Starting phenix.real_space_refine on Wed Sep 17 13:51:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9juj_61827/09_2025/9juj_61827.cif Found real_map, /net/cci-nas-00/data/ceres_data/9juj_61827/09_2025/9juj_61827.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9juj_61827/09_2025/9juj_61827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9juj_61827/09_2025/9juj_61827.map" model { file = "/net/cci-nas-00/data/ceres_data/9juj_61827/09_2025/9juj_61827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9juj_61827/09_2025/9juj_61827.cif" } 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= 0.003 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 41 5.16 5 C 5736 2.51 5 N 1543 2.21 5 O 1651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8971 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1165, 8971 Classifications: {'peptide': 1165} Link IDs: {'PTRANS': 30, 'TRANS': 1134} Chain breaks: 1 Time building chain proxies: 2.09, per 1000 atoms: 0.23 Number of scatterers: 8971 At special positions: 0 Unit cell: (106.02, 102.3, 123.69, 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 41 16.00 O 1651 8.00 N 1543 7.00 C 5736 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: 0.85 Conformation dependent library (CDL) restraints added in 354.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 6 sheets defined 66.5% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 37 through 75 removed outlier: 4.031A pdb=" N LEU A 58 " --> pdb=" O HIS A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix removed outlier: 3.871A pdb=" N ASN A 75 " --> pdb=" O SER A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 133 Processing helix chain 'A' and resid 134 through 140 removed outlier: 3.672A pdb=" N PHE A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 158 removed outlier: 4.921A pdb=" N ALA A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VAL A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 187 Processing helix chain 'A' and resid 187 through 236 Proline residue: A 199 - end of helix Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 245 through 299 Processing helix chain 'A' and resid 303 through 347 Proline residue: A 326 - end of helix removed outlier: 3.557A pdb=" N HIS A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.712A pdb=" N ARG A 353 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN A 354 " --> pdb=" O ILE A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 354' Processing helix chain 'A' and resid 409 through 417 removed outlier: 3.751A pdb=" N VAL A 413 " --> pdb=" O LYS A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 472 through 483 removed outlier: 3.711A pdb=" N ALA A 480 " --> pdb=" O ILE A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 491 Processing helix chain 'A' and resid 509 through 523 Processing helix chain 'A' and resid 540 through 546 Processing helix chain 'A' and resid 678 through 693 removed outlier: 4.240A pdb=" N GLN A 682 " --> pdb=" O ALA A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 729 removed outlier: 3.558A pdb=" N TYR A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 785 Processing helix chain 'A' and resid 788 through 794 removed outlier: 3.638A pdb=" N PHE A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 842 Processing helix chain 'A' and resid 845 through 852 Processing helix chain 'A' and resid 852 through 869 Processing helix chain 'A' and resid 873 through 878 removed outlier: 4.009A pdb=" N HIS A 878 " --> pdb=" O LEU A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 891 Processing helix chain 'A' and resid 891 through 899 Processing helix chain 'A' and resid 900 through 954 Proline residue: A 914 - end of helix Processing helix chain 'A' and resid 958 through 1001 Proline residue: A 984 - end of helix Processing helix chain 'A' and resid 1067 through 1073 removed outlier: 3.634A pdb=" N ILE A1072 " --> pdb=" O VAL A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1100 Processing helix chain 'A' and resid 1116 through 1124 removed outlier: 3.523A pdb=" N HIS A1124 " --> pdb=" O ILE A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1139 Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'A' and resid 1164 through 1180 removed outlier: 3.660A pdb=" N LYS A1180 " --> pdb=" O ALA A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1212 