Starting phenix.real_space_refine on Wed Jun 11 05:56:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9axa_43931/06_2025/9axa_43931.cif Found real_map, /net/cci-nas-00/data/ceres_data/9axa_43931/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9axa_43931/06_2025/9axa_43931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9axa_43931/06_2025/9axa_43931.map" model { file = "/net/cci-nas-00/data/ceres_data/9axa_43931/06_2025/9axa_43931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9axa_43931/06_2025/9axa_43931.cif" } resolution = 4.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.18, per 1000 atoms: 0.58 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: 2.77 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.26 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: 4.10 Time building geometry restraints manager: 3.31 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 380 or resid 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: 0.580 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: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.290 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.530 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.20), 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 TRP 0.093 0.003 TRP E 230 HIS 0.014 0.001 HIS E 180 PHE 0.039 0.002 PHE F 176 TYR 0.051 0.002 TYR F 48 ARG 0.012 0.001 ARG E 224 Details of bonding type rmsd hydrogen bonds : bond 0.12792 ( 709) hydrogen bonds : angle 6.61953 ( 2085) covalent geometry : bond 0.00442 (12657) covalent geometry : angle 0.98155 (17062) *********************** 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 : 1.505 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: 0.2321 time to fit residues: 78.9908 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 : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 138 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 = 0.3605 r_free = 0.3605 target = 0.075580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.055841 restraints weight = 63034.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.057507 restraints weight = 39603.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.058659 restraints weight = 28632.882| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12657 Z= 0.191 Angle : 0.631 7.298 17062 Z= 0.336 Chirality : 0.043 0.139 1882 Planarity : 0.006 0.152 2171 Dihedral : 5.565 63.509 1734 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.29 % Favored : 95.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1515 helix: 0.79 (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 TRP 0.029 0.002 TRP E 230 HIS 0.005 0.001 HIS D 145 PHE 0.018 0.002 PHE F 176 TYR 0.024 0.002 TYR F 48 ARG 0.010 0.001 ARG E 224 Details of bonding type rmsd hydrogen bonds : bond 0.04352 ( 709) hydrogen bonds : angle 5.18853 ( 2085) covalent geometry : bond 0.00402 (12657) covalent geometry : angle 0.63145 (17062) *********************** 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 : 1.342 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: A 393 GLU cc_start: 0.9112 (tt0) cc_final: 0.8650 (tt0) REVERT: A 447 ASP cc_start: 0.9357 (m-30) cc_final: 0.9022 (m-30) REVERT: A 469 MET cc_start: 0.8889 (ppp) cc_final: 0.8247 (ppp) REVERT: A 486 ASP cc_start: 0.8518 (t0) cc_final: 0.7916 (t0) REVERT: A 534 TYR cc_start: 0.9261 (t80) cc_final: 0.8609 (t80) REVERT: B 341 CYS cc_start: 0.8737 (m) cc_final: 0.8459 (m) REVERT: C 350 MET cc_start: 0.4937 (ppp) cc_final: 0.4561 (ppp) REVERT: C 412 MET cc_start: 0.6412 (ppp) cc_final: 0.5827 (ppp) REVERT: C 442 MET cc_start: 0.7975 (tpt) cc_final: 0.7749 (tmm) REVERT: C 446 ILE cc_start: 0.9528 (mt) cc_final: 0.8317 (mt) REVERT: C 447 ASP cc_start: 0.9106 (t0) cc_final: 0.8577 (t0) REVERT: C 552 ASN cc_start: 0.8993 (p0) cc_final: 0.8346 (p0) REVERT: D 143 MET cc_start: 0.8360 (tpp) cc_final: 0.8043 (tpp) REVERT: D 249 MET cc_start: 0.9363 (tmm) cc_final: 0.8974 (tmm) REVERT: D 256 MET cc_start: 0.9329 (pmm) cc_final: 0.9072 (pmm) REVERT: E 181 TYR cc_start: 0.8665 (t80) cc_final: 0.8307 (t80) REVERT: E 220 MET cc_start: 0.7248 (ptp) cc_final: 0.7045 (ptp) REVERT: F 1 MET cc_start: 0.3581 (tpt) cc_final: 0.3242 (tpt) REVERT: F 124 LYS cc_start: 0.8896 (pptt) cc_final: 0.8627 (pptt) outliers start: 1 outliers final: 0 residues processed: 207 average time/residue: 0.2082 time to fit residues: 64.3061 Evaluate side-chains 150 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.2980 chunk 145 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.076655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.056961 restraints weight = 61693.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.058638 restraints weight = 38869.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.059808 restraints weight = 28024.491| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1497 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= 0.126 Angle : 0.582 6.356 17062 Z= 0.305 Chirality : 0.043 0.140 1882 Planarity : 0.004 0.058 2171 Dihedral : 5.332 62.530 1734 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.96 % Favored : 95.91 % Rotamer: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.21), residues: 1515 helix: 1.05 (0.18), residues: 861 sheet: -0.36 (0.59), residues: 76 loop : -0.93 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 511 HIS 0.003 0.001 HIS D 145 PHE 0.016 0.001 PHE F 176 TYR 0.022 0.001 TYR F 48 ARG 0.005 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 709) hydrogen bonds : angle 4.97047 ( 2085) covalent geometry : bond 0.00265 (12657) covalent geometry : angle 0.58203 (17062) *********************** 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 213 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 2.109 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: 0.9084 (tt0) cc_final: 0.8580 (tt0) REVERT: A 447 ASP cc_start: 0.9268 (m-30) cc_final: 0.8895 (m-30) REVERT: A 469 MET cc_start: 0.8726 (ppp) cc_final: 0.8121 (ppp) REVERT: A 486 ASP cc_start: 0.8767 (t0) cc_final: 0.8006 (t0) REVERT: B 341 CYS cc_start: 0.8819 (m) cc_final: 0.8569 (m) REVERT: C 350 MET cc_start: 0.4951 (ppp) cc_final: 0.4607 (ppp) REVERT: C 412 MET cc_start: 0.6338 (ppp) cc_final: 0.5713 (ppp) REVERT: C 442 MET cc_start: 0.7942 (tpt) cc_final: 0.7733 (tmm) REVERT: C 446 ILE cc_start: 0.9526 (mt) cc_final: 0.8313 (mt) REVERT: C 447 ASP cc_start: 0.9121 (t0) cc_final: 0.8573 (t0) REVERT: C 552 ASN cc_start: 0.8979 (p0) cc_final: 0.8280 (p0) REVERT: D 143 MET cc_start: 0.8374 (tpp) cc_final: 0.7939 (tpp) REVERT: D 146 MET cc_start: 0.7755 (tpt) cc_final: 0.7229 (tpp) REVERT: D 249 MET cc_start: 0.9412 (tmm) cc_final: 0.9006 (tmm) REVERT: E 1 MET cc_start: 0.5952 (tpp) cc_final: 0.5503 (tmm) REVERT: E 162 MET cc_start: 0.2155 (mtt) cc_final: 0.1942 (mtp) REVERT: E 220 MET cc_start: 0.7185 (ptp) cc_final: 0.6781 (ptp) REVERT: F 1 MET cc_start: 0.3683 (tpt) cc_final: 0.3462 (tpp) REVERT: F 124 LYS cc_start: 0.8943 (pptt) cc_final: 0.8488 (pptt) REVERT: F 155 MET cc_start: 0.7682 (ptp) cc_final: 0.7340 (ptp) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.2322 time to fit residues: 74.3159 Evaluate side-chains 159 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 24 optimal weight: 0.0000 chunk 146 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 102 optimal weight: 0.3980 chunk 100 optimal weight: 0.8980 overall best weight: 0.7986 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.076649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.056754 restraints weight = 62088.