Starting phenix.real_space_refine on Sat Aug 23 13:52:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9axa_43931/08_2025/9axa_43931.cif Found real_map, /net/cci-nas-00/data/ceres_data/9axa_43931/08_2025/9axa_43931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9axa_43931/08_2025/9axa_43931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9axa_43931/08_2025/9axa_43931.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9axa_43931/08_2025/9axa_43931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9axa_43931/08_2025/9axa_43931.map" } resolution = 4.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 80 5.16 5 C 7902 2.51 5 N 2115 2.21 5 O 2318 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12421 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2207 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 12, 'TRANS': 260} Chain breaks: 2 Chain: "B" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2186 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 12, 'TRANS': 265} Chain breaks: 2 Chain: "C" Number of atoms: 2224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2224 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 2 Chain: "D" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2166 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 2 Chain: "E" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1785 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1785 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'A1AHE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'A1AHE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.84, per 1000 atoms: 0.23 Number of scatterers: 12421 At special positions: 0 Unit cell: (92.3355, 162.945, 101.388, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 2 15.00 F 4 9.00 O 2318 8.00 N 2115 7.00 C 7902 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 499.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2924 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 9 sheets defined 59.9% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 383 through 399 removed outlier: 3.865A pdb=" N LYS A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 435 Processing helix chain 'A' and resid 441 through 462 Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 526 through 542 removed outlier: 3.809A pdb=" N ASP A 530 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 569 through 573 removed outlier: 4.096A pdb=" N LYS A 572 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 589 removed outlier: 3.623A pdb=" N VAL A 589 " --> pdb=" O VAL A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 611 Processing helix chain 'B' and resid 53 through 59 removed outlier: 3.698A pdb=" N LYS B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 150 through 159 removed outlier: 3.533A pdb=" N VAL B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 184 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 231 through 237 Processing helix chain 'B' and resid 241 through 259 removed outlier: 4.057A pdb=" N ASP B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 331 through 342 Processing helix chain 'B' and resid 351 through 357 Processing helix chain 'B' and resid 358 through 367 Processing helix chain 'B' and resid 370 through 380 Processing helix chain 'C' and resid 383 through 399 removed outlier: 3.727A pdb=" N PHE C 387 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 389 " --> pdb=" O GLU C 385 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 Processing helix chain 'C' and resid 441 through 462 Processing helix chain 'C' and resid 508 through 512 removed outlier: 3.829A pdb=" N TRP C 511 " --> pdb=" O SER C 508 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET C 512 " --> pdb=" O VAL C 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 508 through 512' Processing helix chain 'C' and resid 513 through 519 Processing helix chain 'C' and resid 526 through 544 removed outlier: 3.786A pdb=" N ASP C 530 " --> pdb=" O SER C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 563 removed outlier: 3.679A pdb=" N ILE C 557 " --> pdb=" O ASN C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 589 removed outlier: 3.503A pdb=" N VAL C 589 " --> pdb=" O VAL C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 612 removed outlier: 3.509A pdb=" N ILE C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 104 through 116 Processing helix chain 'D' and resid 117 through 121 removed outlier: 3.687A pdb=" N CYS D 121 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 159 Processing helix chain 'D' and resid 162 through 185 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 241 through 259 removed outlier: 4.147A pdb=" N ASP D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 331 through 342 Processing helix chain 'D' and resid 351 through 356 Processing helix chain 'D' and resid 358 through 367 Processing helix chain 'D' and resid 370 through 380 Processing helix chain 'E' and resid 2 through 16 Processing helix chain 'E' and resid 18 through 32 Processing helix chain 'E' and resid 37 through 70 Processing helix chain 'E' and resid 79 through 111 removed outlier: 5.850A pdb=" N ILE E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 133 Processing helix chain 'E' and resid 137 through 162 removed outlier: 3.756A pdb=" N LYS E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 183 Processing helix chain 'E' and resid 186 through 204 Processing helix chain 'E' and resid 205 through 208 removed outlier: 3.713A pdb=" N LEU E 208 " --> pdb=" O LEU E 