removed outlier: 3.917A pdb=" N ARG A1212 " --> pdb=" O ALA A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1255 removed outlier: 3.613A pdb=" N GLY A1254 " --> pdb=" O ASN A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1264 removed outlier: 3.788A pdb=" N MET A1259 " --> pdb=" O ILE A1255 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 370 Processing sheet with id=AA2, first strand: chain 'A' and resid 399 through 401 removed outlier: 6.157A pdb=" N ILE A 399 " --> pdb=" O THR A 558 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 446 through 449 removed outlier: 3.840A pdb=" N VAL A 449 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 577 through 578 Processing sheet with id=AA5, first strand: chain 'A' and resid 1045 through 1048 removed outlier: 5.435A pdb=" N LEU A1045 " --> pdb=" O HIS A1028 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1102 through 1103 removed outlier: 5.980A pdb=" N ALA A1103 " --> pdb=" O LEU A1185 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1791 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: 1.54 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2945 1.35 - 1.47: 1984 1.47 - 1.59: 4140 1.59 - 1.71: 0 1.71 - 1.84: 68 Bond restraints: 9137 Sorted by residual: bond pdb=" N VAL A 235 " pdb=" CA VAL A 235 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.55e+00 bond pdb=" N VAL A 239 " pdb=" CA VAL A 239 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.88e+00 bond pdb=" N VAL A 203 " pdb=" CA VAL A 203 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.79e+00 bond pdb=" N VAL A 230 " pdb=" CA VAL A 230 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.75e+00 bond pdb=" N ILE A 204 " pdb=" CA ILE A 204 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 8.05e+00 ... (remaining 9132 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 11893 2.07 - 4.13: 437 4.13 - 6.20: 33 6.20 - 8.26: 2 8.26 - 10.33: 1 Bond angle restraints: 12366 Sorted by residual: angle pdb=" C THR A1128 " pdb=" CA THR A1128 " pdb=" CB THR A1128 " ideal model delta sigma weight residual 116.54 112.04 4.50 1.15e+00 7.56e-01 1.53e+01 angle pdb=" C ASN A 484 " pdb=" CA ASN A 484 " pdb=" CB ASN A 484 " ideal model delta sigma weight residual 116.34 110.87 5.47 1.40e+00 5.10e-01 1.53e+01 angle pdb=" CA GLU A1150 " pdb=" CB GLU A1150 " pdb=" CG GLU A1150 " ideal model delta sigma weight residual 114.10 121.27 -7.17 2.00e+00 2.50e-01 1.29e+01 angle pdb=" CB MET A 157 " pdb=" CG MET A 157 " pdb=" SD MET A 157 " ideal model delta sigma weight residual 112.70 102.37 10.33 3.00e+00 1.11e-01 1.18e+01 angle pdb=" N ILE A 201 " pdb=" CA ILE A 201 " pdb=" C ILE A 201 " ideal model delta sigma weight residual 110.62 107.23 3.39 1.02e+00 9.61e-01 1.10e+01 ... (remaining 12361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4919 17.93 - 35.85: 442 35.85 - 53.78: 69 53.78 - 71.70: 26 71.70 - 89.62: 7 Dihedral angle restraints: 5463 sinusoidal: 2109 harmonic: 3354 Sorted by residual: dihedral pdb=" CA ARG A 844 " pdb=" C ARG A 844 " pdb=" N LEU A 845 " pdb=" CA LEU A 845 " ideal model delta harmonic sigma weight residual 180.00 162.25 17.75 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA PHE A 552 " pdb=" C PHE A 552 " pdb=" N MET A 553 " pdb=" CA MET A 553 " ideal model delta harmonic sigma weight residual -180.00 -163.24 -16.76 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" C ILE A 341 " pdb=" N ILE A 341 " pdb=" CA ILE A 341 " pdb=" CB ILE A 341 " ideal model delta harmonic sigma weight residual -122.00 -130.26 8.26 0 2.50e+00 1.60e-01 1.09e+01 ... (remaining 5460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1221 0.069 - 0.138: 172 0.138 - 0.206: 32 0.206 - 0.275: 2 0.275 - 0.344: 1 Chirality restraints: 1428 Sorted by residual: chirality pdb=" CB ILE A 341 " pdb=" CA ILE A 341 " pdb=" CG1 ILE A 341 " pdb=" CG2 ILE A 341 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CB VAL A 235 " pdb=" CA VAL A 235 " pdb=" CG1 VAL A 235 " pdb=" CG2 VAL A 235 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ILE A 201 " pdb=" N ILE A 201 " pdb=" C ILE A 201 " pdb=" CB ILE A 201 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1425 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 238 " 0.235 9.50e-02 1.11e+02 1.05e-01 6.79e+00 pdb=" NE ARG A 238 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 