Starting phenix.real_space_refine on Tue Mar 3 14:45:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9upc_64391/03_2026/9upc_64391.cif Found real_map, /net/cci-nas-00/data/ceres_data/9upc_64391/03_2026/9upc_64391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9upc_64391/03_2026/9upc_64391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9upc_64391/03_2026/9upc_64391.map" model { file = "/net/cci-nas-00/data/ceres_data/9upc_64391/03_2026/9upc_64391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9upc_64391/03_2026/9upc_64391.cif" } resolution = 3.14 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= 0.026 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 46 5.16 5 C 3927 2.51 5 N 1051 2.21 5 O 1135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6159 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2778 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2772 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 16, 'TRANS': 330} Conformer: "B" Number of residues, atoms: 347, 2772 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 16, 'TRANS': 330} bond proxies already assigned to first conformer: 2823 Chain: "B" Number of atoms: 2945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2945 Classifications: {'peptide': 362} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 353} Chain breaks: 2 Chain: "C" Number of atoms: 436 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 50, 426 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Conformer: "B" Number of residues, atoms: 50, 426 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} bond proxies already assigned to first conformer: 426 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS C 37 " occ=0.46 ... (18 atoms not shown) pdb=" NE2BHIS C 37 " occ=0.54 Time building chain proxies: 1.76, per 1000 atoms: 0.29 Number of scatterers: 6159 At special positions: 0 Unit cell: (64.78, 100.04, 104.14, 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 46 16.00 O 1135 8.00 N 1051 7.00 C 3927 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: 0.53 Conformation dependent library (CDL) restraints added in 328.4 milliseconds 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 2 sheets defined 67.2% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 642 through 653 Processing helix chain 'A' and resid 693 through 707 Processing helix chain 'A' and resid 715 through 736 Processing helix chain 'A' and resid 741 through 762 Processing helix chain 'A' and resid 771 through 795 Processing helix chain 'A' and resid 802 through 813 removed outlier: 3.755A pdb=" N GLY A 808 " --> pdb=" O ALA A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 826 removed outlier: 4.481A pdb=" N ARG A 822 " --> pdb=" O GLY A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 849 Processing helix chain 'A' and resid 851 through 861 Processing helix chain 'A' and resid 863 through 869 Processing helix chain 'A' and resid 873 through 888 removed outlier: 3.645A pdb=" N ILE A 877 " --> pdb=" O TYR A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 904 removed outlier: 3.683A pdb=" N VAL A 904 " --> pdb=" O LEU A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 922 through 924 No H-bonds generated for 'chain 'A' and resid 922 through 924' Processing helix chain 'A' and resid 951 through 957 Processing helix chain 'A' and resid 961 through 968 removed outlier: 3.580A pdb=" N GLY A 968 " --> pdb=" O GLU A 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 20 removed outlier: 3.544A pdb=" N TYR B 9 " --> pdb=" O THR B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 30 removed outlier: 3.629A pdb=" N CYS B 25 " --> pdb=" O ASP B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 59 through 75 removed outlier: 3.672A pdb=" N GLY B 73 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN B 74 " --> pdb=" O TYR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 98 removed outlier: 3.619A pdb=" N LYS B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 127 Processing helix chain 'B' and resid 136 through 152 Processing helix chain 'B' and resid 155 through 159 removed outlier: 3.707A pdb=" N GLY B 159 " --> pdb=" O THR B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 168 through 183 Processing helix chain 'B' and resid 184 through 195 removed outlier: 3.744A pdb=" N CYS B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Proline residue: B 190 - end of helix Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.852A pdb=" N TYR B 204 " --> pdb=" O