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.058450 restraints weight = 39023.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.059638 restraints weight = 28153.514| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12657 Z= 0.119 Angle : 0.587 6.806 17062 Z= 0.303 Chirality : 0.043 0.142 1882 Planarity : 0.004 0.053 2171 Dihedral : 5.121 63.238 1734 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.03 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1515 helix: 1.17 (0.18), residues: 859 sheet: -0.39 (0.56), residues: 81 loop : -0.88 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 247 HIS 0.005 0.001 HIS E 180 PHE 0.020 0.001 PHE F 176 TYR 0.018 0.001 TYR F 48 ARG 0.004 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 709) hydrogen bonds : angle 4.78970 ( 2085) covalent geometry : bond 0.00250 (12657) covalent geometry : angle 0.58670 (17062) *********************** 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 218 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.544 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: 0.9062 (tt0) cc_final: 0.8524 (tt0) REVERT: A 447 ASP cc_start: 0.9248 (m-30) cc_final: 0.8891 (m-30) REVERT: A 469 MET cc_start: 0.8659 (ppp) cc_final: 0.8038 (ppp) REVERT: A 486 ASP cc_start: 0.8754 (t0) cc_final: 0.7945 (t0) REVERT: A 534 TYR cc_start: 0.9369 (t80) cc_final: 0.8557 (t80) REVERT: C 350 MET cc_start: 0.5172 (ppp) cc_final: 0.4674 (ppp) REVERT: C 412 MET cc_start: 0.6261 (ppp) cc_final: 0.5631 (ppp) REVERT: C 442 MET cc_start: 0.7962 (tpt) cc_final: 0.7740 (tmm) REVERT: C 446 ILE cc_start: 0.9525 (mt) cc_final: 0.8192 (mt) REVERT: C 447 ASP cc_start: 0.9158 (t0) cc_final: 0.8601 (t0) REVERT: C 552 ASN cc_start: 0.9025 (p0) cc_final: 0.8291 (p0) REVERT: D 146 MET cc_start: 0.7671 (tpt) cc_final: 0.7156 (tpp) REVERT: D 249 MET cc_start: 0.9421 (tmm) cc_final: 0.8978 (tmm) REVERT: E 162 MET cc_start: 0.2286 (mtt) cc_final: 0.1926 (mtp) REVERT: E 220 MET cc_start: 0.7836 (ptp) cc_final: 0.7488 (ptp) REVERT: F 15 GLN cc_start: 0.8684 (mt0) cc_final: 0.8419 (mp10) REVERT: F 124 LYS cc_start: 0.8992 (pptt) cc_final: 0.8509 (pptt) REVERT: F 155 MET cc_start: 0.7787 (ptp) cc_final: 0.7413 (ptp) REVERT: F 220 MET cc_start: 0.8040 (mmp) cc_final: 0.7840 (mmp) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2198 time to fit residues: 72.6040 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 : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 110 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 141 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 115 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.073520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.053926 restraints weight = 64930.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.055543 restraints weight = 41214.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.056681 restraints weight = 29936.304| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12657 Z= 0.218 Angle : 0.676 9.193 17062 Z= 0.354 Chirality : 0.045 0.170 1882 Planarity : 0.005 0.048 2171 Dihedral : 5.341 63.130 1734 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.28 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.21), residues: 1515 helix: 1.03 (0.17), residues: 866 sheet: -0.62 (0.51), residues: 92 loop : -0.93 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP F 230 HIS 0.007 0.002 HIS F 180 PHE 0.030 0.002 PHE F 176 TYR 0.024 0.002 TYR F 181 ARG 0.006 0.001 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.04149 ( 709) hydrogen bonds : angle 5.01463 ( 2085) covalent geometry : bond 0.00463 (12657) covalent geometry : angle 0.67600 (17062) *********************** 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 