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 205 through 208' Processing helix chain 'E' and resid 209 through 231 removed outlier: 3.694A pdb=" N ILE E 219 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU E 222 " --> pdb=" O LEU E 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 15 Processing helix chain 'F' and resid 18 through 32 Processing helix chain 'F' and resid 37 through 70 Processing helix chain 'F' and resid 79 through 111 removed outlier: 5.893A pdb=" N ILE F 108 " --> pdb=" O ASP F 104 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LYS F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 134 Processing helix chain 'F' and resid 137 through 162 Processing helix chain 'F' and resid 166 through 183 Processing helix chain 'F' and resid 186 through 205 Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 209 through 231 removed outlier: 4.131A pdb=" N ILE F 219 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU F 222 " --> pdb=" O LEU F 218 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 350 through 354 removed outlier: 6.364A pdb=" N LEU A 351 " --> pdb=" O LYS A 367 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS A 367 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 353 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 417 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 418 " --> pdb=" O MET A 412 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 410 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN A 422 " --> pdb=" O PHE A 408 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N PHE A 408 " --> pdb=" O GLN A 422 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AA3, first strand: chain 'A' and resid 474 through 477 Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 87 removed outlier: 3.670A pdb=" N LEU B 92 " --> pdb=" O HIS B 87 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 139 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 131 " --> pdb=" O CYS B 142 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLU B 144 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N PHE B 129 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 196 through 198 Processing sheet with id=AA6, first strand: chain 'C' and resid 365 through 367 removed outlier: 3.582A pdb=" N VAL C 372 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE C 419 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 418 " --> pdb=" O MET C 412 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET C 412 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY C 410 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N GLN C 422 " --> pdb=" O PHE C 408 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N PHE C 408 " --> pdb=" O GLN C 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 426 through 428 removed outlier: 3.901A pdb=" N SER C 427 " --> pdb=" O LEU C 476 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 68 through 73 removed outlier: 6.429A pdb=" N LYS D 70 " --> pdb=" O SER D 86 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER D 86 " --> pdb=" O LYS D 70 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS D 97 " --> pdb=" O ILE D 141 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE D 141 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE D 99 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D 139 " --> pdb=" O ILE D 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 149 through 150 709 hydrogen bonds defined for protein. 2085 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: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3382 1.34 - 1.46: 2453 1.46 - 1.58: 6674 1.58 - 1.70: 12 1.70 - 1.82: 136 Bond restraints: 12657 Sorted by residual: bond pdb=" N GLU C 343 " pdb=" CA GLU C 343 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.39e+00 bond pdb=" N MET A 519 " pdb=" CA MET A 519 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.55e+00 bond pdb=" C21 A1AHE D 401 " pdb=" N22 A1AHE D 401 " ideal model delta sigma weight residual 1.306 1.357 -0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" N MET D 219 " pdb=" CA MET D 219 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.31e+00 bond pdb=" C21 A1AHE B 401 " pdb=" N22 A1AHE B 401 " ideal model delta sigma weight residual 1.306 1.355 -0.049 2.00e-02 2.50e+03 6.03e+00 ... (remaining 12652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 16515 2.48 - 4.97: 428 4.97 - 7.45: 95 7.45 - 9.94: 19 9.94 - 12.42: 5 Bond angle restraints: 17062 Sorted by residual: angle pdb=" CB MET A 412 " pdb=" CG MET A 412 " pdb=" SD MET A 412 " ideal model delta sigma weight residual 112.70 124.57 -11.87 3.00e+00 1.11e-01 1.57e+01 angle pdb=" N GLU A 607 " pdb=" CA GLU A 607 " pdb=" CB GLU A 607 " ideal model delta sigma weight residual 110.28 116.38 -6.10 1.55e+00 4.16e-01 1.55e+01 angle pdb=" N GLN A 520 " pdb=" CA GLN A 520 " pdb=" C GLN A 520 " ideal model delta sigma weight residual 113.55 108.82 4.73 1.26e+00 6.30e-01 1.41e+01 angle pdb=" CA LYS F 124 " pdb=" CB LYS F 124 " pdb=" CG LYS F 124 " ideal model delta sigma weight residual 114.10 121.59 -7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" C ALA E 16 " pdb=" N GLU E 17 " pdb=" CA GLU E 17 " ideal model delta sigma weight residual 122.61 128.45 -5.84 1.56e+00 4.11e-01 1.40e+01 ... (remaining 17057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 6981 17.81 - 35.61: 598 35.61 - 53.42: 117 53.42 - 71.22: 36 71.22 - 89.03: 9 Dihedral angle restraints: 7741 sinusoidal: 3224 harmonic: 4517 Sorted by residual: dihedral pdb=" CD ARG A 518 " pdb=" NE ARG A 518 " pdb=" CZ ARG A 518 " pdb=" NH1 ARG A 518 " ideal model delta sinusoidal sigma weight residual 0.00 40.09 -40.09 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" CA LEU C 510 " pdb=" C LEU C 510 " pdb=" N TRP C 511 " pdb=" CA TRP C 511 " ideal model delta harmonic sigma weight residual -180.00 -157.12 -22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ILE F 219 " pdb=" C ILE F 219 " pdb=" N MET F 220 " pdb=" CA MET F 220 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 7738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1312 0.050 - 0.100: 421 0.100 - 0.151: 121 0.151 - 0.201: 23 0.201 - 0.251: 5 Chirality restraints: 1882 Sorted by residual: chirality pdb=" CG LEU E 193 " pdb=" CB LEU E 193 " pdb=" CD1 LEU E 193 " pdb=" CD2 LEU E 193 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB THR E 98 " pdb=" CA THR E 98 " pdb=" OG1 THR E 98 " pdb=" CG2 THR E 98 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB VAL A 589 " pdb=" CA VAL A 589 " pdb=" CG1 VAL A 589 " pdb=" CG2 VAL A 589 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1879 not shown) Planarity restraints: 2171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 518 " 0.709 9.50e-02 1.11e+02 3.18e-01 6.15e+01 pdb=" NE ARG A 518 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG A 518 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 518 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 518 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 230 " -0.033 2.00e-02 2.50e+03 3.53e-02 3.12e+01 pdb=" CG TRP E 230 " 0.093 2.00e-02 2.50e+03 pdb=" CD1 TRP E 230 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP E 230 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 230 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP E 230 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 230 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 230 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 230 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP E 230 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 518 " -0.352 9.50e-02 1.11e+02 1.58e-01 1.52e+01 pdb=" NE ARG C 518 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG C 518 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 518 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 518 " -0.012 2.00e-02 2.50e+03 ... (remaining 2168 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2207 2.77 - 3.30: 12363 3.30 - 3.83: 21449 3.83 - 4.37: 23896 4.37 - 4.90: 40024 Nonbonded interactions: 99939 Sorted by model distance: nonbonded pdb=" O TYR D 229 " pdb=" OG SER D 248 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR C 383 " pdb=" OE1 GLN C 386 " model vdw 2.249 3.040 nonbonded pdb=" OD1 ASP F 113 " pdb=" OG SER F 116 " model vdw 2.260 3.040 nonbonded pdb=" O LEU E 227 " pdb=" OG1 THR E 231 " model vdw 2.261 3.040 nonbonded pdb=" OG SER B 150 " pdb=" OE1 GLN B 153 " model vdw 2.266 3.040 ... (remaining 99934 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' and (resid 342 through 354 or resid 362 through 376 or resid 382 thro \ ugh 625)) selection = (chain 'C' and (resid 342 through 354 or resid 362 through 494 or resid 500 thro \ ugh 625)) } ncs_group { reference = (chain 'B' and (resid 59 through 72 or resid 81 through 401)) selection = (chain 'D' and (resid 59 through 72 or resid 81 through 380 or resid 401)) } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 0.540 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.270 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 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 : 0.004 0.060 12657 Z= 0.228 Angle : 0.982 12.420 17062 Z= 0.503 Chirality : 0.055 0.251 1882 Planarity : 0.010 0.318 2171 Dihedral : 14.516 89.027 4817 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.29 % Favored : 95.58 % Rotamer: Outliers : 0.44 % Allowed : 0.44 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.20), residues: 1515 helix: -0.11 (0.17), residues: 847 sheet: -0.48 (0.60), residues: 78 loop : -1.30 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 224 TYR 0.051 0.002 TYR F 48 PHE 0.039 0.002 PHE F 176 TRP 0.093 0.003 TRP E 230 HIS 0.014 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00442 (12657) covalent geometry : angle 0.98155 (17062) hydrogen bonds : bond 0.12792 ( 709) hydrogen bonds : angle 6.61953 ( 2085) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 231 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.9082 (tt0) cc_final: 0.8771 (tt0) REVERT: A 447 ASP cc_start: 0.9258 (m-30) cc_final: 0.8903 (m-30) REVERT: A 469 MET cc_start: 0.8571 (ppp) cc_final: 0.8325 (ppp) REVERT: A 486 ASP cc_start: 0.8437 (t0) cc_final: 0.7818 (t0) REVERT: A 512 MET cc_start: 0.7463 (ptp) cc_final: 0.7079 (ptp) REVERT: A 534 TYR cc_start: 0.9160 (t80) cc_final: 0.8235 (t80) REVERT: A 581 MET cc_start: 0.6617 (ptt) cc_final: 0.6305 (ptt) REVERT: B 143 MET cc_start: 0.9009 (tpt) cc_final: 0.8688 (tpp) REVERT: B 341 CYS cc_start: 0.8706 (m) cc_final: 0.8345 (m) REVERT: C 350 MET cc_start: 0.5904 (ppp) cc_final: 0.5400 (ppp) REVERT: C 392 ASN cc_start: 0.9038 (m110) cc_final: 0.8655 (t0) REVERT: C 412 MET cc_start: 0.6581 (ppp) cc_final: 0.6061 (ppp) REVERT: C 442 MET cc_start: 0.8299 (tpt) cc_final: 0.7796 (tmm) REVERT: C 446 ILE cc_start: 0.9506 (mt) cc_final: 0.8367 (mt) REVERT: C 447 ASP cc_start: 0.9039 (t0) cc_final: 0.8535 (t0) REVERT: C 462 LYS cc_start: 0.8945 (tttt) cc_final: 0.8687 (tttt) REVERT: C 464 ILE cc_start: 0.9108 (mm) cc_final: 0.8609 (mp) REVERT: C 532 TYR cc_start: 0.8799 (t80) cc_final: 0.8507 (t80) REVERT: C 552 