LYS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 223 removed outlier: 3.586A pdb=" N VAL B 210 " --> pdb=" O THR B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 240 removed outlier: 3.577A pdb=" N GLU B 230 " --> pdb=" O PHE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'B' and resid 244 through 262 Proline residue: B 257 - end of helix Processing helix chain 'B' and resid 267 through 274 Processing helix chain 'B' and resid 277 through 287 removed outlier: 4.061A pdb=" N GLU B 281 " --> pdb=" O MET B 277 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 301 Processing helix chain 'B' and resid 301 through 309 Processing helix chain 'B' and resid 316 through 330 removed outlier: 4.294A pdb=" N ILE B 320 " --> pdb=" O LYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 349 removed outlier: 3.637A pdb=" N PHE B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 349 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 371 removed outlier: 3.518A pdb=" N ALA B 365 " --> pdb=" O GLN B 361 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET B 370 " --> pdb=" O ASN B 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 62 Processing sheet with id=AA1, first strand: chain 'A' and resid 896 through 897 Processing sheet with id=AA2, first strand: chain 'B' and resid 265 through 266 331 hydrogen bonds defined for protein. 971 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2021 1.34 - 1.46: 1263 1.46 - 1.58: 2942 1.58 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 6294 Sorted by residual: bond pdb=" CB PHE A 806 " pdb=" CG PHE A 806 " ideal model delta sigma weight residual 1.502 1.474 0.028 2.30e-02 1.89e+03 1.53e+00 bond pdb=" N PRO B 46 " pdb=" CA PRO B 46 " ideal model delta sigma weight residual 1.469 1.477 -0.009 7.40e-03 1.83e+04 1.41e+00 bond pdb=" N GLY A 930 " pdb=" CA GLY A 930 " ideal model delta sigma weight residual 1.449 1.466 -0.017 1.45e-02 4.76e+03 1.33e+00 bond pdb=" CB CYS B 362 " pdb=" SG CYS B 362 " ideal model delta sigma weight residual 1.808 1.772 0.036 3.30e-02 9.18e+02 1.22e+00 bond pdb=" CB CYS A 868 " pdb=" SG CYS A 868 " ideal model delta sigma weight residual 1.808 1.778 0.030 3.30e-02 9.18e+02 8.23e-01 ... (remaining 6289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 7968 1.03 - 2.07: 443 2.07 - 3.10: 66 3.10 - 4.13: 18 4.13 - 5.16: 6 Bond angle restraints: 8501 Sorted by residual: angle pdb=" N HIS B 372 " pdb=" CA HIS B 372 " pdb=" C HIS B 372 " ideal model delta sigma weight residual 111.81 107.11 4.70 1.44e+00 4.82e-01 1.07e+01 angle pdb=" N ILE A 734 " pdb=" CA ILE A 734 " pdb=" C ILE A 734 " ideal model delta sigma weight residual 110.72 108.03 2.69 1.01e+00 9.80e-01 7.08e+00 angle pdb=" N ILE B 195 " pdb=" CA ILE B 195 " pdb=" C ILE B 195 " ideal model delta sigma weight residual 110.09 106.47 3.62 1.50e+00 4.44e-01 5.81e+00 angle pdb=" N VAL A 904 " pdb=" CA VAL A 904 " pdb=" C VAL A 904 " ideal model delta sigma weight residual 111.67 109.53 2.14 9.50e-01 1.11e+00 5.08e+00 angle pdb=" CA TYR A 720 " pdb=" CB TYR A 720 " pdb=" CG TYR A 720 " ideal model delta sigma weight residual 113.90 110.44 3.46 1.80e+00 3.09e-01 3.70e+00 ... (remaining 8496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 3451 17.73 - 35.46: 278 35.46 - 53.19: 64 53.19 - 70.93: 14 70.93 - 88.66: 2 Dihedral angle restraints: 3809 sinusoidal: 1555 harmonic: 2254 Sorted by residual: dihedral pdb=" CA CYS A 868 " pdb=" C CYS A 868 " pdb=" N LEU A 869 " pdb=" CA LEU A 869 " ideal model delta harmonic sigma weight residual 180.00 153.75 26.25 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA HIS B 372 " pdb=" C HIS B 372 " pdb=" N VAL B 373 " pdb=" CA VAL B 373 " ideal model delta harmonic sigma weight residual -180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA HIS A 828 " pdb=" C HIS A 828 " pdb=" N PRO A 829 " pdb=" CA PRO A 829 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 3806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 568 0.026 - 0.052: 254 0.052 - 0.079: 83 0.079 - 0.105: 22 0.105 - 0.131: 8 Chirality restraints: 935 Sorted by residual: chirality pdb=" CA VAL A 974 " pdb=" N VAL A 974 " pdb=" C VAL A 974 " pdb=" CB VAL A 974 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA PHE A 806 " pdb=" N PHE A 806 " pdb=" C PHE A 806 " pdb=" CB PHE A 806 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA ILE B 195 " pdb=" N ILE B 195 " pdb=" C ILE B 195 " pdb=" CB ILE B 195 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 932 not shown) Planarity restraints: 