Starting phenix.real_space_refine on Thu Nov 14 15:03:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jf0_36205/11_2024/8jf0_36205.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jf0_36205/11_2024/8jf0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jf0_36205/11_2024/8jf0_36205.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jf0_36205/11_2024/8jf0_36205.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jf0_36205/11_2024/8jf0_36205.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jf0_36205/11_2024/8jf0_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-5513/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: 5.11, per 1000 atoms: 0.78 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: 1.66 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: 0.68 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: 1.80 Time building geometry restraints manager: 1.90 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: 0.00 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: 0.880 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.060 Process input model: 19.940 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:3.120 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= 1.002 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 *********************** 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 : 0.811 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: 0.1979 time to fit residues: 70.1141 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 : 0.970 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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= 0.287 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 *********************** 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 : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 PHE cc_start: 0.7222 (t80) cc_final: 0.6291 (m-80) REVERT: A 334 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8156 (pp20) REVERT: A 363 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8546 (mm-30) REVERT: A 407 MET cc_start: 0.8913 (mmm) cc_final: 0.8655 (mmm) REVERT: A 488 GLU cc_start: 0.8716 (mp0) cc_final: 0.8238 (tp30) REVERT: B 255 PHE cc_start: 0.7221 (t80) cc_final: 0.6290 (m-80) REVERT: B 334 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8156 (pp20) REVERT: B 363 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8544 (mm-30) REVERT: B 407 MET cc_start: 0.8910 (mmm) cc_final: 0.8652 (mmm) REVERT: B 488 GLU cc_start: 0.8716 (mp0) cc_final: 0.8239 (tp30) outliers start: 22 outliers final: 10 residues processed: 180 average time/residue: 0.1643 time to fit residues: 40.6068 Evaluate side-chains 150 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 334 GLU 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 334 GLU 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 43 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 64 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 0.0370 chunk 78 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- 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 B 478 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6728 Z= 0.252 Angle : 0.675 7.718 9178 Z= 0.342 Chirality : 0.044 0.142 1110 Planarity : 0.004 0.032 1140 Dihedral : 3.784 12.902 916 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 5.07 % Allowed : 15.77 % Favored : 79.15 % 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: 0.69 (0.28), residues: 856 helix: 0.87 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -0.46 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 149 HIS 0.008 0.001 HIS A 147 PHE 0.015 0.002 PHE B 466 TYR 0.014 0.002 TYR B 340 ARG 0.003 0.001 ARG A 126 *********************** 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 194 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8134 (pp20) REVERT: A 410 LEU cc_start: 0.9303 (mp) cc_final: 0.9087 (mp) REVERT: A 451 ASP cc_start: 0.8475 (t70) cc_final: 0.8205 (t0) REVERT: A 512 ASP cc_start: 0.8790 (t0) cc_final: 0.8560 (t0) REVERT: B 334 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8133 (pp20) REVERT: B 410 LEU cc_start: 0.9301 (mp) cc_final: 0.9085 (mp) REVERT: B 451 ASP cc_start: 0.8474 (t70) cc_final: 0.8205 (t0) REVERT: B 512 ASP cc_start: 0.8789 (t0) cc_final: 0.8561 (t0) outliers start: 36 outliers final: 18 residues processed: 172 average time/residue: 0.1630 time to fit residues: 38.9645 Evaluate side-chains 144 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 135 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 334 GLU 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 135 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 334 GLU 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 