ASN cc_start: 0.8958 (p0) cc_final: 0.8219 (p0) REVERT: D 65 ASP cc_start: 0.8666 (p0) cc_final: 0.7865 (m-30) REVERT: D 94 MET cc_start: 0.3473 (tpt) cc_final: 0.1539 (mmm) REVERT: D 143 MET cc_start: 0.7849 (tpp) cc_final: 0.7485 (mmt) REVERT: D 208 ASP cc_start: 0.8991 (m-30) cc_final: 0.8756 (m-30) REVERT: D 230 MET cc_start: 0.6926 (tmm) cc_final: 0.4199 (ppp) REVERT: D 247 TRP cc_start: 0.8680 (t60) cc_final: 0.8148 (t60) REVERT: D 249 MET cc_start: 0.9378 (tmm) cc_final: 0.9005 (tmm) REVERT: E 25 PHE cc_start: 0.8383 (m-80) cc_final: 0.8122 (m-80) REVERT: F 124 LYS cc_start: 0.8799 (pptt) cc_final: 0.8234 (pptt) REVERT: F 155 MET cc_start: 0.7434 (ptp) cc_final: 0.6946 (ptp) outliers start: 6 outliers final: 0 residues processed: 233 average time/residue: 0.1048 time to fit residues: 36.0583 Evaluate side-chains 170 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.075544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.055760 restraints weight = 62899.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.057422 restraints weight = 39529.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.058571 restraints weight = 28634.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.059228 restraints weight = 22843.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.059863 restraints weight = 19782.716| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12657 Z= 0.190 Angle : 0.632 7.193 17062 Z= 0.336 Chirality : 0.043 0.140 1882 Planarity : 0.005 0.135 2171 Dihedral : 5.558 63.517 1734 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 0.07 % Allowed : 4.30 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.21), residues: 1515 helix: 0.78 (0.18), residues: 861 sheet: -0.35 (0.59), residues: 76 loop : -1.00 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 518 TYR 0.024 0.002 TYR F 48 PHE 0.017 0.002 PHE F 176 TRP 0.027 0.002 TRP E 230 HIS 0.005 0.001 HIS D 145 Details of bonding type rmsd covalent geometry : bond 0.00398 (12657) covalent geometry : angle 0.63179 (17062) hydrogen bonds : bond 0.04383 ( 709) hydrogen bonds : angle 5.18285 ( 2085) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.9088 (tt0) cc_final: 0.8641 (tt0) REVERT: A 447 ASP cc_start: 0.9343 (m-30) cc_final: 0.9004 (m-30) REVERT: A 469 MET cc_start: 0.8866 (ppp) cc_final: 0.8219 (ppp) REVERT: A 486 ASP cc_start: 0.8517 (t0) cc_final: 0.7935 (t0) REVERT: B 341 CYS cc_start: 0.8711 (m) cc_final: 0.8436 (m) REVERT: C 350 MET cc_start: 0.4859 (ppp) cc_final: 0.4509 (ppp) REVERT: C 412 MET cc_start: 0.6384 (ppp) cc_final: 0.5796 (ppp) REVERT: C 446 ILE cc_start: 0.9531 (mt) cc_final: 0.8307 (mt) REVERT: C 447 ASP cc_start: 0.9085 (t0) cc_final: 0.8547 (t0) REVERT: C 552 ASN cc_start: 0.8998 (p0) cc_final: 0.8351 (p0) REVERT: D 143 MET cc_start: 0.8329 (tpp) cc_final: 0.8045 (tpp) REVERT: D 249 MET cc_start: 0.9367 (tmm) cc_final: 0.8964 (tmm) REVERT: D 256 MET cc_start: 0.9308 (pmm) cc_final: 0.9041 (pmm) REVERT: E 180 HIS cc_start: 0.7876 (m170) cc_final: 0.7634 (m170) REVERT: E 181 TYR cc_start: 0.8599 (t80) cc_final: 0.8180 (t80) REVERT: E 220 MET cc_start: 0.7208 (ptp) cc_final: 0.6835 (ptp) REVERT: F 1 MET cc_start: 0.3531 (tpt) cc_final: 0.3197 (tpt) REVERT: F 124 LYS cc_start: 0.8896 (pptt) cc_final: 0.8624 (pptt) REVERT: F 220 MET cc_start: 0.8045 (mmp) cc_final: 0.7843 (mmp) outliers start: 1 outliers final: 0 residues processed: 207 average time/residue: 0.0983 time to fit residues: 30.7739 Evaluate side-chains 149 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 1 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.074493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.054756 restraints weight = 64215.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.056390 restraints weight = 40335.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.057524 restraints weight = 29295.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.058295 restraints weight = 23434.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.058828 restraints weight = 20085.615| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12657 Z= 0.187 Angle : 0.623 6.524 17062 Z= 0.330 Chirality : 0.044 0.144 1882 Planarity : 0.005 0.052 2171 Dihedral : 5.465 63.535 1734 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.36 % Favored : 95.51 % Rotamer: Outliers : 0.07 % Allowed : 4.60 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.21), residues: 1515 helix: 0.97 (0.18), residues: 860 sheet: -0.36 (0.56), residues: 81 loop : -1.04 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 148 TYR 0.020 0.002 TYR F 48 PHE 0.027 0.002 PHE F 176 TRP 0.016 0.002 TRP C 511 HIS 0.006 0.001 HIS D 145 Details of bonding type rmsd covalent geometry : bond 0.00396 (12657) covalent geometry : angle 0.62307 (17062) hydrogen bonds : bond 0.04166 ( 709) hydrogen bonds : angle 5.00447 ( 2085) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.9129 (tt0) cc_final: 0.8664 (tt0) REVERT: A 447 ASP cc_start: 0.9331 (m-30) cc_final: 0.8995 (m-30) REVERT: A 469 MET cc_start: 0.8911 (ppp) cc_final: 0.8140 (ppp) REVERT: A 486 ASP cc_start: 0.8525 (t0) cc_final: 0.7918 (t0) REVERT: B 190 ASP cc_start: 0.8454 (m-30) cc_final: 0.8055 (m-30) REVERT: B 341 CYS cc_start: 0.8821 (m) cc_final: 0.8618 (m) REVERT: C 350 MET cc_start: 0.5109 (ppp) cc_final: 0.4742 (ppp) REVERT: C 412 MET cc_start: 0.6409 (ppp) cc_final: 0.5747 (ppp) REVERT: C 447 ASP cc_start: 0.9154 (t0) cc_final: 0.8582 (t0) REVERT: D 143 MET cc_start: 0.8446 (tpp) cc_final: 0.8080 (tpp) REVERT: D 146 MET cc_start: 0.7698 (tpt) cc_final: 0.7180 (tpp) REVERT: D 249 MET cc_start: 0.9476 (tmm) cc_final: 0.9063 (tmm) REVERT: D 256 MET cc_start: 0.9299 (pmm) cc_final: 0.9071 (pmm) REVERT: E 1 MET cc_start: 0.6113 (tpp) cc_final: 0.5702 (tmm) REVERT: E 162 MET cc_start: 0.2685 (mtt) cc_final: 0.2311 (mtp) REVERT: E 180 HIS cc_start: 0.7790 (m170) cc_final: 0.7565 (m170) REVERT: E 220 MET cc_start: 0.7190 (ptp) cc_final: 0.6804 (ptp) REVERT: F 1 MET cc_start: 0.3826 (tpt) cc_final: 0.3450 (tpp) REVERT: F 124 LYS cc_start: 0.8983 (pptt) cc_final: 0.8523 (pptt) REVERT: F 155 MET cc_start: 0.7455 (ptp) cc_final: 0.7226 (ptp) outliers start: 1 outliers final: 0 residues processed: 206 average time/residue: 0.1019 time to fit residues: 31.7819 Evaluate side-chains 148 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 96 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 75 optimal weight: 0.0470 chunk 123 optimal weight: 3.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.076042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.056085 restraints weight = 62623.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.057811 restraints weight = 39069.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.059001 restraints weight = 28056.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.059817 restraints weight = 22229.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.060350 restraints weight = 18903.581| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12657 Z= 0.119 Angle : 0.594 6.645 17062 Z= 0.307 Chirality : 0.043 0.162 1882 Planarity : 0.004 0.054 2171 Dihedral : 5.214 63.388 1734 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.16 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.21), residues: 1515 helix: 1.14 (0.18), residues: 858 sheet: -0.50 (0.55), residues: 81 loop : -0.95 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 148 TYR 0.022 0.001 TYR A 534 PHE 0.016 0.001 PHE B 53 TRP 0.012 0.001 TRP D 247 HIS 0.004 0.001 HIS C 460 Details of bonding type rmsd covalent geometry : bond 0.00253 (12657) covalent geometry : angle 0.59449 (17062) hydrogen bonds : bond 0.03901 ( 709) hydrogen bonds : angle 4.83525 ( 2085) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.9061 (tt0) cc_final: 0.8544 (tt0) REVERT: A 447 ASP cc_start: 0.9220 (m-30) cc_final: 0.8885 (m-30) REVERT: A 469 MET cc_start: 0.8673 (ppp) cc_final: 0.7977 (ppp) REVERT: A 486 ASP cc_start: 0.8454 (t0) cc_final: 0.7821 (t0) REVERT: B 190 ASP cc_start: 0.8569 (m-30) cc_final: 0.8343 (m-30) REVERT: B 204 ILE cc_start: 0.8958 (mp) cc_final: 0.8710 (mp) REVERT: C 350 MET cc_start: 0.5209 (ppp) cc_final: 0.4752 (ppp) REVERT: C 412 MET cc_start: 0.6320 (ppp) cc_final: 0.5879 (ppp) REVERT: C 446 ILE cc_start: 0.9536 (mt) cc_final: 0.8961 (mm) REVERT: C 447 ASP cc_start: 0.9148 (t0) cc_final: 0.8557 (t0) REVERT: D 146 MET cc_start: 0.7672 (tpt) cc_final: 0.7189 (tpp) REVERT: D 249 MET cc_start: 0.9432 (tmm) cc_final: 0.8969 (tmm) REVERT: E 162 MET cc_start: 0.2213 (mtt) cc_final: 0.1857 (mtp) REVERT: F 124 LYS cc_start: 0.8959 (pptt) cc_final: 0.8509 (pptt) REVERT: F 155 MET cc_start: 0.7683 (ptp) cc_final: 0.7326 (ptp) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.0963 time to fit residues: 30.8537 Evaluate side-chains 154 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 115 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 47 optimal weight: 0.0070 chunk 145 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 71 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.076222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.056469 restraints weight = 62877.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.058188 restraints weight = 39136.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.059366 restraints weight = 28148.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.060188 restraints weight = 22319.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.060742 restraints weight = 18979.467| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12657 Z= 0.114 Angle : 0.601 7.596 17062 Z= 0.309 Chirality : 0.043 0.191 1882 Planarity : 0.004 0.048 2171 Dihedral : 5.103 63.701 1734 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.42 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.21), residues: 1515 helix: 1.27 (0.18), residues: 856 sheet: -0.57 (0.55), residues: 82 loop : -0.91 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 148 TYR 0.024 0.001 TYR A 534 PHE 0.017 0.001 PHE F 176 TRP 0.022 0.001 TRP F 230 HIS 0.005 0.001 HIS C 460 Details of bonding type rmsd covalent geometry : bond 0.00240 (12657) covalent geometry : angle 0.60082 (17062) hydrogen bonds : bond 0.03882 ( 709) hydrogen bonds : angle 4.76690 ( 2085) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.9065 (tt0) cc_final: 0.8617 (tt0) REVERT: A 447 ASP cc_start: 0.9284 (m-30) cc_final: 0.8959 (m-30) REVERT: A 469 MET cc_start: 0.8574 (ppp) cc_final: 0.7938 (ppp) REVERT: A 486 ASP cc_start: 0.8458 (t0) cc_final: 0.7791 (t0) REVERT: B 190 ASP cc_start: 0.8636 (m-30) cc_final: 0.8355 (m-30) REVERT: B 196 ILE cc_start: 0.9382 (pt) cc_final: 0.9050 (tp) REVERT: B 204 ILE cc_start: 0.8828 (mp) cc_final: 0.8485 (mp) REVERT: C 350 MET cc_start: 0.5625 (ppp) cc_final: 0.4943 (ppp) REVERT: C 412 MET cc_start: 0.6278 (ppp) cc_final: 0.5837 (ppp) REVERT: C 447 ASP cc_start: 0.9162 (t0) cc_final: 0.8562 (t0) REVERT: C 464 ILE cc_start: 0.9223 (mm) cc_final: 0.8984 (mm) REVERT: D 146 MET cc_start: 0.7719 (tpt) cc_final: 0.7253 (tpp) REVERT: D 249 MET cc_start: 0.9388 (tmm) cc_final: 0.8971 (tmm) REVERT: D 256 MET cc_start: 0.9210 (pmm) cc_final: 0.8887 (pmm) REVERT: E 1 MET cc_start: 0.5383 (tpp) cc_final: 0.4756 (tmm) REVERT: E 22 MET cc_start: 0.8188 (ppp) cc_final: 0.7963 (ppp) REVERT: E 144 ILE cc_start: 0.8899 (pt) cc_final: 0.8465 (tt) REVERT: F 124 LYS cc_start: 0.8972 (pptt) cc_final: 0.8499 (pptt) REVERT: F 155 MET cc_start: 0.7685 (ptp) cc_final: 0.7363 (ptp) REVERT: F 181 TYR cc_start: 0.8407 (t80) cc_final: 0.7779 (t80) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.0892 time to fit residues: 28.3592 Evaluate side-chains 151 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 32 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 0.0030 chunk 133 optimal weight: 0.