238 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 238 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 238 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 721 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C LEU A 721 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU A 721 " 0.011 2.00e-02 2.50e+03 pdb=" N SER A 722 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 711 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C GLY A 711 " 0.028 2.00e-02 2.50e+03 pdb=" O GLY A 711 " -0.010 2.00e-02 2.50e+03 pdb=" N SER A 712 " -0.009 2.00e-02 2.50e+03 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1100 2.75 - 3.29: 9959 3.29 - 3.83: 15785 3.83 - 4.36: 18071 4.36 - 4.90: 30413 Nonbonded interactions: 75328 Sorted by model distance: nonbonded pdb=" OE1 GLU A 116 " pdb=" NE2 GLN A 159 " model vdw 2.215 3.120 nonbonded pdb=" O TRP A 441 " pdb=" NE2 GLN A 445 " model vdw 2.249 3.120 nonbonded pdb=" NE2 GLN A 842 " pdb=" O TRP A 843 " model vdw 2.257 3.120 nonbonded pdb=" O GLY A1254 " pdb=" NH1 ARG A1258 " model vdw 2.262 3.120 nonbonded pdb=" NH2 ARG A 123 " pdb=" O ILE A 151 " model vdw 2.271 3.120 ... (remaining 75323 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: 0.860 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.530 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 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 : 0.005 0.060 9137 Z= 0.334 Angle : 0.760 10.327 12366 Z= 0.521 Chirality : 0.051 0.344 1428 Planarity : 0.005 0.105 1572 Dihedral : 14.448 89.625 3305 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.21 % Allowed : 1.16 % Favored : 98.63 % 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 aren not related in a simple way. whole: 0.13 (0.24), residues: 1161 helix: 1.17 (0.19), residues: 749 sheet: -0.22 (1.26), residues: 25 loop : -2.11 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 569 TYR 0.016 0.001 TYR A 908 PHE 0.024 0.001 PHE A 552 TRP 0.013 0.001 TRP A 188 HIS 0.009 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 9137) covalent geometry : angle 0.76043 (12366) hydrogen bonds : bond 0.11949 ( 603) hydrogen bonds : angle 5.41510 ( 1791) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.7108 (mt) cc_final: 0.6565 (mm) REVERT: A 162 ILE cc_start: 0.7938 (pt) cc_final: 0.7687 (pt) REVERT: A 273 MET cc_start: 0.6642 (mmm) cc_final: 0.6250 (mtm) REVERT: A 442 LEU cc_start: 0.6467 (mp) cc_final: 0.5741 (tp) REVERT: A 511 GLN cc_start: 0.4254 (tp-100) cc_final: 0.3535 (tp-100) REVERT: A 736 MET cc_start: 0.6061 (ttp) cc_final: 0.5788 (ttp) REVERT: A 1114 THR cc_start: 0.6996 (t) cc_final: 0.6493 (p) REVERT: A 1118 GLU cc_start: 0.7115 (pt0) cc_final: 0.6347 (tm-30) outliers start: 2 outliers final: 1 residues processed: 166 average time/residue: 0.1123 time to fit residues: 24.4970 Evaluate side-chains 95 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0010 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.9166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 445 GLN A 506 GLN A 682 GLN A 797 ASN A 911 ASN A1073 GLN A1246 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.238928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.176217 restraints weight = 9529.309| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 1.75 r_work: 0.4025 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3916 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9137 Z= 0.152 Angle : 0.586 8.180 12366 Z= 0.315 Chirality : 0.040 0.154 1428 Planarity : 0.004 0.035 1572 Dihedral : 4.369 57.425 1256 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.00 % Allowed : 9.27 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.25), residues: 1161 helix: 1.65 (0.19), residues: 754 sheet: -0.62 (1.23), residues: 25 loop : -1.87 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1199 TYR 0.021 0.002 TYR A 295 PHE 0.025 0.002 PHE A 552 TRP 0.012 0.001 TRP A 441 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9137) covalent geometry : angle 0.58636 (12366) hydrogen bonds : bond 0.04843 ( 603) hydrogen bonds : angle 4.19454 ( 1791) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7849 (ptpp) cc_final: 0.7511 (mttp) REVERT: A 273 MET cc_start: 0.7720 (mmm) cc_final: 0.7076 (mtp) REVERT: A 442 LEU cc_start: 0.6794 (mp) cc_final: 0.6000 (tp) REVERT: A 470 ASP cc_start: 0.8042 (m-30) cc_final: 0.7793 (m-30) REVERT: A 511 GLN cc_start: 0.4753 (tp-100) cc_final: 0.3963 (tp-100) REVERT: A 997 PHE cc_start: 0.6990 (m-10) cc_final: 0.6631 (m-80) REVERT: A 1001 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7572 (m-30) outliers start: 19 outliers final: 9 residues processed: 131 average time/residue: 0.0941 time to fit residues: 17.3911 Evaluate side-chains 102 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 921 TRP Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1054 THR Chi-restraints excluded: chain A residue 1068 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 46 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 GLN A1219 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.219333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.164086 restraints weight = 9464.690| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.75 r_work: 0.3779 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9137 Z= 0.231 Angle : 0.680 9.281 12366 Z= 0.367 Chirality : 0.045 0.161 1428 Planarity : 0.005 0.047 1572 Dihedral : 4.510 22.059 1254 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.27 % Allowed : 13.80 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.24), residues: 1161 helix: 0.98 (0.18), residues: 758 sheet: -1.06 (1.18), residues: 25 loop : -1.97 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 468 TYR 0.022 0.002 TYR A 279 PHE 0.030 0.003 PHE A 552 TRP 0.014 0.002 TRP A 946 HIS 0.008 0.002 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 9137) covalent geometry : angle 0.67952 (12366) hydrogen bonds : bond 0.05819 ( 603) hydrogen bonds : angle 4.45120 ( 1791) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.323 Fit side-chains REVERT: A 154 ASP cc_start: 0.8198 (t70) cc_final: 0.7973 (t0) REVERT: A 248 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7358 (ttm-80) REVERT: A 273 MET cc_start: 0.7717 (mmm) cc_final: 0.7112 (mtp) REVERT: A 341 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8167 (mm) REVERT: A 440 ARG cc_start: 0.7526 (ttp80) cc_final: 0.7140 (ttm110) REVERT: A 442 LEU cc_start: 0.7085 (mp) cc_final: 0.6589 (tp) REVERT: A 521 MET cc_start: 0.6158 (mmm) cc_final: 0.5819 (mmm) REVERT: A 811 ASN cc_start: 0.7758 (p0) cc_final: 0.7253 (t0) REVERT: A 853 PHE cc_start: 0.7585 (t80) cc_final: 0.7355 (t80) REVERT: A 893 ARG cc_start: 0.7587 (ptp90) cc_final: 0.6305 (ptm160) REVERT: A 970 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7223 (mmt) REVERT: A 986 PHE cc_start: 0.5182 (OUTLIER) cc_final: 0.4724 (m-80) REVERT: A 1118 GLU cc_start: 0.6699 (pt0) cc_final: 0.6001 (tm-30) outliers start: 31 outliers final: 16 residues processed: 154 average time/residue: 0.0970 time to fit residues: 20.9753 Evaluate side-chains 122 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 921 TRP Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 986 PHE Chi-restraints excluded: chain A residue 1054 THR Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1186 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 80 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 GLN A1073 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.220615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.162219 restraints weight = 9448.339| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.03 r_work: 0.3846 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9137 Z= 0.157 Angle : 0.581 10.502 12366 Z= 0.312 Chirality : 0.040 0.155 1428 Planarity : 0.004 0.041 1572 Dihedral : 4.164 19.160 1254 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.06 % Allowed : 17.49 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.24), residues: 1161 helix: 1.32 (0.19), residues: 762 sheet: -0.48 (1.32), residues: 20 loop : -2.03 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1002 TYR 0.020 0.002 TYR A 295 PHE 0.023 0.001 PHE A 552 TRP 0.015 0.001 TRP A 188 HIS 0.008 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9137) covalent geometry : angle 0.58122 (12366) hydrogen bonds : bond 0.04987 ( 603) hydrogen bonds : angle 4.21497 ( 1791) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 157 MET cc_start: 0.5297 (ttm) cc_final: 0.4704 (ttm) REVERT: A 273 MET cc_start: 0.7423 (mmm) cc_final: 0.6793 (mtp) REVERT: A 319 LEU cc_start: 0.8188 (tt) cc_final: 0.7653 (mp) REVERT: A 341 