207 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.373 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: A 393 GLU cc_start: 0.9191 (tt0) cc_final: 0.8763 (tt0) REVERT: A 447 ASP cc_start: 0.9310 (m-30) cc_final: 0.9006 (m-30) REVERT: A 469 MET cc_start: 0.8693 (ppp) cc_final: 0.8028 (ppp) REVERT: A 486 ASP cc_start: 0.8517 (t0) cc_final: 0.7922 (t0) REVERT: B 190 ASP cc_start: 0.8614 (m-30) cc_final: 0.8297 (m-30) REVERT: B 341 CYS cc_start: 0.8842 (m) cc_final: 0.8592 (m) REVERT: C 350 MET cc_start: 0.5232 (ppp) cc_final: 0.4851 (ppp) REVERT: C 412 MET cc_start: 0.6413 (ppp) cc_final: 0.5973 (ppp) REVERT: C 442 MET cc_start: 0.8077 (tpt) cc_final: 0.7800 (tmm) REVERT: C 446 ILE cc_start: 0.9517 (mt) cc_final: 0.8239 (mt) REVERT: C 447 ASP cc_start: 0.9215 (t0) cc_final: 0.8675 (t0) REVERT: D 146 MET cc_start: 0.7904 (tpt) cc_final: 0.7405 (tpp) REVERT: D 249 MET cc_start: 0.9477 (tmm) cc_final: 0.9055 (tmm) REVERT: E 1 MET cc_start: 0.5436 (tpp) cc_final: 0.4838 (tmm) REVERT: E 22 MET cc_start: 0.8110 (ppp) cc_final: 0.7864 (ppp) REVERT: E 144 ILE cc_start: 0.8948 (pt) cc_final: 0.8512 (tt) REVERT: E 180 HIS cc_start: 0.7805 (m170) cc_final: 0.7460 (m170) REVERT: E 220 MET cc_start: 0.7916 (ptp) cc_final: 0.7484 (ptp) REVERT: F 155 MET cc_start: 0.7701 (ptp) cc_final: 0.7453 (ptp) REVERT: F 181 TYR cc_start: 0.7995 (t80) cc_final: 0.7553 (t80) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2118 time to fit residues: 66.6951 Evaluate side-chains 150 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 34 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 135 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 43 optimal weight: 0.0980 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 75 optimal weight: 0.0470 chunk 119 optimal weight: 9.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.075826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.055907 restraints weight = 63504.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.057639 restraints weight = 39475.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.058845 restraints weight = 28234.719| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12657 Z= 0.118 Angle : 0.611 9.264 17062 Z= 0.314 Chirality : 0.043 0.197 1882 Planarity : 0.004 0.047 2171 Dihedral : 5.069 63.815 1734 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.49 % Favored : 95.45 % Rotamer: Outliers : 0.07 % Allowed : 2.00 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1515 helix: 1.24 (0.18), residues: 857 sheet: -0.54 (0.55), residues: 82 loop : -0.92 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 511 HIS 0.005 0.001 HIS D 119 PHE 0.016 0.001 PHE A 599 TYR 0.021 0.001 TYR B 240 ARG 0.006 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 709) hydrogen bonds : angle 4.78917 ( 2085) covalent geometry : bond 0.00249 (12657) covalent geometry : angle 0.61073 (17062) *********************** 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: 1 poor density : 209 time to evaluate : 1.358 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: 0.9121 (tt0) cc_final: 0.8803 (tt0) REVERT: A 447 ASP cc_start: 0.9296 (m-30) cc_final: 0.8979 (m-30) REVERT: A 456 MET cc_start: 0.8863 (mmt) cc_final: 0.8550 (mmt) REVERT: A 468 ASP cc_start: 0.8697 (p0) cc_final: 0.8492 (p0) REVERT: A 469 MET cc_start: 0.8682 (ppp) cc_final: 0.8062 (ppp) REVERT: A 486 ASP cc_start: 0.8460 (t0) cc_final: 0.7821 (t0) REVERT: B 204 ILE cc_start: 0.8944 (mp) cc_final: 0.8696 (mp) REVERT: C 350 MET cc_start: 0.5849 (ppp) cc_final: 0.5158 (ppp) REVERT: C 412 MET cc_start: 0.6171 (ppp) cc_final: 0.5532 (ppp) REVERT: C 446 ILE cc_start: 0.9541 (mt) cc_final: 0.8249 (mt) REVERT: C 447 ASP cc_start: 0.9198 (t0) cc_final: 0.8669 (t0) REVERT: C 462 