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.076260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.056536 restraints weight = 62815.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.058246 restraints weight = 39244.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.059454 restraints weight = 28201.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.060254 restraints weight = 22239.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.060847 restraints weight = 18872.873| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12657 Z= 0.119 Angle : 0.615 9.077 17062 Z= 0.318 Chirality : 0.043 0.202 1882 Planarity : 0.004 0.047 2171 Dihedral : 5.032 64.661 1734 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.62 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.21), residues: 1515 helix: 1.28 (0.18), residues: 856 sheet: -0.61 (0.54), residues: 82 loop : -0.89 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 169 TYR 0.014 0.001 TYR E 128 PHE 0.027 0.001 PHE E 25 TRP 0.013 0.001 TRP D 247 HIS 0.006 0.001 HIS F 180 Details of bonding type rmsd covalent geometry : bond 0.00249 (12657) covalent geometry : angle 0.61534 (17062) hydrogen bonds : bond 0.03879 ( 709) hydrogen bonds : angle 4.76704 ( 2085) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.9061 (tt0) cc_final: 0.8567 (tt0) REVERT: A 447 ASP cc_start: 0.9287 (m-30) cc_final: 0.8966 (m-30) REVERT: A 469 MET cc_start: 0.8636 (ppp) cc_final: 0.7977 (ppp) REVERT: A 486 ASP cc_start: 0.8735 (t0) cc_final: 0.7909 (t0) REVERT: A 532 TYR cc_start: 0.8553 (t80) cc_final: 0.8253 (t80) REVERT: B 196 ILE cc_start: 0.9399 (pt) cc_final: 0.9051 (tp) REVERT: B 204 ILE cc_start: 0.8702 (mp) cc_final: 0.8319 (mp) REVERT: C 350 MET cc_start: 0.5622 (ppp) cc_final: 0.4953 (ppp) REVERT: C 412 MET cc_start: 0.6250 (ppp) cc_final: 0.5814 (ppp) REVERT: C 446 ILE cc_start: 0.9556 (mt) cc_final: 0.8915 (mm) REVERT: C 447 ASP cc_start: 0.9176 (t0) cc_final: 0.8585 (t0) REVERT: C 462 LYS cc_start: 0.8989 (tttt) cc_final: 0.8729 (tttt) REVERT: D 249 MET cc_start: 0.9436 (tmm) cc_final: 0.9017 (tmm) REVERT: E 22 MET cc_start: 0.8208 (ppp) cc_final: 0.7938 (ppp) REVERT: E 144 ILE cc_start: 0.8915 (pt) cc_final: 0.8480 (tt) REVERT: E 153 GLU cc_start: 0.9362 (mp0) cc_final: 0.9108 (mp0) REVERT: E 220 MET cc_start: 0.7873 (ptp) cc_final: 0.7662 (ptp) REVERT: F 124 LYS cc_start: 0.8921 (pptt) cc_final: 0.8483 (pptt) REVERT: F 181 TYR cc_start: 0.8412 (t80) cc_final: 0.8006 (t80) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.0926 time to fit residues: 29.8276 Evaluate side-chains 156 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 0.0980 chunk 70 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 141 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.076278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.056389 restraints weight = 63135.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.058148 restraints weight = 39328.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.059383 restraints weight = 28150.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.060235 restraints weight = 22179.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.060826 restraints weight = 18748.811| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12657 Z= 0.117 Angle : 0.607 10.209 17062 Z= 0.309 Chirality : 0.043 0.154 1882 Planarity : 0.004 0.047 2171 Dihedral : 5.030 65.955 1734 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.29 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.21), residues: 1515 helix: 1.35 (0.18), residues: 856 sheet: -0.52 (0.52), residues: 91 loop : -0.89 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 148 TYR 0.020 0.001 TYR A 534 PHE 0.015 0.001 PHE A 599 TRP 0.019 0.001 TRP C 511 HIS 0.005 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00250 (12657) covalent geometry : angle 0.60669 (17062) hydrogen bonds : bond 0.03712 ( 709) hydrogen bonds : angle 4.66912 ( 2085) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.9053 (tt0) cc_final: 0.8547 (tt0) REVERT: A 442 MET cc_start: 0.8290 (ppp) cc_final: 0.8069 (ppp) REVERT: A 447 ASP cc_start: 0.9292 (m-30) cc_final: 0.8954 (m-30) REVERT: A 469 MET cc_start: 0.8539 (ppp) cc_final: 0.7977 (ppp) REVERT: A 486 ASP cc_start: 0.8701 (t0) cc_final: 0.7928 (t0) REVERT: A 517 ILE cc_start: 0.8399 (mm) cc_final: 0.8074 (mm) REVERT: A 532 TYR cc_start: 0.8484 (t80) cc_final: 0.8250 (t80) REVERT: B 196 ILE cc_start: 0.9396 (pt) cc_final: 0.9044 (tp) REVERT: B 204 ILE cc_start: 0.8687 (mp) cc_final: 0.8308 (mp) REVERT: B 354 GLN cc_start: 0.8705 (mt0) cc_final: 0.8438 (mt0) REVERT: C 350 MET cc_start: 0.5649 (ppp) cc_final: 0.5013 (ppp) REVERT: C 412 MET cc_start: 0.6092 (ppp) cc_final: 0.5440 (ppp) REVERT: C 447 ASP cc_start: 0.9185 (t0) cc_final: 0.8597 (t0) REVERT: D 146 MET cc_start: 0.7871 (tpt) cc_final: 0.7301 (tpp) REVERT: D 219 MET cc_start: 0.9105 (ptp) cc_final: 