Starting phenix.real_space_refine on Sat May 10 17:00:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jf0_36205/05_2025/8jf0_36205.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jf0_36205/05_2025/8jf0_36205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jf0_36205/05_2025/8jf0_36205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jf0_36205/05_2025/8jf0_36205.map" model { file = "/net/cci-nas-00/data/ceres_data/8jf0_36205/05_2025/8jf0_36205.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jf0_36205/05_2025/8jf0_36205.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.005 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 50 5.16 5 C 4304 2.51 5 N 1064 2.21 5 O 1160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6578 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3289 Classifications: {'peptide': 436} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 412} Chain breaks: 3 Restraints were copied for chains: B Time building chain proxies: 5.21, per 1000 atoms: 0.79 Number of scatterers: 6578 At special positions: 0 Unit cell: (83.0003, 98.4936, 77.4669, 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 50 16.00 O 1160 8.00 N 1064 7.00 C 4304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 1.2 seconds 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1568 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 74.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 46 through 59 removed outlier: 3.645A pdb=" N GLY A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.792A pdb=" N PHE A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 100 removed outlier: 4.073A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 removed outlier: 3.534A pdb=" N ALA A 120 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 Processing helix chain 'A' and resid 145 through 174 Proline residue: A 151 - end of helix removed outlier: 3.827A pdb=" N GLU A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 183 removed outlier: 3.809A pdb=" N ALA A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 180 " --> pdb=" O PRO A 176 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ASN A 181 " --> pdb=" O GLY A 177 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TYR A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 199 removed outlier: 3.705A pdb=" N THR A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) Proline residue: A 190 - end of helix removed outlier: 3.608A pdb=" N GLY A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 Processing helix chain 'A' and resid 210 through 226 removed outlier: 3.738A pdb=" N CYS A 216 " --> pdb=" O GLY A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 274 Processing helix chain 'A' and resid 317 through 345 removed outlier: 3.962A pdb=" N ALA A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 374 Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.643A pdb=" N THR A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 removed outlier: 3.553A pdb=" N THR A 417 " --> pdb=" O ILE A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 444 removed outlier: 3.921A pdb=" N CYS A 433 " --> pdb=" O GLY A 429 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 478 removed outlier: 3.840A pdb=" N PHE A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Proline residue: A 472 - end of helix Processing helix chain 'A' and resid 479 through 482 removed outlier: 3.994A pdb=" N ILE A 482 " --> pdb=" O PRO A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 486 through 498 Processing helix chain 'A' and resid 499 through 515 Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'B' and resid 46 through 59 removed outlier: 3.645A pdb=" N GLY B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.792A pdb=" N PHE B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 100 removed outlier: 4.073A pdb=" N VAL B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR B 85 " --> pdb=" O GLN B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.534A pdb=" N ALA B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 136 Processing helix chain 'B' and resid 145 through 174 Proline residue: B 151 - end of helix removed outlier: 3.827A pdb=" N GLU B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 