1095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 265 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.35e+00 pdb=" N PRO B 266 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 266 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 266 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 899 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO A 900 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 900 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 900 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 45 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO B 46 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 46 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 46 " -0.022 5.00e-02 4.00e+02 ... (remaining 1092 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 2416 2.87 - 3.38: 6818 3.38 - 3.89: 10781 3.89 - 4.39: 12981 4.39 - 4.90: 20395 Nonbonded interactions: 53391 Sorted by model distance: nonbonded pdb=" OD2 ASP C 45 " pdb=" O ASN C 47 " model vdw 2.363 3.040 nonbonded pdb=" O GLU A 964 " pdb=" OE1 GLU A 964 " model vdw 2.459 3.040 nonbonded pdb=" O ASP B 76 " pdb=" OD1 ASP B 76 " model vdw 2.461 3.040 nonbonded pdb=" OE1 GLU A 764 " pdb=" O THR A 948 " model vdw 2.465 3.040 nonbonded pdb=" O LEU A 743 " pdb=" OG SER A 746 " model vdw 2.469 3.040 ... (remaining 53386 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.42 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: 0.970 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.660 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 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 0.036 6294 Z= 0.152 Angle : 0.562 5.165 8501 Z= 0.327 Chirality : 0.034 0.131 935 Planarity : 0.004 0.052 1095 Dihedral : 13.765 88.657 2341 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.14 % Favored : 93.72 % Rotamer: Outliers : 1.77 % Allowed : 8.10 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.91 (0.31), residues: 753 helix: -0.05 (0.23), residues: 477 sheet: None (None), residues: 0 loop : -1.47 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 878 TYR 0.014 0.001 TYR B 330 PHE 0.020 0.002 PHE A 806 TRP 0.007 0.001 TRP C 27 HIS 0.005 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6294) covalent geometry : angle 0.56202 ( 8501) hydrogen bonds : bond 0.13344 ( 331) hydrogen bonds : angle 6.40722 ( 971) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 709 MET cc_start: 0.7055 (mtt) cc_final: 0.6565 (mtt) REVERT: A 767 MET cc_start: 0.6608 (mmt) cc_final: 0.6098 (mmt) REVERT: A 907 MET cc_start: 0.6988 (tmm) cc_final: 0.6754 (tmm) REVERT: B 20 ARG cc_start: 0.8271 (mmm-85) cc_final: 0.7839 (mmm160) REVERT: B 137 MET cc_start: 0.8037 (mtp) cc_final: 0.7728 (mtp) REVERT: B 143 GLU cc_start: 0.7092 (tp30) cc_final: 0.6593 (mt-10) REVERT: B 176 PHE cc_start: 0.8816 (m-80) cc_final: 0.8401 (m-80) REVERT: B 261 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7329 (mp) REVERT: C 49 GLU cc_start: 0.7594 (mp0) cc_final: 0.7289 (mp0) outliers start: 12 outliers final: 6 residues processed: 126 average time/residue: 0.0632 time to fit residues: 11.0151 Evaluate side-chains 106 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 737 GLN Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 868 CYS Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 317 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.229348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.198414 restraints weight = 28611.060| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 6.12 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4263 r_free = 0.4263 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4263 r_free = 0.4263 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6294 Z= 0.175 Angle : 0.654 10.207 8501 Z= 0.338 Chirality : 0.041 0.204 935 Planarity : 0.004 0.051 1095 Dihedral : 6.747 59.591 838 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.94 % Favored : 94.93 % Rotamer: Outliers : 2.65 % Allowed : 10.01 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.64 (0.31), residues: 753 helix: 0.11 (0.23), residues: 485 sheet: None (None), residues: 0 loop : -1.28 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 726 TYR 0.015 0.001 TYR B 330 PHE 0.060 0.002 PHE A 806 TRP 0.013 0.002 TRP A 719 HIS 0.006 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 6294) covalent geometry : angle 0.65408 ( 8501) hydrogen bonds : bond 0.05241 ( 331) hydrogen bonds : angle 5.16584 ( 971) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.227 Fit side-chains REVERT: A 