77 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.5449 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= 0.246 Angle : 0.667 7.213 9178 Z= 0.334 Chirality : 0.044 0.136 1110 Planarity : 0.004 0.034 1140 Dihedral : 3.857 15.107 916 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 5.35 % Allowed : 16.90 % Favored : 77.75 % 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: 1.05 (0.28), residues: 856 helix: 1.11 (0.20), residues: 622 sheet: None (None), residues: 0 loop : -0.21 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 149 HIS 0.008 0.001 HIS B 147 PHE 0.011 0.002 PHE B 255 TYR 0.012 0.002 TYR A 340 ARG 0.002 0.000 ARG B 522 *********************** 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 186 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 PHE cc_start: 0.7048 (t80) cc_final: 0.6471 (p90) REVERT: A 304 ARG cc_start: 0.8100 (tpp-160) cc_final: 0.7801 (ttp80) REVERT: A 334 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8126 (pp20) REVERT: A 407 MET cc_start: 0.8852 (mmm) cc_final: 0.8484 (mmm) REVERT: A 512 ASP cc_start: 0.8803 (t0) cc_final: 0.8568 (t0) REVERT: B 255 PHE cc_start: 0.7048 (t80) cc_final: 0.6472 (p90) REVERT: B 304 ARG cc_start: 0.8098 (tpp-160) cc_final: 0.7801 (ttp80) REVERT: B 334 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8126 (pp20) REVERT: B 407 MET cc_start: 0.8852 (mmm) cc_final: 0.8487 (mmm) REVERT: B 512 ASP cc_start: 0.8803 (t0) cc_final: 0.8570 (t0) outliers start: 38 outliers final: 24 residues processed: 168 average time/residue: 0.1488 time to fit residues: 34.9926 Evaluate side-chains 162 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 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 147 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 334 GLU 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 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 147 HIS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 334 GLU 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 69 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 42 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 20 optimal weight: 0.0040 overall best weight: 3.1398 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6728 Z= 0.230 Angle : 0.672 12.410 9178 Z= 0.327 Chirality : 0.045 0.208 1110 Planarity : 0.004 0.034 1140 Dihedral : 3.828 14.924 916 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.80 % Allowed : 19.86 % Favored : 76.34 % 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: 1.14 (0.28), residues: 856 helix: 1.16 (0.20), residues: 622 sheet: None (None), residues: 0 loop : -0.12 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 149 HIS 0.007 0.001 HIS B 147 PHE 0.011 0.001 PHE B 200 TYR 0.012 0.002 TYR B 340 ARG 0.002 0.000 ARG B 289 *********************** 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 173 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 PHE cc_start: 0.6799 (t80) cc_final: 0.6198 (p90) REVERT: A 258 MET cc_start: 0.8229 (mtm) cc_final: 0.7970 (mtm) REVERT: A 304 ARG cc_start: 0.8161 (tpp-160) cc_final: 0.7905 (ttp80) REVERT: A 334 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8141 (pp20) REVERT: A 407 MET cc_start: 0.8903 (mmm) cc_final: 0.8538 (mmm) REVERT: A 512 ASP cc_start: 0.8830 (t0) cc_final: 0.8617 (t0) REVERT: B 255 PHE cc_start: 0.6797 (t80) cc_final: 0.6197 (p90) REVERT: B 258 MET cc_start: 0.8231 (mtm) cc_final: 0.7971 (mtm) REVERT: B 304 ARG cc_start: 0.8161 (tpp-160) cc_final: 0.7905 (ttp80) REVERT: B 334 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8140 (pp20) REVERT: B 407 MET cc_start: 0.8905 (mmm) cc_final: 0.8538 (mmm) REVERT: B 451 ASP cc_start: 0.8522 (t0) cc_final: 0.8314 (t0) REVERT: B 512 ASP cc_start: 0.8829 (t0) cc_final: 0.8618 (t0) outliers start: 27 outliers final: 16 residues processed: 160 average time/residue: 0.1492 time to fit residues: 33.2054 Evaluate side-chains 154 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 89 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 334 GLU 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 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 334 GLU 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 27 optimal weight: 5.9990 chunk 74 optimal weight: 30.0000 chunk 16 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 43 optimal weight: 30.0000 chunk 80 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 150 HIS B 491 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6728 Z= 0.274 Angle : 0.681 9.883 9178 Z= 0.337 Chirality : 0.045 0.150 1110 Planarity : 0.004 0.034 1140 Dihedral : 3.881 14.611 916 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.38 % Allowed : 20.42 % 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: 1.04 (0.28), residues: 856 helix: 1.04 (0.20), residues: 620 sheet: None (None), residues: 0 loop : -0.01 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 149 HIS 0.012 0.002 HIS B 147 PHE 0.013 0.002 PHE B 200 TYR 0.012 0.002 TYR A 340 ARG 0.002 0.000 ARG A 522 *********************** 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 164 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 ARG cc_start: 0.8216 (tpp-160) cc_final: 0.7980 (ttp80) REVERT: A 334 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8166 (pp20) REVERT: A 407 MET cc_start: 0.8911 (mmm) cc_final: 0.8663 (mmm) REVERT: B 304 ARG cc_start: 0.8217 (tpp-160) cc_final: 0.7981 (ttp80) REVERT: B 334 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8166 (pp20) REVERT: B 407 MET cc_start: 0.8913 (mmm) cc_final: 0.8663 (mmm) REVERT: B 451 ASP cc_start: 0.8680 (t0) cc_final: 0.8436 (t0) outliers start: 24 outliers final: 18 residues processed: 150 average time/residue: 0.1633 time to fit residues: 34.1860 Evaluate side-chains 150 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 89 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 334 GLU 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 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 263 THR Chi-restraints excluded: chain B residue 334 GLU 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 9 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 51 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS A 150 HIS B 147 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.6117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6728 Z= 0.215 Angle : 0.683 9.682 9178 Z= 0.332 Chirality : 0.045 0.305 1110 Planarity : 0.004 0.030 1140 Dihedral : 3.849 14.496 916 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.52 % Allowed : 22.68 % Favored : 73.80 % 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: 1.28 (0.28), residues: 856 helix: 1.27 (0.20), residues: 620 sheet: None (None), residues: 0 loop : -0.10 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 149 HIS 0.019 0.002 HIS A 147 PHE 0.011 0.002 PHE A 200 TYR 0.011 0.002 TYR A 340 ARG 0.001 0.000 ARG B 289 *********************** 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: 25 poor density : 137 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 ARG cc_start: 0.8221 (tpp-160) cc_final: 0.7944 (ttp80) REVERT: A 334 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8190 (pp20) REVERT: A 407 MET cc_start: 0.8961 (mmm) cc_final: 0.8541 (mmm) REVERT: A 512 ASP cc_start: 0.8808 (t0) cc_final: 0.8571 (t0) REVERT: B 304 ARG cc_start: 0.8222 (tpp-160) cc_final: 0.7947 (ttp80) REVERT: B 334 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8190 (pp20) REVERT: B 407 MET cc_start: 0.8961 (mmm) cc_final: 0.8574 (mmm) REVERT: B 451 ASP cc_start: 0.8684 (t0) cc_final: 0.8402 (t0) REVERT: B 512 ASP cc_start: 0.8809 (t0) cc_final: 0.8571 (t0) outliers start: 25 outliers final: 20 residues processed: 152 average time/residue: 0.1490 time to fit residues: 31.7268 Evaluate side-chains 154 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 145 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 334 GLU 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 145 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 334 GLU 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 24 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 52 optimal weight: 0.0170 chunk 56 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 65 optimal weight: 40.0000 chunk 75 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 overall best weight: 5.0026 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 6728 Z= 0.309 Angle : 0.728 9.414 9178 Z= 0.361 Chirality : 0.047 0.317 1110 Planarity : 0.004 0.030 1140 Dihedral : 4.056 16.009 916 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.37 % Allowed : 22.68 % Favored : 72.96 % 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: 1.03 (0.29), residues: 856 helix: 1.04 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -0.03 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 149 HIS 0.014 0.002 HIS B 147 PHE 0.015 0.002 PHE B 200 TYR 0.015 0.002 TYR A 136 ARG 0.002 0.000 ARG B 522 *********************** 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 170 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 ARG cc_start: 0.8264 (tpp-160) cc_final: 0.7926 (ttp80) REVERT: A 407 MET cc_start: 0.8910 (mmm) cc_final: 0.8503 (mmm) REVERT: B 304 ARG cc_start: 0.8264 (tpp-160) cc_final: 0.7928 (ttp80) REVERT: B 407 MET cc_start: 0.8934 (mmm) cc_final: 0.8538 (mmm) REVERT: B 451 ASP cc_start: 0.8718 (t0) cc_final: 0.8424 (t0) outliers start: 31 outliers final: 25 residues processed: 158 average time/residue: 0.1453 time to fit residues: 32.0296 Evaluate side-chains 153 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 60 ILE Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 179 LEU 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 60 ILE 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 147 HIS Chi-restraints excluded: chain B residue 179 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 73 optimal weight: 0.0670 chunk 76 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.6541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6728 Z= 0.217 Angle : 0.798 16.529 9178 Z= 0.367 Chirality : 0.045 0.208 1110 Planarity : 0.004 0.026 1140 Dihedral : 4.085 23.497 916 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.24 % Allowed : 24.37 % Favored : 72.39 % 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: 1.24 (0.29), residues: 856 helix: 1.19 (0.21), residues: 620 sheet: None (None), residues: 0 loop : 0.04 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 149 HIS 0.021 0.003 HIS B 147 PHE 0.010 0.001 PHE B 420 TYR 0.013 0.002 TYR B 136 ARG 0.003 0.000 ARG B 206 *********************** 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 165 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.8827 (mmm) cc_final: 0.8482 (mmm) REVERT: B 407 MET cc_start: 0.8859 (mmm) cc_final: 0.8525 (mmm) REVERT: B 451 ASP cc_start: 0.8715 (t0) cc_final: 0.8384 (t0) outliers start: 23 outliers final: 17 residues processed: 155 average time/residue: 0.1479 time to fit residues: 32.7306 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 : 0.939 ------------------------------------------------------------------------------- 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 81 GLN Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain B residue 52 TYR Chi-restraints excluded: chain B residue 60 ILE 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 179 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 425 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.6717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6728 Z= 0.241 Angle : 0.824 16.070 9178 Z= 0.375 Chirality : 0.047 0.363 1110 Planarity : 0.004 0.030 1140 Dihedral : 4.013 18.879 916 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.68 % Allowed : 25.49 % Favored : 71.83 % 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: 1.12 (0.28), residues: 856 helix: 1.13 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -0.07 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 311 HIS 0.016 0.002 HIS A 147 PHE 0.026 0.002 PHE A 255 TYR 0.019 0.002 TYR B 136 ARG 0.002 0.000 ARG B 289 ********************** 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 159 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.8951 (mmm) cc_final: 0.8593 (mmm) REVERT: B 407 MET cc_start: 0.8889 (mmm) cc_final: 0.8560 (mmm) REVERT: B 451 ASP cc_start: 0.8718 (t0) cc_final: 0.8381 (t0) outliers start: 19 outliers final: 19 residues processed: 151 average time/residue: 0.1465 time to fit residues: 31.5655 Evaluate side-chains 156 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 81 GLN Chi-restraints excluded: chain A residue 89 CYS 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 179 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain B residue 52 TYR Chi-restraints excluded: chain B residue 60 ILE 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 345 LEU Chi-restraints excluded: chain B residue 425 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.129537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.103122 restraints weight = 15339.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.106318 restraints weight = 9153.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.108557 restraints weight = 6616.544| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.6971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6728 Z= 0.220 Angle : 0.833 16.221 9178 Z= 0.380 Chirality : 0.047 0.343 1110 Planarity : 0.004 0.025 1140 Dihedral : 4.079 19.973 916 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.82 % Allowed : 25.35 % Favored : 71.83 % 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: 1.23 (0.28), residues: 856 helix: 1.21 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -0.00 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 265 HIS 0.019 0.002 HIS B 147 PHE 0.015 0.002 PHE A 255 TYR 0.013 0.002 TYR A 136 ARG 0.003 0.000 ARG B 206 =============================================================================== Job complete usr+sys time: 1503.62 seconds wall clock time: 28 minutes 30.94 seconds (1710.94 seconds total)