166 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 183 removed outlier: 3.809A pdb=" N ALA B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 180 " --> pdb=" O PRO B 176 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ASN B 181 " --> pdb=" O GLY B 177 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TYR B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 199 removed outlier: 3.705A pdb=" N THR B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) Proline residue: B 190 - end of helix removed outlier: 3.608A pdb=" N GLY B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 Processing helix chain 'B' and resid 210 through 226 removed outlier: 3.738A pdb=" N CYS B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 274 Processing helix chain 'B' and resid 317 through 345 removed outlier: 3.962A pdb=" N ALA B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 374 Processing helix chain 'B' and resid 396 through 413 removed outlier: 3.643A pdb=" N THR B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 421 removed outlier: 3.553A pdb=" N THR B 417 " --> pdb=" O ILE B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 444 removed outlier: 3.921A pdb=" N CYS B 433 " --> pdb=" O GLY B 429 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 478 removed outlier: 3.840A pdb=" N PHE B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER B 464 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Proline residue: B 472 - end of helix Processing helix chain 'B' and resid 479 through 482 removed outlier: 3.994A pdb=" N ILE B 482 " --> pdb=" O PRO B 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 479 through 482' Processing helix chain 'B' and resid 486 through 498 Processing helix chain 'B' and resid 499 through 515 Processing helix chain 'B' and resid 518 through 523 418 hydrogen bonds defined for protein. 1254 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: 1.87 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1112 1.32 - 1.45: 1686 1.45 - 1.57: 3850 1.57 - 1.70: 4 1.70 - 1.82: 76 Bond restraints: 6728 Sorted by residual: bond pdb=" C ASP A 205 " pdb=" N ARG A 206 " ideal model delta sigma weight residual 1.335 1.404 -0.069 1.31e-02 5.83e+03 2.81e+01 bond pdb=" C ASP B 205 " pdb=" N ARG B 206 " ideal model delta sigma weight residual 1.335 1.404 -0.069 1.31e-02 5.83e+03 2.81e+01 bond pdb=" C ILE B 222 " pdb=" O ILE B 222 " ideal model delta sigma weight residual 1.237 1.295 -0.059 1.13e-02 7.83e+03 2.69e+01 bond pdb=" C ILE A 222 " pdb=" O ILE A 222 " ideal model delta sigma weight residual 1.237 1.295 -0.059 1.13e-02 7.83e+03 2.69e+01 bond pdb=" C ARG B 456 " pdb=" O ARG B 456 " ideal model delta sigma weight residual 1.236 1.285 -0.049 1.16e-02 7.43e+03 1.75e+01 ... (remaining 6723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 5204 1.43 - 2.87: 2928 2.87 - 4.30: 920 4.30 - 5.74: 110 5.74 - 7.17: 16 Bond angle restraints: 9178 Sorted by residual: angle pdb=" O ASP A 205 " pdb=" C ASP A 205 " pdb=" N ARG A 206 " ideal model delta sigma weight residual 122.07 128.06 -5.99 1.03e+00 9.43e-01 3.38e+01 angle pdb=" O ASP B 205 " pdb=" C ASP B 205 " pdb=" N ARG B 206 " ideal model delta sigma weight residual 122.07 128.06 -5.99 1.03e+00 9.43e-01 3.38e+01 angle pdb=" N GLN B 287 " pdb=" CA GLN B 287 " pdb=" C GLN B 287 " ideal model delta sigma weight residual 114.04 107.87 6.17 1.24e+00 6.50e-01 2.47e+01 angle pdb=" N GLN A 287 " pdb=" CA GLN A 287 " pdb=" C GLN A 287 " ideal model delta sigma weight residual 114.04 107.87 6.17 1.24e+00 6.50e-01 2.47e+01 angle pdb=" CA PHE A 200 " pdb=" CB PHE A 200 " pdb=" CG PHE A 200 " ideal model delta sigma weight residual 113.80 118.63 -4.83 1.00e+00 1.00e+00 2.34e+01 ... (remaining 9173 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 14.06: 3598 14.06 - 28.12: 220 28.12 - 42.17: 44 42.17 - 56.23: 20 56.23 - 70.29: 24 Dihedral angle restraints: 3906 sinusoidal: 1452 harmonic: 2454 Sorted by residual: dihedral pdb=" N LYS A 128 " pdb=" CA LYS A 128 " pdb=" CB LYS A 128 " pdb=" CG LYS A 128 " ideal model delta sinusoidal sigma weight residual -180.00 -121.07 -58.93 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LYS B 128 " pdb=" CA LYS B 128 " pdb=" CB LYS B 128 " pdb=" CG LYS B 128 " ideal model delta sinusoidal sigma weight residual -180.00 -121.07 -58.93 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA ILE B 369 " pdb=" CB ILE B 369 " pdb=" CG1 ILE B 369 " pdb=" CD1 ILE B 369 " ideal model delta sinusoidal sigma weight residual 180.00 122.31 57.69 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 544 0.050 - 0.100: 350 0.100 - 0.150: 152 0.150 - 0.200: 58 0.200 - 0.250: 6 Chirality restraints: 1110 Sorted by residual: chirality pdb=" CA VAL A 450 " pdb=" N VAL A 450 " pdb=" C VAL A 450 " pdb=" CB VAL A 450 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA VAL B 450 " pdb=" N VAL B 450 " pdb=" C VAL B 450 " pdb=" CB VAL B 450 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA PRO B 151 " pdb=" N PRO B 151 " pdb=" C PRO B 151 " pdb=" CB PRO B 151 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1107 not shown) Planarity restraints: 1140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 466 " -0.035 2.00e-02 2.50e+03 2.82e-02 1.39e+01 pdb=" CG PHE B 466 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE B 466 " 0.051 2.00e-02 2.50e+03 pdb=" CD2 PHE B 466 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE B 466 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 PHE B 466 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 466 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 466 " 0.035 2.00e-02 2.50e+03 2.82e-02 1.39e+01 pdb=" CG PHE A 466 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE A 466 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 PHE A 466 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE A 466 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 PHE A 466 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 466 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 340 " 0.039 2.00e-02 2.50e+03 2.10e-02 8.82e+00 pdb=" CG TYR A 340 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 340 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 340 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR A 340 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 340 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 340 " 0.023 2.00e-02 2.50e+03 pdb=" OH TYR A 340 " 0.010 2.00e-02 2.50e+03 ... (remaining 1137 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 488 2.77 - 3.30: 7642 3.30 - 3.83: 11118 3.83 - 4.37: 14817 4.37 - 4.90: 23097 Nonbonded interactions: 57162 Sorted by model distance: nonbonded pdb=" O PHE A 325 " pdb=" OG1 THR A 328 " model vdw 2.235 3.040 nonbonded pdb=" O PHE B 325 " pdb=" OG1 THR B 328 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR A 340 " pdb=" NH1 ARG A 344 " model vdw 2.338 3.120 nonbonded pdb=" OH TYR B 340 " pdb=" NH1 ARG B 344 " model vdw 2.338 3.120 nonbonded pdb=" O VAL A 460 " pdb=" OG SER A 464 " model vdw 2.378 3.040 ... (remaining 57157 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 0.070 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.500 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.015 0.082 6728 Z= 1.134 Angle : 1.804 7.172 9178 Z= 1.397 Chirality : 0.077 0.250 1110 Planarity : 0.010 0.094 1140 Dihedral : 12.099 70.286 2338 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.28 % Allowed : 4.79 % Favored : 94.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.25), residues: 856 helix: -1.51 (0.18), residues: 572 sheet: None (None), residues: 0 loop : -2.08 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.007 TRP B 127 HIS 0.011 0.004 HIS A 210 PHE 0.051 0.006 PHE A 466 TYR 0.039 0.007 TYR A 340 ARG 0.032 0.004 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.23971 ( 418) hydrogen bonds : angle 7.70625 ( 1254) covalent geometry : bond 0.01520 ( 6728) covalent geometry : angle 1.80408 ( 9178) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 258 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 HIS cc_start: 0.8949 (t-90) cc_final: 0.8544 (t70) REVERT: A 186 LEU cc_start: 0.8793 (mt) cc_final: 0.8420 (mp) REVERT: A 295 ASP cc_start: 0.8215 (t70) cc_final: 0.7565 (t0) REVERT: A 363 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8331 (mm-30) REVERT: A 451 ASP cc_start: 0.8389 (t70) cc_final: 0.8180 (t0) REVERT: B 77 HIS cc_start: 