709 MET cc_start: 0.6840 (mtt) cc_final: 0.6442 (mtt) REVERT: A 886 ASN cc_start: 0.7812 (t0) cc_final: 0.7590 (t0) REVERT: A 907 MET cc_start: 0.6741 (tmm) cc_final: 0.6471 (tmm) REVERT: B 20 ARG cc_start: 0.8059 (mmm-85) cc_final: 0.7754 (mmm-85) REVERT: B 143 GLU cc_start: 0.7170 (tp30) cc_final: 0.6657 (mt-10) REVERT: B 200 LEU cc_start: 0.5820 (OUTLIER) cc_final: 0.5409 (pp) REVERT: C 49 GLU cc_start: 0.7853 (mp0) cc_final: 0.7350 (mp0) outliers start: 18 outliers final: 9 residues processed: 112 average time/residue: 0.0724 time to fit residues: 11.0460 Evaluate side-chains 103 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain C residue 61 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.229767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.200050 restraints weight = 19040.772| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 4.02 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4264 r_free = 0.4264 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4263 r_free = 0.4263 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6294 Z= 0.164 Angle : 0.636 9.637 8501 Z= 0.327 Chirality : 0.040 0.216 935 Planarity : 0.004 0.048 1095 Dihedral : 6.035 58.956 830 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.81 % Favored : 95.06 % Rotamer: Outliers : 2.65 % Allowed : 11.93 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.61 (0.31), residues: 753 helix: 0.13 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -1.28 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 883 TYR 0.026 0.002 TYR A 720 PHE 0.018 0.002 PHE A 852 TRP 0.011 0.002 TRP A 719 HIS 0.006 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 6294) covalent geometry : angle 0.63630 ( 8501) hydrogen bonds : bond 0.04886 ( 331) hydrogen bonds : angle 4.99403 ( 971) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.220 Fit side-chains REVERT: B 20 ARG cc_start: 0.8084 (mmm-85) cc_final: 0.7710 (mmm-85) REVERT: B 143 GLU cc_start: 0.7088 (tp30) cc_final: 0.6607 (mt-10) REVERT: B 146 MET cc_start: 0.7566 (mmm) cc_final: 0.6907 (tmm) REVERT: B 200 LEU cc_start: 0.5896 (OUTLIER) cc_final: 0.5500 (pp) REVERT: C 49 GLU cc_start: 0.7799 (mp0) cc_final: 0.7422 (mp0) outliers start: 18 outliers final: 12 residues processed: 111 average time/residue: 0.0631 time to fit residues: 9.8091 Evaluate side-chains 109 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 372 HIS Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain C residue 61 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.5980 chunk 71 optimal weight: 9.9990 chunk 17 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 807 GLN A 810 ASN A 886 ASN B 98 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.229952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.202209 restraints weight = 13627.700| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 3.36 r_work: 0.4161 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4159 r_free = 0.4159 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4159 r_free = 0.4159 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6294 Z= 0.150 Angle : 0.626 10.160 8501 Z= 0.322 Chirality : 0.040 0.205 935 Planarity : 0.004 0.046 1095 Dihedral : 5.974 58.910 830 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.34 % Favored : 94.53 % Rotamer: Outliers : 3.09 % Allowed : 13.11 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.57 (0.31), residues: 753 helix: 0.20 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -1.34 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 883 TYR 0.020 0.001 TYR A 720 PHE 0.021 0.002 PHE A 806 TRP 0.015 0.002 TRP A 719 HIS 0.004 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6294) covalent geometry : angle 0.62618 ( 8501) hydrogen bonds : bond 0.04644 ( 331) hydrogen bonds : angle 4.89464 ( 971) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: B 143 GLU cc_start: 0.7222 (tp30) cc_final: 0.6547 (mt-10) REVERT: B 146 MET cc_start: 0.7599 (mmm) cc_final: 0.6894 (tmm) REVERT: B 176 PHE cc_start: 0.8724 (m-80) cc_final: 0.8410 (m-80) REVERT: B 200 LEU cc_start: 0.6026 (OUTLIER) cc_final: 0.5506 (pp) REVERT: C 49 GLU cc_start: 0.7759 (mp0) cc_final: 0.7364 (mp0) outliers start: 21 outliers final: 13 residues processed: 114 average time/residue: 0.0626 time to fit residues: 10.0345 Evaluate side-chains 112 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 TRP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 372 HIS Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain C residue 61 