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.8043 (mm) REVERT: A 442 LEU cc_start: 0.7094 (mp) cc_final: 0.6637 (tp) REVERT: A 893 ARG cc_start: 0.7811 (ptp90) cc_final: 0.6650 (ptm160) REVERT: A 970 MET cc_start: 0.7353 (mmt) cc_final: 0.7015 (mmp) REVERT: A 986 PHE cc_start: 0.5009 (OUTLIER) cc_final: 0.4497 (m-80) REVERT: A 1100 LYS cc_start: 0.7623 (mtpt) cc_final: 0.7252 (mttp) REVERT: A 1118 GLU cc_start: 0.6671 (pt0) cc_final: 0.5988 (tm-30) REVERT: A 1129 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7784 (tm-30) REVERT: A 1187 ASP cc_start: 0.7369 (t0) cc_final: 0.7110 (t70) outliers start: 29 outliers final: 17 residues processed: 140 average time/residue: 0.0887 time to fit residues: 17.9434 Evaluate side-chains 124 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 921 TRP Chi-restraints excluded: chain A residue 986 PHE Chi-restraints excluded: chain A residue 1054 THR Chi-restraints excluded: chain A residue 1186 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 38 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 GLN A1162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.218957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.156463 restraints weight = 9319.253| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.82 r_work: 0.3800 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.5926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9137 Z= 0.218 Angle : 0.648 8.424 12366 Z= 0.349 Chirality : 0.043 0.159 1428 Planarity : 0.005 0.047 1572 Dihedral : 4.432 21.849 1254 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.90 % Allowed : 18.55 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.24), residues: 1161 helix: 1.07 (0.18), residues: 766 sheet: -1.89 (1.12), residues: 27 loop : -2.04 (0.28), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1179 TYR 0.017 0.002 TYR A 279 PHE 0.022 0.002 PHE A 552 TRP 0.015 0.002 TRP A 188 HIS 0.008 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 9137) covalent geometry : angle 0.64804 (12366) hydrogen bonds : bond 0.05513 ( 603) hydrogen bonds : angle 4.47818 ( 1791) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.361 Fit side-chains REVERT: A 157 MET cc_start: 0.5499 (OUTLIER) cc_final: 0.4495 (ttm) REVERT: A 273 MET cc_start: 0.7681 (mmm) cc_final: 0.7025 (mtp) REVERT: A 440 ARG cc_start: 0.7201 (mpt180) cc_final: 0.6877 (mpt180) REVERT: A 442 LEU cc_start: 0.6989 (mp) cc_final: 0.6788 (tp) REVERT: A 444 GLN cc_start: 0.7141 (mt0) cc_final: 0.6270 (tm-30) REVERT: A 811 ASN cc_start: 0.7790 (p0) cc_final: 0.7507 (t0) REVERT: A 893 ARG cc_start: 0.7926 (ptp90) cc_final: 0.6998 (ptm160) REVERT: A 970 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7335 (mmp) REVERT: A 986 PHE cc_start: 0.5266 (OUTLIER) cc_final: 0.4762 (m-80) REVERT: A 1100 LYS cc_start: 0.7758 (mtpt) cc_final: 0.7410 (mttp) REVERT: A 1118 GLU cc_start: 0.6324 (pt0) cc_final: 0.5549 (tm-30) REVERT: A 1153 LYS cc_start: 0.6378 (mtmm) cc_final: 0.6134 (ptpp) outliers start: 37 outliers final: 24 residues processed: 140 average time/residue: 0.0943 time to fit residues: 18.7676 Evaluate side-chains 134 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 921 TRP Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 986 PHE Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1054 THR Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1186 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 51 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 90 optimal weight: 0.0770 chunk 68 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 ASN A1246 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.219398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.166172 restraints weight = 9316.052| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.74 r_work: 0.3779 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.5997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9137 Z= 0.133 Angle : 0.561 7.928 12366 Z= 0.299 Chirality : 0.040 0.152 1428 Planarity : 0.004 0.046 1572 Dihedral : 4.131 18.508 1254 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.74 % Allowed : 20.23 % Favored : 77.03 % 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 aren not related in a simple way. whole: 0.52 (0.25), residues: 1161 helix: 1.49 (0.19), residues: 762 sheet: -1.71 (1.16), residues: 27 loop : -1.98 