0.8949 (t-90) cc_final: 0.8545 (t70) REVERT: B 186 LEU cc_start: 0.8793 (mt) cc_final: 0.8419 (mp) REVERT: B 295 ASP cc_start: 0.8212 (t70) cc_final: 0.7561 (t0) REVERT: B 363 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8330 (mm-30) REVERT: B 451 ASP cc_start: 0.8391 (t70) cc_final: 0.8181 (t0) outliers start: 2 outliers final: 0 residues processed: 260 average time/residue: 0.1612 time to fit residues: 56.3395 Evaluate side-chains 172 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 77 HIS A 147 HIS A 230 ASN A 478 ASN B 50 GLN B 77 HIS B 147 HIS B 230 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.129214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.102808 restraints weight = 15262.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.106275 restraints weight = 8930.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.108522 restraints weight = 6350.532| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6728 Z= 0.199 Angle : 0.735 8.528 9178 Z= 0.380 Chirality : 0.045 0.166 1110 Planarity : 0.005 0.026 1140 Dihedral : 3.764 12.405 916 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.10 % Allowed : 14.51 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.27), residues: 856 helix: 0.25 (0.19), residues: 618 sheet: None (None), residues: 0 loop : -1.05 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 149 HIS 0.009 0.002 HIS B 147 PHE 0.011 0.002 PHE B 502 TYR 0.018 0.002 TYR A 340 ARG 0.003 0.001 ARG A 522 Details of bonding type rmsd hydrogen bonds : bond 0.06776 ( 418) hydrogen bonds : angle 5.12463 ( 1254) covalent geometry : bond 0.00434 ( 6728) covalent geometry : angle 0.73544 ( 9178) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 PHE cc_start: 0.8222 (t80) cc_final: 0.7884 (t80) REVERT: A 97 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7714 (mm-40) REVERT: A 255 PHE cc_start: 0.6623 (t80) cc_final: 0.6161 (m-80) REVERT: A 363 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7842 (mm-30) REVERT: A 407 MET cc_start: 0.8569 (mmm) cc_final: 0.8291 (mmm) REVERT: B 56 PHE cc_start: 0.8228 (t80) cc_final: 0.7896 (t80) REVERT: B 97 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7712 (mm-40) REVERT: B 255 PHE cc_start: 0.6622 (t80) cc_final: 0.6161 (m-80) REVERT: B 363 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7841 (mm-30) REVERT: B 407 MET cc_start: 0.8565 (mmm) cc_final: 0.8287 (mmm) outliers start: 22 outliers final: 10 residues processed: 180 average time/residue: 0.1479 time to fit residues: 36.5619 Evaluate side-chains 148 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 493 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 43 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 2 optimal weight: 0.0020 chunk 14 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS A 473 ASN B 147 HIS B 473 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.131723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.105540 restraints weight = 15702.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.109158 restraints weight = 9102.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.111497 restraints weight = 6461.764| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6728 Z= 0.146 Angle : 0.656 7.813 9178 Z= 0.329 Chirality : 0.043 0.144 1110 Planarity : 0.004 0.032 1140 Dihedral : 3.690 12.700 916 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.51 % Allowed : 16.76 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.28), residues: 856 helix: 1.11 (0.20), residues: 618 sheet: None (None), residues: 0 loop : -0.48 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 149 HIS 0.008 0.001 HIS B 147 PHE 0.013 0.001 PHE B 466 TYR 0.013 0.002 TYR B 340 ARG 0.004 0.001 ARG B 126 Details of bonding type rmsd hydrogen bonds : bond 0.05394 ( 418) hydrogen bonds : angle 4.48459 ( 1254) covalent geometry : bond 0.00317 ( 6728) covalent geometry : angle 0.65583 ( 9178) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7704 (mp10) REVERT: A 255 PHE cc_start: 0.6153 (t80) cc_final: 0.5910 (m-80) REVERT: A 407 MET cc_start: 0.8651 (mmm) cc_final: 0.8440 (mmm) REVERT: A 451 ASP cc_start: 0.8195 (t70) cc_final: 0.7973 (t0) REVERT: B 81 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7699 (mp10) REVERT: B 255 PHE cc_start: 0.6145 (t80) cc_final: 0.5907 (m-80) REVERT: B 407 MET cc_start: 0.8653 (mmm) cc_final: 0.8442 (mmm) REVERT: B 451 ASP cc_start: 0.8199 (t70) cc_final: 0.7975 (t0) outliers start: 32 outliers final: 12 residues processed: 184 average time/residue: 0.1557 time to fit residues: 39.4535 Evaluate side-chains 144 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain B residue 52 TYR Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 493 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 1 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 13 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS B 147 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.130839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.103759 restraints weight = 15548.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.107215 restraints weight = 9139.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.109524 restraints weight = 6533.325| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6728 Z= 0.145 Angle : 0.650 7.564 9178 Z= 0.322 Chirality : 0.043 0.135 1110 Planarity : 0.004 0.033 1140 Dihedral : 3.660 12.740 916 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.94 % Allowed : 19.86 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.28), residues: 856 helix: 1.36 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -0.17 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 149 HIS 0.008 0.001 HIS A 147 PHE 0.016 0.002 PHE A 420 TYR 0.012 0.002 TYR A 340 ARG 0.002 0.000 ARG B 522 Details of bonding type rmsd hydrogen bonds : bond 0.05188 ( 418) hydrogen bonds : angle 4.32507 ( 1254) covalent geometry : bond 0.00321 ( 6728) covalent geometry : angle 0.65038 ( 9178) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7956 (tm-30) REVERT: A 407 MET cc_start: 0.8555 (mmm) cc_final: 0.8337 (mmm) REVERT: A 408 LEU cc_start: 0.9194 (pp) cc_final: 0.8969 (pp) REVERT: B 133 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7955 (tm-30) REVERT: B 407 MET cc_start: 0.8559 (mmm) cc_final: 0.8341 (mmm) REVERT: B 408 LEU cc_start: 0.9197 (pp) cc_final: 0.8972 (pp) outliers start: 28 outliers final: 18 residues processed: 172 average time/residue: 0.1417 time to fit residues: 34.5566 Evaluate side-chains 160 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain B residue 52 TYR Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 493 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 33 optimal weight: 0.0980 chunk 73 optimal weight: 40.0000 chunk 60 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS B 147 HIS B 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.126762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.099833 restraints weight = 15559.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.103105 restraints weight = 9278.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.105222 restraints weight = 6709.588| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6728 Z= 0.201 Angle : 0.689 7.250 9178 Z= 0.346 Chirality : 0.046 0.183 1110 Planarity : 0.004 0.035 1140 Dihedral : 3.808 12.842 916 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.51 % Allowed : 18.87 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.28), residues: 856 helix: 1.03 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -0.20 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 149 HIS 0.019 0.002 HIS B 147 PHE 0.020 0.002 PHE A 420 TYR 0.013 0.002 TYR A 340 ARG 0.003 0.000 ARG B 522 Details of bonding type rmsd hydrogen bonds : bond 0.05781 ( 418) hydrogen bonds : angle 4.46327 ( 1254) covalent geometry : bond 0.00458 ( 6728) covalent geometry : angle 0.68948 ( 9178) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.8662 (mmm) cc_final: 0.8229 (mmm) REVERT: A 408 LEU cc_start: 0.9228 (pp) cc_final: 0.9025 (pp) REVERT: B 407 MET cc_start: 0.8659 (mmm) cc_final: 0.8227 (mmm) REVERT: B 408 LEU cc_start: 0.9230 (pp) cc_final: 0.9025 (pp) outliers start: 32 outliers final: 22 residues processed: 164 average time/residue: 0.1525 time to fit residues: 35.3333 Evaluate side-chains 164 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain B residue 52 TYR Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 493 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 19 optimal weight: 20.0000 chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 62 optimal weight: 30.0000 chunk 78 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS B 147 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.126856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.099981 restraints weight = 15282.