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 20 optimal weight: 0.1980 chunk 16 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.233862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.204820 restraints weight = 29122.234| |-----------------------------------------------------------------------------| r_work (start): 0.4311 rms_B_bonded: 6.15 r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4310 r_free = 0.4310 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4310 r_free = 0.4310 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6294 Z= 0.136 Angle : 0.607 7.686 8501 Z= 0.312 Chirality : 0.039 0.219 935 Planarity : 0.004 0.043 1095 Dihedral : 5.844 59.363 830 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.81 % Favored : 95.06 % Rotamer: Outliers : 3.53 % Allowed : 14.14 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.42 (0.31), residues: 753 helix: 0.34 (0.24), residues: 488 sheet: None (None), residues: 0 loop : -1.33 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 883 TYR 0.023 0.001 TYR A 720 PHE 0.022 0.002 PHE A 806 TRP 0.015 0.002 TRP A 719 HIS 0.004 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6294) covalent geometry : angle 0.60652 ( 8501) hydrogen bonds : bond 0.04298 ( 331) hydrogen bonds : angle 4.73513 ( 971) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 886 ASN cc_start: 0.7716 (t160) cc_final: 0.7166 (t0) REVERT: B 20 ARG cc_start: 0.7890 (mmm-85) cc_final: 0.7641 (mmm-85) REVERT: B 143 GLU cc_start: 0.7048 (tp30) cc_final: 0.6598 (mt-10) REVERT: B 146 MET cc_start: 0.7210 (mmm) cc_final: 0.6661 (tmm) REVERT: B 200 LEU cc_start: 0.5726 (OUTLIER) cc_final: 0.5267 (pp) REVERT: C 49 GLU cc_start: 0.7876 (mp0) cc_final: 0.7470 (mp0) outliers start: 24 outliers final: 15 residues processed: 125 average time/residue: 0.0600 time to fit residues: 10.7569 Evaluate side-chains 117 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 TRP Chi-restraints excluded: chain A residue 754 PHE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 372 HIS Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain C residue 61 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 23 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 0.5980 chunk 36 optimal weight: 8.9990 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 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 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.232051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.203005 restraints weight = 21907.807| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 5.09 r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4299 r_free = 0.4299 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4299 r_free = 0.4299 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6294 Z= 0.155 Angle : 0.632 8.062 8501 Z= 0.324 Chirality : 0.040 0.227 935 Planarity : 0.004 0.040 1095 Dihedral : 5.803 57.064 830 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.39 % Rotamer: Outliers : 3.24 % Allowed : 15.76 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.39 (0.31), residues: 753 helix: 0.35 (0.23), residues: 482 sheet: None (None), residues: 0 loop : -1.25 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 883 TYR 0.014 0.001 TYR B 369 PHE 0.040 0.002 PHE B 176 TRP 0.015 0.002 TRP A 719 HIS 0.005 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6294) covalent geometry : angle 0.63182 ( 8501) hydrogen bonds : bond 0.04426 ( 331) hydrogen bonds : angle 4.78226 ( 971) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.221 Fit side-chains REVERT: A 877 ILE cc_start: 0.4993 (OUTLIER) cc_final: 0.3951 (mm) REVERT: B 143 GLU cc_start: 0.6977 (tp30) cc_final: 0.6504 (mt-10) REVERT: B 146 MET cc_start: 0.7270 (mmm) cc_final: 0.6613 (tmm) REVERT: B 200 LEU cc_start: 0.5711 (OUTLIER) cc_final: 0.5297 (pp) REVERT: B 302 GLU cc_start: 0.6248 (mt-10) cc_final: 0.6033 (mt-10) REVERT: C 49 GLU cc_start: 0.7617 (mp0) cc_final: 0.7218 (mp0) outliers start: 22 outliers final: 16 residues processed: 118 average time/residue: 0.0605 time to fit residues: 10.0415 Evaluate side-chains 119 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 719 TRP Chi-restraints excluded: chain A residue 754 PHE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 372 HIS Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain C residue 61 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 55 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 27 optimal weight: 0.0770 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.227957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.197643 