LYS cc_start: 0.8992 (ttmt) cc_final: 0.8772 (tttt) REVERT: D 228 SER cc_start: 0.9232 (p) cc_final: 0.8941 (m) REVERT: D 249 MET cc_start: 0.9409 (tmm) cc_final: 0.9033 (tmm) REVERT: D 256 MET cc_start: 0.9324 (pmm) cc_final: 0.9019 (pmm) REVERT: E 144 ILE cc_start: 0.8927 (pt) cc_final: 0.8496 (tt) REVERT: E 153 GLU cc_start: 0.9379 (mp0) cc_final: 0.9138 (mp0) REVERT: E 220 MET cc_start: 0.7918 (ptp) cc_final: 0.7708 (ptp) REVERT: F 119 PHE cc_start: 0.8605 (t80) cc_final: 0.8349 (t80) REVERT: F 124 LYS cc_start: 0.8910 (pptt) cc_final: 0.8454 (pptt) REVERT: F 181 TYR cc_start: 0.8347 (t80) cc_final: 0.7901 (t80) outliers start: 1 outliers final: 0 residues processed: 210 average time/residue: 0.2246 time to fit residues: 69.7511 Evaluate side-chains 162 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.578 ------------------------------------------------------------------------------- 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: 8.9990 chunk 112 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 81 optimal weight: 0.0570 chunk 130 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.075923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.056212 restraints weight = 62792.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.057950 restraints weight = 38992.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.059165 restraints weight = 27943.551| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12657 Z= 0.118 Angle : 0.620 10.097 17062 Z= 0.317 Chirality : 0.043 0.160 1882 Planarity : 0.004 0.046 2171 Dihedral : 5.005 65.014 1734 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.62 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.21), residues: 1515 helix: 1.26 (0.18), residues: 858 sheet: -0.59 (0.54), residues: 82 loop : -0.89 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 511 HIS 0.004 0.001 HIS E 180 PHE 0.028 0.001 PHE F 176 TYR 0.014 0.001 TYR A 574 ARG 0.007 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 709) hydrogen bonds : angle 4.74993 ( 2085) covalent geometry : bond 0.00252 (12657) covalent geometry : angle 0.62028 (17062) *********************** 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 215 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.351 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: A 393 GLU cc_start: 0.9076 (tt0) cc_final: 0.8563 (tt0) REVERT: A 447 ASP cc_start: 0.9290 (m-30) cc_final: 0.8970 (m-30) REVERT: A 456 MET cc_start: 0.8856 (mmt) cc_final: 0.8515 (mmt) REVERT: A 469 MET cc_start: 0.8648 (ppp) cc_final: 0.8008 (ppp) REVERT: A 486 ASP cc_start: 0.8403 (t0) cc_final: 0.7814 (t0) REVERT: A 532 TYR cc_start: 0.8543 (t80) cc_final: 0.8269 (t80) REVERT: C 350 MET cc_start: 0.5829 (ppp) cc_final: 0.5189 (ppp) REVERT: C 412 MET cc_start: 0.6130 (ppp) cc_final: 0.5503 (ppp) REVERT: C 447 ASP cc_start: 0.9176 (t0) cc_final: 0.8613 (t0) REVERT: C 462 LYS cc_start: 0.9054 (ttmt) cc_final: 0.8827 (tttt) REVERT: D 94 MET cc_start: 0.3429 (tpt) cc_final: 0.2389 (tpp) REVERT: D 146 MET cc_start: 0.7841 (tpt) cc_final: 0.7289 (tpp) REVERT: D 219 MET cc_start: 0.9126 (ptp) cc_final: 0.8853 (ptp) REVERT: D 228 SER cc_start: 0.9205 (p) cc_final: 0.8897 (m) REVERT: D 249 MET cc_start: 0.9444 (tmm) cc_final: 0.8995 (tmm) REVERT: E 1 MET cc_start: 0.5723 (tpp) cc_final: 0.5207 (tmm) REVERT: E 144 ILE cc_start: 0.8928 (pt) cc_final: 0.8483 (tt) REVERT: E 220 MET cc_start: 0.7917 (ptp) cc_final: 0.7708 (ptp) REVERT: F 1 MET cc_start: 0.5242 (tpp) cc_final: 0.4481 (tmm) REVERT: F 124 LYS cc_start: 0.8925 (pptt) cc_final: 0.8465 (pptt) REVERT: F 155 MET cc_start: 0.7656 (ptp) cc_final: 0.7408 (ptp) REVERT: F 181 TYR cc_start: 0.8341 (t80) cc_final: 0.7876 (t80) REVERT: F 220 MET cc_start: 0.8120 (mmp) cc_final: 0.7795 (mmp) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2092 time to fit residues: 67.7392 Evaluate side-chains 155 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 52 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 141 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 119 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.075610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.055746 restraints weight = 64785.