4203 (ttt) REVERT: A 162 HIS cc_start: 0.7563 (OUTLIER) cc_final: 0.6464 (m90) REVERT: A 258 GLU cc_start: 0.7744 (mp0) cc_final: 0.7443 (pt0) REVERT: A 333 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6726 (tm130) REVERT: A 490 TYR cc_start: 0.7198 (m-80) cc_final: 0.6683 (m-80) REVERT: A 632 ASN cc_start: 0.5751 (t0) cc_final: 0.5145 (m-40) REVERT: A 1208 LEU cc_start: 0.5135 (OUTLIER) cc_final: 0.4213 (mm) REVERT: A 1301 LEU cc_start: 0.6922 (mp) cc_final: 0.6717 (mp) outliers start: 24 outliers final: 17 residues processed: 125 average time/residue: 0.0774 time to fit residues: 13.3529 Evaluate side-chains 126 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 1028 VAL Chi-restraints excluded: chain A residue 1070 THR Chi-restraints excluded: chain A residue 1107 ASN Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1240 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 3 optimal weight: 0.0370 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 ASN ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 HIS ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.208922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.192626 restraints weight = 8048.625| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 1.43 r_work: 0.3850 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7614 Z= 0.142 Angle : 0.619 8.982 10270 Z= 0.333 Chirality : 0.044 0.222 1164 Planarity : 0.004 0.061 1270 Dihedral : 5.214 26.107 974 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.63 % Allowed : 18.02 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.28), residues: 891 helix: 1.42 (0.24), residues: 467 sheet: -1.16 (0.76), residues: 39 loop : -2.04 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 76 TYR 0.017 0.001 TYR A 696 PHE 0.015 0.001 PHE A 87 TRP 0.018 0.002 TRP A 507 HIS 0.006 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 7614) covalent geometry : angle 0.61946 / 0.33 (10270) hydrogen bonds : bond 0.04742 / 3.13 ( 372) hydrogen bonds : angle 4.58242 / 3.17 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1436.63 seconds wall clock time: 25 minutes 36.90 seconds (1536.90 seconds total)