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1002 TYR 0.023 0.001 TYR A 295 PHE 0.028 0.001 PHE A 552 TRP 0.017 0.001 TRP A 441 HIS 0.006 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9137) covalent geometry : angle 0.56094 (12366) hydrogen bonds : bond 0.04761 ( 603) hydrogen bonds : angle 4.24993 ( 1791) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 MET cc_start: 0.7649 (mmm) cc_final: 0.6946 (mtp) REVERT: A 319 LEU cc_start: 0.8299 (tt) cc_final: 0.7932 (mp) REVERT: A 342 PHE cc_start: 0.8042 (m-10) cc_final: 0.7834 (m-10) REVERT: A 416 ILE cc_start: 0.7834 (tt) cc_final: 0.7337 (mt) REVERT: A 440 ARG cc_start: 0.7049 (mpt180) cc_final: 0.6806 (mpt180) REVERT: A 444 GLN cc_start: 0.7137 (mt0) cc_final: 0.6347 (mm-40) REVERT: A 893 ARG cc_start: 0.7849 (ptp90) cc_final: 0.6990 (ptm160) REVERT: A 986 PHE cc_start: 0.4907 (OUTLIER) cc_final: 0.4339 (m-80) REVERT: A 1100 LYS cc_start: 0.7786 (mtpt) cc_final: 0.7438 (mttp) REVERT: A 1118 GLU cc_start: 0.6459 (pt0) cc_final: 0.5584 (tm-30) REVERT: A 1129 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7802 (tm-30) REVERT: A 1153 LYS cc_start: 0.6396 (mtmm) cc_final: 0.6114 (ptpp) REVERT: A 1187 ASP cc_start: 0.7555 (t0) cc_final: 0.7338 (t0) outliers start: 26 outliers final: 14 residues processed: 137 average time/residue: 0.0945 time to fit residues: 18.4648 Evaluate side-chains 120 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 986 PHE Chi-restraints excluded: chain A residue 1054 THR Chi-restraints excluded: chain A residue 1186 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.219238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.162975 restraints weight = 9438.372| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 1.75 r_work: 0.3837 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.6221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9137 Z= 0.138 Angle : 0.566 7.193 12366 Z= 0.301 Chirality : 0.040 0.149 1428 Planarity : 0.004 0.043 1572 Dihedral : 4.050 18.328 1254 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.42 % Allowed : 21.07 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.24), residues: 1161 helix: 1.49 (0.19), residues: 763 sheet: -1.62 (1.17), residues: 27 loop : -1.99 (0.28), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1002 TYR 0.022 0.001 TYR A 295 PHE 0.024 0.002 PHE A 552 TRP 0.013 0.001 TRP A 188 HIS 0.003 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9137) covalent geometry : angle 0.56562 (12366) hydrogen bonds : bond 0.04753 ( 603) hydrogen bonds : angle 4.18609 ( 1791) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.8315 (tpp) cc_final: 0.8075 (mmm) REVERT: A 273 MET cc_start: 0.7423 (mmm) cc_final: 0.6762 (mtp) REVERT: A 319 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7883 (mp) REVERT: A 416 ILE cc_start: 0.7814 (tt) cc_final: 0.7367 (mt) REVERT: A 440 ARG cc_start: 0.7192 (mpt180) cc_final: 0.6951 (mpt180) REVERT: A 444 GLN cc_start: 0.7096 (mt0) cc_final: 0.6348 (mm-40) REVERT: A 893 ARG cc_start: 0.7895 (ptp90) cc_final: 0.7010 (ptm160) REVERT: A 986 PHE cc_start: 0.5008 (OUTLIER) cc_final: 0.4460 (m-80) REVERT: A 1036 ARG cc_start: 0.5881 (mmm-85) cc_final: 0.5401 (mtm180) REVERT: A 1100 LYS cc_start: 0.7831 (mtpt) cc_final: 0.7465 (mttp) REVERT: A 1118 GLU cc_start: 0.6337 (pt0) cc_final: 0.5457 (tm-30) REVERT: A 1129 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7896 (tm-30) REVERT: A 1153 LYS cc_start: 0.6378 (mtmm) cc_final: 0.6132 (ptpp) outliers start: 23 outliers final: 18 residues processed: 133 average time/residue: 0.0964 time to fit residues: 18.0773 Evaluate side-chains 123 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 986 PHE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1054 THR Chi-restraints excluded: chain A residue 1186 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.212511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.158545 restraints weight = 9465.281| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.90 r_work: 0.3713 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.6696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9137 Z= 0.190 Angle : 0.630 12.994 12366 Z= 0.335 Chirality : 0.042 0.151 1428 Planarity : 0.004 0.044 1572 Dihedral : 4.324 21.145 1254 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.16 % Allowed : 20.97 