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.103135 restraints weight = 9144.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.105266 restraints weight = 6620.860| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6728 Z= 0.188 Angle : 0.696 7.345 9178 Z= 0.347 Chirality : 0.044 0.150 1110 Planarity : 0.004 0.035 1140 Dihedral : 3.903 13.354 916 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.94 % Allowed : 19.44 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.28), residues: 856 helix: 1.04 (0.20), residues: 620 sheet: None (None), residues: 0 loop : -0.06 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 149 HIS 0.005 0.001 HIS B 147 PHE 0.018 0.002 PHE A 420 TYR 0.011 0.002 TYR B 340 ARG 0.002 0.000 ARG B 289 Details of bonding type rmsd hydrogen bonds : bond 0.05500 ( 418) hydrogen bonds : angle 4.37501 ( 1254) covalent geometry : bond 0.00430 ( 6728) covalent geometry : angle 0.69564 ( 9178) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: A 95 LEU cc_start: 0.9260 (tp) cc_final: 0.9010 (tt) REVERT: A 407 MET cc_start: 0.8702 (mmm) cc_final: 0.8285 (mmm) REVERT: A 408 LEU cc_start: 0.9270 (pp) cc_final: 0.9067 (pp) REVERT: B 68 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: B 95 LEU cc_start: 0.9265 (tp) cc_final: 0.9016 (tt) REVERT: B 407 MET cc_start: 0.8709 (mmm) cc_final: 0.8286 (mmm) REVERT: B 408 LEU cc_start: 0.9272 (pp) cc_final: 0.9068 (pp) outliers start: 28 outliers final: 22 residues processed: 158 average time/residue: 0.1366 time to fit residues: 30.9354 Evaluate side-chains 164 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain B residue 52 TYR Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 493 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 58 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 70 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS A 491 GLN B 147 HIS B 491 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.123477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.096633 restraints weight = 15482.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.099696 restraints weight = 9230.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.101545 restraints weight = 6721.941| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 6728 Z= 0.267 Angle : 0.769 9.519 9178 Z= 0.388 Chirality : 0.049 0.271 1110 Planarity : 0.005 0.037 1140 Dihedral : 4.212 22.682 916 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.51 % Allowed : 21.41 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.28), residues: 856 helix: 0.73 (0.20), residues: 620 sheet: None (None), residues: 0 loop : -0.18 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 149 HIS 0.023 0.003 HIS B 147 PHE 0.032 0.003 PHE A 255 TYR 0.013 0.002 TYR A 307 ARG 0.002 0.000 ARG B 522 Details of bonding type rmsd hydrogen bonds : bond 0.06372 ( 418) hydrogen bonds : angle 4.63225 ( 1254) covalent geometry : bond 0.00616 ( 6728) covalent geometry : angle 0.76939 ( 9178) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: A 95 LEU cc_start: 0.9290 (tp) cc_final: 0.9039 (tt) REVERT: A 328 THR cc_start: 0.8299 (m) cc_final: 0.8098 (m) REVERT: A 407 MET cc_start: 0.8729 (mmm) cc_final: 0.8280 (mmm) REVERT: B 68 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: B 95 LEU cc_start: 0.9294 (tp) cc_final: 0.9046 (tt) REVERT: B 328 THR cc_start: 0.8297 (m) cc_final: 0.8093 (m) REVERT: B 407 MET cc_start: 0.8733 (mmm) cc_final: 0.8284 (mmm) REVERT: B 408 LEU cc_start: 0.9303 (pp) cc_final: 0.9103 (pp) outliers start: 32 outliers final: 20 residues processed: 146 average time/residue: 0.1311 time to fit residues: 27.6476 Evaluate side-chains 148 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain B residue 52 TYR Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 89 CYS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 493 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 48 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 chunk 52 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 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 147 HIS A 226 GLN B 147 HIS B 491 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.130192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.103587 restraints weight = 15384.