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.057465 restraints weight = 40244.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.058676 restraints weight = 29002.734| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2554 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= 0.130 Angle : 0.635 10.080 17062 Z= 0.324 Chirality : 0.044 0.158 1882 Planarity : 0.004 0.045 2171 Dihedral : 5.014 66.284 1734 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.88 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.22), residues: 1515 helix: 1.28 (0.18), residues: 855 sheet: -0.64 (0.54), residues: 82 loop : -0.87 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 511 HIS 0.006 0.001 HIS C 460 PHE 0.029 0.002 PHE F 176 TYR 0.020 0.001 TYR F 130 ARG 0.004 0.000 ARG F 56 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 709) hydrogen bonds : angle 4.78411 ( 2085) covalent geometry : bond 0.00281 (12657) covalent geometry : angle 0.63463 (17062) *********************** 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 211 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.378 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: A 393 GLU cc_start: 0.9104 (tt0) cc_final: 0.8586 (tt0) REVERT: A 447 ASP cc_start: 0.9245 (m-30) cc_final: 0.8877 (m-30) REVERT: A 469 MET cc_start: 0.8736 (ppp) cc_final: 0.8045 (ppp) REVERT: A 486 ASP cc_start: 0.8486 (t0) cc_final: 0.7853 (t0) REVERT: B 308 MET cc_start: 0.6713 (tmm) cc_final: 0.6494 (tmm) REVERT: C 350 MET cc_start: 0.5927 (ppp) cc_final: 0.5266 (ppp) REVERT: C 412 MET cc_start: 0.6066 (ppp) cc_final: 0.5445 (ppp) REVERT: C 442 MET cc_start: 0.7890 (tpt) cc_final: 0.7541 (tmm) REVERT: C 446 ILE cc_start: 0.9535 (mt) cc_final: 0.9023 (mm) REVERT: C 447 ASP cc_start: 0.9222 (t0) cc_final: 0.8697 (t0) REVERT: D 146 MET cc_start: 0.7902 (tpt) cc_final: 0.7327 (tpp) REVERT: D 219 MET cc_start: 0.9146 (ptp) cc_final: 0.8772 (ptp) REVERT: D 228 SER cc_start: 0.9233 (p) cc_final: 0.8880 (m) REVERT: D 249 MET cc_start: 0.9441 (tmm) cc_final: 0.9007 (tmm) REVERT: E 144 ILE cc_start: 0.8921 (pt) cc_final: 0.8495 (tt) REVERT: E 220 MET cc_start: 0.8090 (ptp) cc_final: 0.7818 (ptp) REVERT: F 26 MET cc_start: 0.9164 (mtp) cc_final: 0.8908 (mtp) REVERT: F 124 LYS cc_start: 0.8945 (pptt) cc_final: 0.8517 (pptt) REVERT: F 220 MET cc_start: 0.8087 (mmp) cc_final: 0.7877 (mmp) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.2200 time to fit residues: 69.4620 Evaluate side-chains 150 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 113 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.075488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.055610 restraints weight = 63912.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.057330 restraints weight = 39856.