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.24), residues: 1161 helix: 1.16 (0.18), residues: 763 sheet: -1.71 (1.18), residues: 27 loop : -1.87 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1002 TYR 0.022 0.002 TYR A 295 PHE 0.028 0.002 PHE A 552 TRP 0.013 0.002 TRP A 188 HIS 0.010 0.002 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 9137) covalent geometry : angle 0.63031 (12366) hydrogen bonds : bond 0.05298 ( 603) hydrogen bonds : angle 4.38361 ( 1791) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.8662 (tpp) cc_final: 0.8240 (mmt) REVERT: A 273 MET cc_start: 0.7640 (mmm) cc_final: 0.6974 (mtp) REVERT: A 342 PHE cc_start: 0.8268 (m-10) cc_final: 0.8058 (m-10) REVERT: A 416 ILE cc_start: 0.7813 (tt) cc_final: 0.7327 (mt) REVERT: A 440 ARG cc_start: 0.7360 (mpt180) cc_final: 0.7040 (mpt180) REVERT: A 444 GLN cc_start: 0.7049 (mt0) cc_final: 0.6387 (mm-40) REVERT: A 699 TYR cc_start: 0.6831 (m-80) cc_final: 0.6491 (m-10) REVERT: A 811 ASN cc_start: 0.7734 (p0) cc_final: 0.7474 (t0) REVERT: A 893 ARG cc_start: 0.8079 (ptp90) cc_final: 0.7289 (ptm160) REVERT: A 970 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7347 (mmp) REVERT: A 986 PHE cc_start: 0.5136 (OUTLIER) cc_final: 0.4606 (m-80) REVERT: A 1036 ARG cc_start: 0.6060 (mmm-85) cc_final: 0.5610 (mtm180) REVERT: A 1100 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7656 (mttp) REVERT: A 1118 GLU cc_start: 0.6238 (pt0) cc_final: 0.5327 (tm-30) REVERT: A 1129 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7792 (tm-30) REVERT: A 1153 LYS cc_start: 0.6474 (mtmm) cc_final: 0.6227 (ptpp) outliers start: 30 outliers final: 24 residues processed: 134 average time/residue: 0.1066 time to fit residues: 19.8781 Evaluate side-chains 134 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 986 PHE Chi-restraints excluded: chain A residue 998 GLU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1054 THR Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1186 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 64 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 HIS ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.208889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.154688 restraints weight = 9516.075| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.86 r_work: 0.3697 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.7147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9137 Z= 0.199 Angle : 0.639 12.439 12366 Z= 0.340 Chirality : 0.043 0.268 1428 Planarity : 0.004 0.044 1572 Dihedral : 4.416 20.827 1254 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.27 % Allowed : 21.07 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.24), residues: 1161 helix: 1.04 (0.18), residues: 764 sheet: -2.31 (0.97), residues: 37 loop : -1.91 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1002 TYR 0.022 0.002 TYR A 295 PHE 0.028 0.002 PHE A 552 TRP 0.014 0.001 TRP A 188 HIS 0.010 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 9137) covalent geometry : angle 0.63892 (12366) hydrogen bonds : bond 0.05343 ( 603) hydrogen bonds : angle 4.47093 ( 1791) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.8597 (tpp) cc_final: 0.8231 (mmt) REVERT: A 273 MET cc_start: 0.7464 (mmm) cc_final: 0.6855 (mtp) REVERT: A 416 ILE cc_start: 0.7850 (tt) cc_final: 0.7403 (mt) REVERT: A 440 ARG cc_start: 0.7522 (mpt180) cc_final: 0.7196 (mpt180) REVERT: A 444 GLN cc_start: 0.7025 (mt0) cc_final: 0.6414 (mm-40) REVERT: A 699 TYR cc_start: 0.6882 (m-80) cc_final: 0.6551 (m-10) REVERT: A 734 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6645 (mp0) REVERT: A 811 ASN cc_start: 0.7752 (p0) cc_final: 0.7544 (t0) REVERT: A 893 ARG cc_start: 0.8246 (ptp90) cc_final: 0.7541 (ptm160) REVERT: A 913 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7157 (mm-30) REVERT: A 970 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.7265 (mmp) REVERT: A 986 PHE cc_start: 0.5011 (OUTLIER) cc_final: 0.4478 (m-80) REVERT: A 1036 ARG cc_start: 0.5986 (mmm-85) cc_final: 0.5515 (mtm180) REVERT: A 1100 LYS cc_start: 0.8005 (mtpt) cc_final: 0.7727 (mttp) REVERT: A 1129 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7959 (tm-30) REVERT: A 1153 LYS cc_start: 0.6637 (mtmm) cc_final: 0.6373 (ptpp) outliers start: 31 outliers final: 25 residues processed: 140 average time/residue: 0.1049 time to fit residues: 