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.106939 restraints weight = 9032.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.108841 restraints weight = 6464.290| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.6411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6728 Z= 0.137 Angle : 0.703 12.428 9178 Z= 0.343 Chirality : 0.045 0.295 1110 Planarity : 0.004 0.027 1140 Dihedral : 3.971 21.973 916 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.24 % Allowed : 23.10 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.29), residues: 856 helix: 1.22 (0.20), residues: 622 sheet: None (None), residues: 0 loop : 0.13 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 311 HIS 0.008 0.001 HIS A 147 PHE 0.039 0.002 PHE B 255 TYR 0.018 0.002 TYR A 136 ARG 0.003 0.000 ARG B 206 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 418) hydrogen bonds : angle 4.18261 ( 1254) covalent geometry : bond 0.00299 ( 6728) covalent geometry : angle 0.70310 ( 9178) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.8725 (p) cc_final: 0.8433 (t) REVERT: A 68 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6676 (mp0) REVERT: A 87 PHE cc_start: 0.8833 (m-80) cc_final: 0.8508 (m-80) REVERT: A 95 LEU cc_start: 0.9249 (tp) cc_final: 0.9025 (tt) REVERT: A 407 MET cc_start: 0.8676 (mmm) cc_final: 0.8331 (mmm) REVERT: B 59 THR cc_start: 0.8722 (p) cc_final: 0.8428 (t) REVERT: B 68 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6692 (mp0) REVERT: B 87 PHE cc_start: 0.8855 (m-80) cc_final: 0.8508 (m-80) REVERT: B 95 LEU cc_start: 0.9253 (tp) cc_final: 0.9032 (tt) REVERT: B 407 MET cc_start: 0.8661 (mmm) cc_final: 0.8252 (mmm) outliers start: 23 outliers final: 15 residues processed: 163 average time/residue: 0.1321 time to fit residues: 30.8192 Evaluate side-chains 153 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 52 TYR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 345 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 0.0170 chunk 81 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS A 226 GLN B 147 HIS B 150 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.131468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.104775 restraints weight = 15512.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.108070 restraints weight = 9094.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.110251 restraints weight = 6512.594| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.6651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6728 Z= 0.143 Angle : 0.768 13.723 9178 Z= 0.363 Chirality : 0.046 0.276 1110 Planarity : 0.004 0.027 1140 Dihedral : 3.920 21.458 916 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.96 % Allowed : 25.35 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.28), residues: 856 helix: 1.15 (0.20), residues: 622 sheet: None (None), residues: 0 loop : 0.12 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 149 HIS 0.020 0.002 HIS A 147 PHE 0.033 0.002 PHE B 255 TYR 0.019 0.002 TYR A 136 ARG 0.002 0.000 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.04373 ( 418) hydrogen bonds : angle 4.21416 ( 1254) covalent geometry : bond 0.00315 ( 6728) covalent geometry : angle 0.76805 ( 9178) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6643 (mp0) REVERT: A 87 PHE cc_start: 0.8786 (m-80) cc_final: 0.8432 (m-80) REVERT: A 95 LEU cc_start: 0.9195 (tp) cc_final: 0.8966 (tt) REVERT: A 128 LYS cc_start: 0.8666 (pptt) cc_final: 0.8422 (pptt) REVERT: A 407 MET cc_start: 0.8645 (mmm) cc_final: 0.8328 (mmm) REVERT: A 501 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7933 (ptm) REVERT: B 68 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: B 87 PHE cc_start: 0.8812 (m-80) cc_final: 0.8434 (m-80) REVERT: B 95 LEU cc_start: 0.9198 (tp) cc_final: 0.8974 (tt) REVERT: B 128 LYS cc_start: 0.8660 (pptt) cc_final: 0.8416 (pptt) REVERT: B 407 MET cc_start: 0.8663 (mmm) cc_final: 0.8306 (mmm) REVERT: B 501 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7934 (ptm) outliers start: 21 outliers final: 13 residues processed: 153 average time/residue: 0.1372 time to fit residues: 30.2578 Evaluate side-chains 155 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain B residue 52 TYR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 501 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 20 optimal weight: 0.0570 chunk 76 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS A 226 GLN B 147 HIS B 491 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.130070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.103475 restraints weight = 15652.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.106675 restraints weight = 9175.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.108888 restraints weight = 6596.498| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.6753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6728 Z= 0.152 Angle : 0.777 12.599 9178 Z= 0.369 Chirality : 0.045 0.230 1110 Planarity : 0.004 0.028 1140 Dihedral : 3.986 21.342 916 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.68 % Allowed : 26.06 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.28), residues: 856 helix: 1.06 (0.21), residues: 620 sheet: None (None), residues: 0 loop : 0.02 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 149 HIS 0.017 0.002 HIS B 147 PHE 0.033 0.002 PHE B 255 TYR 0.019 0.002 TYR B 136 ARG 0.002 0.000 ARG B 289 Details of bonding type rmsd hydrogen bonds : bond 0.04571 ( 418) hydrogen bonds : angle 4.27799 ( 1254) covalent geometry : bond 0.00352 ( 6728) covalent geometry : angle 0.77686 ( 9178) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6603 (mp0) REVERT: A 95 LEU cc_start: 0.9203 (tp) cc_final: 0.8976 (tt) REVERT: A 128 LYS cc_start: 0.8672 (pptt) cc_final: 0.8436 (pptt) REVERT: A 254 MET cc_start: 0.5349 (ttp) cc_final: 0.4071 (mtt) REVERT: A 407 MET cc_start: 0.8670 (mmm) cc_final: 0.8422 (mmm) REVERT: B 68 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: B 95 LEU cc_start: 0.9207 (tp) cc_final: 0.8982 (tt) REVERT: B 128 LYS cc_start: 0.8663 (pptt) cc_final: 0.8427 (pptt) REVERT: B 254 MET cc_start: 0.5356 (ttp) cc_final: 0.4081 (mtt) REVERT: B 407 MET cc_start: 0.8686 (mmm) cc_final: 0.8428 (mmm) outliers start: 19 outliers final: 15 residues processed: 158 average time/residue: 0.1378 time to fit residues: 31.2698 Evaluate side-chains 158 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 52 TYR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 20 optimal weight: 6.9990 chunk 57 optimal weight: 0.0770 chunk 66 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 overall best weight: 2.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS B 147 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.128066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.100959 restraints weight = 15651.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.104147 restraints weight = 9335.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.106355 restraints weight = 6763.148| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.6868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6728 Z= 0.159 Angle : 0.778 12.087 9178 Z= 0.371 Chirality : 0.045 0.217 1110 Planarity : 0.004 0.029 1140 Dihedral : 4.059 21.459 916 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.96 % Allowed : 25.77 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.28), residues: 856 helix: 0.97 (0.20), residues: 618 sheet: None (None), residues: 0 loop : 0.06 (0.42), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 149 HIS 0.012 0.002 HIS B 147 PHE 0.031 0.002 PHE B 255 TYR 0.016 0.002 TYR A 136 ARG 0.002 0.000 ARG B 289 Details of bonding type rmsd hydrogen bonds : bond 0.04667 ( 418) hydrogen bonds : angle 4.33400 ( 1254) covalent geometry : bond 0.00369 ( 6728) covalent geometry : angle 0.77771 ( 9178) =============================================================================== Job complete usr+sys time: 2371.38 seconds wall clock time: 42 minutes 14.31 seconds (2534.31 seconds total)