restraints weight = 22490.625| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 5.24 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4263 r_free = 0.4263 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4263 r_free = 0.4263 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6294 Z= 0.167 Angle : 0.657 9.279 8501 Z= 0.337 Chirality : 0.041 0.237 935 Planarity : 0.004 0.038 1095 Dihedral : 5.847 56.477 830 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.39 % Rotamer: Outliers : 3.24 % Allowed : 16.94 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.47 (0.31), residues: 753 helix: 0.28 (0.23), residues: 481 sheet: None (None), residues: 0 loop : -1.26 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 883 TYR 0.015 0.001 TYR B 369 PHE 0.035 0.002 PHE B 176 TRP 0.014 0.002 TRP A 724 HIS 0.005 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 6294) covalent geometry : angle 0.65670 ( 8501) hydrogen bonds : bond 0.04449 ( 331) hydrogen bonds : angle 4.92946 ( 971) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.213 Fit side-chains REVERT: B 143 GLU cc_start: 0.6963 (tp30) cc_final: 0.6430 (mt-10) REVERT: B 146 MET cc_start: 0.7264 (mmm) cc_final: 0.6556 (tmm) REVERT: B 200 LEU cc_start: 0.5742 (OUTLIER) cc_final: 0.5340 (pp) REVERT: B 302 GLU cc_start: 0.6375 (mt-10) cc_final: 0.6078 (mt-10) REVERT: C 49 GLU cc_start: 0.7610 (mp0) cc_final: 0.7201 (mp0) outliers start: 22 outliers final: 16 residues processed: 114 average time/residue: 0.0652 time to fit residues: 10.3546 Evaluate side-chains 117 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 719 TRP Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain C residue 61 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 4 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 57 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.230545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.202167 restraints weight = 15267.669| |-----------------------------------------------------------------------------| r_work (start): 0.4304 rms_B_bonded: 3.63 r_work: 0.4156 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4163 r_free = 0.4163 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4163 r_free = 0.4163 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6294 Z= 0.146 Angle : 0.650 9.646 8501 Z= 0.331 Chirality : 0.040 0.241 935 Planarity : 0.004 0.037 1095 Dihedral : 5.759 56.584 830 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.39 % Rotamer: Outliers : 3.09 % Allowed : 17.08 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.42 (0.31), residues: 753 helix: 0.31 (0.23), residues: 481 sheet: None (None), residues: 0 loop : -1.24 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 883 TYR 0.013 0.001 TYR B 369 PHE 0.032 0.002 PHE A 806 TRP 0.018 0.002 TRP A 724 HIS 0.004 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6294) covalent geometry : angle 0.65042 ( 8501) hydrogen bonds : bond 0.04237 ( 331) hydrogen bonds : angle 4.85417 ( 971) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: B 9 TYR cc_start: 0.7375 (t80) cc_final: 0.6911 (t80) REVERT: B 146 MET cc_start: 0.7407 (mmm) cc_final: 0.6746 (tmm) REVERT: B 176 PHE cc_start: 0.8712 (m-80) cc_final: 0.8373 (m-80) REVERT: B 200 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.5413 (pp) REVERT: B 302 GLU cc_start: 0.6494 (mt-10) cc_final: 0.6243 (mt-10) REVERT: B 370 MET cc_start: 0.5541 (mpp) cc_final: 0.1019 (ptt) REVERT: C 49 GLU cc_start: 0.7651 (mp0) cc_final: 0.7297 (mp0) outliers start: 21 outliers final: 15 residues processed: 114 average time/residue: 0.0566 time to fit residues: 9.2294 Evaluate side-chains 118 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 719 TRP Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 372 HIS Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 377 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.228699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.198575 restraints weight = 18838.063| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 4.14 r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4274 r_free = 0.4274 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4274 r_free = 0.4274 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6294 Z= 0.159 Angle : 0.665 9.500 8501 Z= 0.336 Chirality : 0.040 0.262 935 Planarity : 0.004 0.035 1095 Dihedral : 5.756 56.362 830 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.39 % Rotamer: Outliers : 3.09 % Allowed : 17.67 