20.5412 Evaluate side-chains 141 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 590 GLU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 986 PHE Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 998 GLU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1054 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 112 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 11 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 113 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 HIS A 693 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.214612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.159207 restraints weight = 9485.614| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.89 r_work: 0.3796 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.7139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9137 Z= 0.137 Angle : 0.605 12.475 12366 Z= 0.316 Chirality : 0.040 0.231 1428 Planarity : 0.004 0.044 1572 Dihedral : 4.197 19.749 1254 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.53 % Allowed : 22.23 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.25), residues: 1161 helix: 1.40 (0.19), residues: 764 sheet: -2.24 (0.96), residues: 37 loop : -1.98 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1002 TYR 0.022 0.001 TYR A 295 PHE 0.022 0.001 PHE A 552 TRP 0.011 0.001 TRP A 188 HIS 0.016 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9137) covalent geometry : angle 0.60546 (12366) hydrogen bonds : bond 0.04778 ( 603) hydrogen bonds : angle 4.25747 ( 1791) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8559 (tttt) cc_final: 0.8012 (mttp) REVERT: A 138 PHE cc_start: 0.8108 (m-80) cc_final: 0.7789 (m-80) REVERT: A 273 MET cc_start: 0.7351 (mmm) cc_final: 0.6720 (mtp) REVERT: A 319 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7945 (mp) REVERT: A 416 ILE cc_start: 0.7810 (tt) cc_final: 0.7376 (mt) REVERT: A 440 ARG cc_start: 0.7560 (mpt180) cc_final: 0.7261 (mpt180) REVERT: A 444 GLN cc_start: 0.6757 (mt0) cc_final: 0.6402 (mm-40) REVERT: A 445 GLN cc_start: 0.7194 (mm-40) cc_final: 0.6202 (mp10) REVERT: A 699 TYR cc_start: 0.6668 (m-80) cc_final: 0.6348 (m-10) REVERT: A 811 ASN cc_start: 0.7774 (p0) cc_final: 0.7484 (t0) REVERT: A 893 ARG cc_start: 0.8125 (ptp90) cc_final: 0.7419 (ptp-110) REVERT: A 986 PHE cc_start: 0.4818 (OUTLIER) cc_final: 0.4278 (m-80) REVERT: A 1036 ARG cc_start: 0.5936 (mmm-85) cc_final: 0.5468 (mtm180) REVERT: A 1100 LYS cc_start: 0.7912 (mtpt) cc_final: 0.7611 (mttp) REVERT: A 1118 GLU cc_start: 0.6143 (pt0) cc_final: 0.5205 (tm-30) REVERT: A 1129 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7855 (tm-30) REVERT: A 1153 LYS cc_start: 0.6530 (mtmm) cc_final: 0.6158 (ptpp) outliers start: 24 outliers final: 17 residues processed: 139 average time/residue: 0.1037 time to fit residues: 20.2123 Evaluate side-chains 131 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 860 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 986 PHE Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 998 GLU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1054 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** 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 = 0.4446 r_free = 0.4446 target = 0.210931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.153910 restraints weight = 9505.406| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.41 r_work: 0.3700 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.7310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9137 Z= 0.173 Angle : 0.632 13.171 12366 Z= 0.332 Chirality : 0.042 0.233 1428 Planarity : 0.004 0.044 1572 Dihedral : 4.264 19.519 1254 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.11 % Allowed : 22.44 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.24), residues: 1161 helix: 1.25 (0.18), residues: 765 sheet: -2.25 (0.98), residues: 37 loop : -1.99 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1002 TYR 0.022 0.002 TYR A 295 PHE 0.024 0.002 PHE A 552 TRP 0.012 0.001 TRP A 188 HIS 0.017 0.002 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9137) covalent geometry : angle 0.63184 (12366) hydrogen bonds : bond 0.05085 ( 603) hydrogen bonds : angle 4.31400 ( 1791) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2726.45 seconds wall clock time: 47 minutes 27.14 seconds (2847.14 seconds total)