0.8851 (ptp) REVERT: D 249 MET cc_start: 0.9423 (tmm) cc_final: 0.8988 (tmm) REVERT: E 1 MET cc_start: 0.5392 (tpp) cc_final: 0.4804 (tmm) REVERT: E 144 ILE cc_start: 0.8921 (pt) cc_final: 0.8481 (tt) REVERT: E 220 MET cc_start: 0.7888 (ptp) cc_final: 0.7673 (ptp) REVERT: F 1 MET cc_start: 0.5175 (tpp) cc_final: 0.4422 (tmm) REVERT: F 124 LYS cc_start: 0.8880 (pptt) cc_final: 0.8470 (pptt) REVERT: F 181 TYR cc_start: 0.8655 (t80) cc_final: 0.8128 (t80) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.0921 time to fit residues: 29.8896 Evaluate side-chains 156 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 51 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 121 optimal weight: 0.0470 chunk 83 optimal weight: 0.9980 chunk 50 optimal weight: 0.2980 chunk 113 optimal weight: 10.0000 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.076554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.056516 restraints weight = 63678.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.058274 restraints weight = 39525.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.059496 restraints weight = 28389.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.060352 restraints weight = 22485.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.060940 restraints weight = 19071.967| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12657 Z= 0.117 Angle : 0.626 11.489 17062 Z= 0.319 Chirality : 0.043 0.154 1882 Planarity : 0.004 0.046 2171 Dihedral : 5.051 67.154 1734 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.49 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.22), residues: 1515 helix: 1.36 (0.18), residues: 856 sheet: -0.63 (0.53), residues: 92 loop : -0.82 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 148 TYR 0.013 0.001 TYR F 127 PHE 0.025 0.001 PHE F 176 TRP 0.015 0.001 TRP C 511 HIS 0.004 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00247 (12657) covalent geometry : angle 0.62646 (17062) hydrogen bonds : bond 0.03716 ( 709) hydrogen bonds : angle 4.68189 ( 2085) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.9029 (tt0) cc_final: 0.8495 (tt0) REVERT: A 447 ASP cc_start: 0.9203 (m-30) cc_final: 0.8874 (m-30) REVERT: A 468 ASP cc_start: 0.8560 (p0) cc_final: 0.8360 (p0) REVERT: A 469 MET cc_start: 0.8667 (ppp) cc_final: 0.8142 (ppp) REVERT: A 486 ASP cc_start: 0.8740 (t0) cc_final: 0.7936 (t0) REVERT: A 532 TYR cc_start: 0.8530 (t80) cc_final: 0.8263 (t80) REVERT: B 196 ILE cc_start: 0.9388 (pt) cc_final: 0.9027 (tp) REVERT: B 204 ILE cc_start: 0.8663 (mp) cc_final: 0.8304 (mp) REVERT: B 354 GLN cc_start: 0.8690 (mt0) cc_final: 0.8406 (mt0) REVERT: C 350 MET cc_start: 0.5656 (ppp) cc_final: 0.5024 (ppp) REVERT: C 412 MET cc_start: 0.6036 (ppp) cc_final: 0.5380 (ppp) REVERT: C 446 ILE cc_start: 0.9512 (mt) cc_final: 0.9068 (mm) REVERT: C 447 ASP cc_start: 0.9153 (t0) cc_final: 0.8576 (t0) REVERT: D 103 ILE cc_start: 0.7501 (tp) cc_final: 0.7295 (pt) REVERT: D 146 MET cc_start: 0.7858 (tpt) cc_final: 0.7318 (tpp) REVERT: D 219 MET cc_start: 0.9072 (ptp) cc_final: 0.8719 (ptp) REVERT: D 249 MET cc_start: 0.9432 (tmm) cc_final: 0.9013 (tmm) REVERT: E 144 ILE cc_start: 0.8896 (pt) cc_final: 0.8455 (tt) REVERT: E 220 MET cc_start: 0.7887 (ptp) cc_final: 0.7598 (ptp) REVERT: F 124 LYS cc_start: 0.8889 (pptt) cc_final: 0.8462 (pptt) REVERT: F 155 MET cc_start: 0.7689 (ptp) cc_final: 0.7294 (ptp) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1020 time to fit residues: 33.6982 Evaluate side-chains 156 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 145 optimal weight: 0.0030 chunk 72 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 81 optimal weight: 0.0370 chunk 0 optimal weight: 3.9990 overall best weight: 1.1872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.075092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.055130 restraints weight = 64404.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.056844 restraints weight = 40370.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.058033 restraints weight = 29112.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.058859 restraints weight = 23112.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.059416 restraints weight = 19685.182| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12657 Z= 0.149 Angle : 0.653 11.763 17062 Z= 0.335 Chirality : 0.044 0.170 1882 Planarity : 0.004 0.081 2171 Dihedral : 5.128 68.072 1734 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.95 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.22), residues: 1515 helix: 1.28 (0.18), residues: 857 sheet: -0.61 (0.53), residues: 92 loop : -0.86 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 148 TYR 0.019 0.001 TYR A 534 PHE 0.021 0.001 PHE F 176 TRP 0.017 0.002 TRP C 511 HIS 0.007 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00322 (12657) covalent geometry : angle 0.65345 (17062) hydrogen bonds : bond 0.03819 ( 709) hydrogen bonds : angle 4.77737 ( 2085) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.9039 (tt0) cc_final: 0.8679 (tt0) REVERT: A 447 ASP cc_start: 0.9231 (m-30) cc_final: 0.8885 (m-30) REVERT: A 469 MET cc_start: 0.8683 (ppp) cc_final: 0.8085 (ppp) REVERT: A 486 ASP cc_start: 0.8766 (t0) cc_final: 0.7972 (t0) REVERT: A 532 TYR cc_start: 0.8533 (t80) cc_final: 0.8276 (t80) REVERT: B 110 GLN cc_start: 0.8684 (tp-100) cc_final: 0.8478 (tp-100) REVERT: B 354 GLN cc_start: 0.8689 (mt0) cc_final: 0.8411 (mt0) REVERT: C 350 MET cc_start: 0.5970 (ppp) cc_final: 0.5354 (ppp) REVERT: C 412 MET cc_start: 0.6079 (ppp) cc_final: 0.5454 (ppp) REVERT: C 447 ASP cc_start: 0.9187 (t0) cc_final: 0.8625 (t0) REVERT: D 146 MET cc_start: 0.7921 (tpt) cc_final: 0.7376 (tpp) REVERT: D 219 MET cc_start: 0.9177 (ptp) cc_final: 0.8765 (ptp) REVERT: D 249 MET cc_start: 0.9487 (tmm) cc_final: 0.9026 (tmm) REVERT: E 144 ILE cc_start: 0.8905 (pt) cc_final: 0.8458 (tt) REVERT: F 1 MET cc_start: 0.4474 (tpp) cc_final: 0.4124 (tmm) REVERT: F 26 MET cc_start: 0.9114 (mtp) cc_final: 0.8886 (mtp) REVERT: F 124 LYS cc_start: 0.8898 (pptt) cc_final: 0.8400 (pptt) REVERT: F 155 MET cc_start: 0.7726 (ptp) cc_final: 0.7288 (ptp) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1062 time to fit residues: 32.7459 Evaluate side-chains 147 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 15 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 35 optimal weight: 0.0050 chunk 94 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.076179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.056125 restraints weight = 63266.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.057863 restraints weight = 39505.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.059078 restraints weight = 28460.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.059920 restraints weight = 22534.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.060492 restraints weight = 19145.525| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12657 Z= 0.125 Angle : 0.664 10.645 17062 Z= 0.338 Chirality : 0.044 0.202 1882 Planarity : 0.004 0.075 2171 Dihedral : 5.081 68.963 1734 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.49 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.22), residues: 1515 helix: 1.24 (0.18), residues: 857 sheet: -0.58 (0.53), residues: 92 loop : -0.81 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 148 TYR 0.020 0.001 TYR D 240 PHE 0.020 0.001 PHE F 176 TRP 0.016 0.001 TRP C 511 HIS 0.005 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00268 (12657) covalent geometry : angle 0.66360 (17062) hydrogen bonds : bond 0.03774 ( 709) hydrogen bonds : angle 4.79088 ( 2085) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 MET cc_start: 0.7387 (pmm) cc_final: 0.6515 (pmm) REVERT: A 393 GLU cc_start: 0.8970 (tt0) cc_final: 0.8400 (tt0) REVERT: A 447 ASP cc_start: 0.9149 (m-30) cc_final: 0.8759 (m-30) REVERT: A 469 MET cc_start: 0.8746 (ppp) cc_final: 0.8184 (ppp) REVERT: A 486 ASP cc_start: 0.8720 (t0) cc_final: 0.7912 (t0) REVERT: A 532 TYR cc_start: 0.8528 (t80) cc_final: 0.8251 (t80) REVERT: B 110 GLN cc_start: 0.8791 (tp-100) cc_final: 0.8459 (tp-100) REVERT: B 308 MET cc_start: 0.6747 (tmm) cc_final: 0.5038 (mmp) REVERT: B 354 GLN cc_start: 0.8641 (mt0) cc_final: 0.8344 (mt0) REVERT: C 350 MET cc_start: 0.5946 (ppp) cc_final: 0.5356 (ppp) REVERT: C 393 GLU cc_start: 0.9230 (pm20) cc_final: 0.8867 (pm20) REVERT: C 412 MET cc_start: 0.6038 (ppp) cc_final: 0.5400 (ppp) REVERT: C 442 MET cc_start: 0.7900 (tpt) cc_final: 0.7661 (tmm) REVERT: C 446 ILE cc_start: 0.9536 (mt) cc_final: 0.9066 (mm) REVERT: C 447 ASP cc_start: 0.9179 (t0) cc_final: 0.8625 (t0) REVERT: D 94 MET cc_start: 0.3385 (tpt) cc_final: 0.2348 (mmm) REVERT: D 146 MET cc_start: 0.7878 (tpt) cc_final: 0.7333 (tpp) REVERT: D 219 MET cc_start: 0.9151 (ptp) cc_final: 0.8779 (ptp) REVERT: D 249 MET cc_start: 0.9452 (tmm) cc_final: 0.9024 (tmm) REVERT: E 144 ILE cc_start: 0.8877 (pt) cc_final: 0.8475 (tt) REVERT: E 220 MET cc_start: 0.8046 (ptp) cc_final: 0.7823 (ptp) REVERT: F 1 MET cc_start: 0.5426 (tpp) cc_final: 0.4986 (tmm) REVERT: F 26 MET cc_start: 0.9082 (mtp) cc_final: 0.8723 (mtp) REVERT: F 48 TYR cc_start: 0.8050 (m-80) cc_final: 0.7614 (m-80) REVERT: F 124 LYS cc_start: 0.8895 (pptt) cc_final: 0.8401 (pptt) REVERT: F 155 MET cc_start: 0.7708 (ptp) cc_final: 0.7097 (ptp) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1029 time to fit residues: 32.4329 Evaluate side-chains 149 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 129 optimal weight: 0.0060 chunk 38 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 145 optimal weight: 0.0970 chunk 37 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 28 optimal weight: 0.0770 chunk 81 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.3552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.076477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.056499 restraints weight = 63322.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.058235 restraints weight = 39766.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.059460 restraints weight = 28634.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.060307 restraints weight = 22659.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.060876 restraints weight = 19223.563| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12657 Z= 0.122 Angle : 0.676 10.293 17062 Z= 0.345 Chirality : 0.044 0.158 1882 Planarity : 0.004 0.069 2171 Dihedral : 5.054 70.198 1734 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.62 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.22), residues: 1515 helix: 1.21 (0.18), residues: 856 sheet: -0.56 (0.53), residues: 92 loop : -0.79 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 148 TYR 0.021 0.001 TYR A 534 PHE 0.033 0.002 PHE F 176 TRP 0.016 0.001 TRP C 511 HIS 0.007 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00256 (12657) covalent geometry : angle 0.67636 (17062) hydrogen bonds : bond 0.03810 ( 709) hydrogen bonds : angle 4.84202 ( 2085) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2095.76 seconds wall clock time: 36 minutes 42.59 seconds (2202.59 seconds total)