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.43 (0.31), residues: 753 helix: 0.28 (0.23), residues: 481 sheet: None (None), residues: 0 loop : -1.19 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 883 TYR 0.015 0.001 TYR B 369 PHE 0.048 0.002 PHE A 806 TRP 0.017 0.002 TRP A 724 HIS 0.005 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6294) covalent geometry : angle 0.66451 ( 8501) hydrogen bonds : bond 0.04303 ( 331) hydrogen bonds : angle 4.88864 ( 971) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 9 TYR cc_start: 0.7390 (t80) cc_final: 0.7051 (t80) REVERT: B 146 MET cc_start: 0.7306 (mmm) cc_final: 0.6673 (tmm) REVERT: B 200 LEU cc_start: 0.5760 (OUTLIER) cc_final: 0.5326 (pp) REVERT: B 337 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.5677 (mp10) REVERT: C 49 GLU cc_start: 0.7677 (mp0) cc_final: 0.7295 (mp0) outliers start: 21 outliers final: 16 residues processed: 113 average time/residue: 0.0648 time to fit residues: 10.2906 Evaluate side-chains 118 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 719 TRP Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 337 GLN Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 377 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 0.0470 chunk 35 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.229768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.199618 restraints weight = 17864.556| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 4.01 r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4265 r_free = 0.4265 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4265 r_free = 0.4265 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6294 Z= 0.174 Angle : 0.692 10.191 8501 Z= 0.351 Chirality : 0.041 0.262 935 Planarity : 0.004 0.036 1095 Dihedral : 5.790 55.548 830 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.61 % Favored : 94.26 % Rotamer: Outliers : 3.09 % Allowed : 17.97 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.45 (0.31), residues: 753 helix: 0.24 (0.23), residues: 480 sheet: None (None), residues: 0 loop : -1.13 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 883 TYR 0.016 0.001 TYR B 369 PHE 0.061 0.003 PHE B 176 TRP 0.018 0.002 TRP A 724 HIS 0.005 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 6294) covalent geometry : angle 0.69216 ( 8501) hydrogen bonds : bond 0.04469 ( 331) hydrogen bonds : angle 4.92111 ( 971) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.223 Fit side-chains REVERT: B 9 TYR cc_start: 0.7382 (t80) cc_final: 0.7061 (t80) REVERT: B 146 MET cc_start: 0.7330 (mmm) cc_final: 0.6689 (tmm) REVERT: B 200 LEU cc_start: 0.5756 (OUTLIER) cc_final: 0.5337 (pp) REVERT: B 337 GLN cc_start: 0.6918 (OUTLIER) cc_final: 0.5685 (mp10) REVERT: C 49 GLU cc_start: 0.7697 (mp0) cc_final: 0.7325 (mp0) outliers start: 21 outliers final: 16 residues processed: 115 average time/residue: 0.0627 time to fit residues: 10.1452 Evaluate side-chains 119 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 719 TRP Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 337 GLN Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 377 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.0570 chunk 36 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 25 optimal weight: 0.0470 chunk 54 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.232590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.201197 restraints weight = 22782.602| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 4.73 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4292 r_free = 0.4292 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4292 r_free = 0.4292 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6294 Z= 0.138 Angle : 0.665 9.942 8501 Z= 0.340 Chirality : 0.040 0.268 935 Planarity : 0.004 0.038 1095 Dihedral : 5.743 56.331 830 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.39 % Rotamer: Outliers : 2.80 % Allowed : 18.11 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.44 (0.31), residues: 753 helix: 0.23 (0.23), residues: 480 sheet: None (None), residues: 0 loop : -1.10 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 883 TYR 0.011 0.001 TYR B 369 PHE 0.057 0.003 PHE B 176 TRP 0.016 0.002 TRP A 724 HIS 0.005 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6294) covalent geometry : angle 0.66530 ( 8501) hydrogen bonds : bond 0.04135 ( 331) hydrogen bonds : angle 4.84152 ( 971) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1422.19 seconds wall clock time: 25 minutes 10.96 seconds (1510.96 seconds total)