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.058536 restraints weight = 28791.306| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12657 Z= 0.133 Angle : 0.641 11.022 17062 Z= 0.326 Chirality : 0.044 0.166 1882 Planarity : 0.004 0.082 2171 Dihedral : 5.045 67.506 1734 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.75 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.22), residues: 1515 helix: 1.23 (0.18), residues: 858 sheet: -0.67 (0.55), residues: 82 loop : -0.85 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 511 HIS 0.006 0.001 HIS A 477 PHE 0.021 0.001 PHE E 176 TYR 0.017 0.001 TYR D 240 ARG 0.009 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 709) hydrogen bonds : angle 4.77691 ( 2085) covalent geometry : bond 0.00286 (12657) covalent geometry : angle 0.64077 (17062) *********************** 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 206 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.322 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: A 393 GLU cc_start: 0.9104 (tt0) cc_final: 0.8586 (tt0) REVERT: A 447 ASP cc_start: 0.9130 (m-30) cc_final: 0.8769 (m-30) REVERT: A 469 MET cc_start: 0.8729 (ppp) cc_final: 0.8031 (ppp) REVERT: A 486 ASP cc_start: 0.8470 (t0) cc_final: 0.7835 (t0) REVERT: A 532 TYR cc_start: 0.8583 (t80) cc_final: 0.8271 (t80) REVERT: B 110 GLN cc_start: 0.8810 (tp-100) cc_final: 0.8471 (tp-100) REVERT: C 350 MET cc_start: 0.6260 (ppp) cc_final: 0.5625 (ppp) REVERT: C 412 MET cc_start: 0.6025 (ppp) cc_final: 0.5424 (ppp) REVERT: C 442 MET cc_start: 0.7841 (tpt) cc_final: 0.7499 (tmm) REVERT: C 446 ILE cc_start: 0.9506 (mt) cc_final: 0.9037 (mm) REVERT: C 447 ASP cc_start: 0.9220 (t0) cc_final: 0.8715 (t0) REVERT: C 462 LYS cc_start: 0.9088 (ttmt) cc_final: 0.8837 (tttt) REVERT: D 103 ILE cc_start: 0.6865 (tp) cc_final: 0.6426 (pt) REVERT: D 146 MET cc_start: 0.7895 (tpt) cc_final: 0.7347 (tpp) REVERT: D 219 MET cc_start: 0.9150 (ptp) cc_final: 0.8747 (ptp) REVERT: D 228 SER cc_start: 0.9192 (p) cc_final: 0.8854 (m) REVERT: D 249 MET cc_start: 0.9432 (tmm) cc_final: 0.8987 (tmm) REVERT: D 256 MET cc_start: 0.9369 (pmm) cc_final: 0.9131 (pmm) REVERT: E 144 ILE cc_start: 0.8910 (pt) cc_final: 0.8470 (tt) REVERT: E 220 MET cc_start: 0.8004 (ptp) cc_final: 0.7593 (ptp) REVERT: F 26 MET cc_start: 0.9141 (mtp) cc_final: 0.8863 (mtp) REVERT: F 124 LYS cc_start: 0.8835 (pptt) cc_final: 0.8444 (pptt) REVERT: F 155 MET cc_start: 0.7792 (ptp) cc_final: 0.7482 (ptp) REVERT: F 220 MET cc_start: 0.8101 (mmp) cc_final: 0.7887 (mmp) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2114 time to fit residues: 65.4480 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 : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 113 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.071646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.052014 restraints weight = 65832.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.053644 restraints weight = 41152.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.054763 restraints weight = 29785.556| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 12657 Z= 0.264 Angle : 0.781 11.782 17062 Z= 0.409 Chirality : 0.048 0.187 1882 Planarity : 0.005 0.075 2171 Dihedral : 5.623 68.753 1734 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.81 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1515 helix: 0.75 (0.17), residues: 858 sheet: -0.86 (0.49), residues: 91 loop : -1.08 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 511 HIS 0.011 0.002 HIS F 180 PHE 0.025 0.002 PHE E 176 TYR 0.023 0.002 TYR F 151 ARG 0.015 0.001 ARG F 148 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 709) hydrogen bonds : angle 5.18739 ( 2085) covalent geometry : bond 0.00560 (12657) covalent geometry : angle 0.78084 (17062) ********************** 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 193 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.9227 (tt0) cc_final: 0.8827 (tt0) REVERT: A 447 ASP cc_start: 0.9226 (m-30) cc_final: 0.8673 (m-30) REVERT: A 469 MET cc_start: 0.8964 (ppp) cc_final: 0.8112 (ppp) REVERT: A 486 ASP cc_start: 0.8539 (t0) cc_final: 0.7915 (t0) REVERT: B 110 GLN cc_start: 0.8806 (tp-100) cc_final: 0.8460 (tp-100) REVERT: B 190 ASP cc_start: 0.8140 (m-30) cc_final: 0.7812 (m-30) REVERT: B 230 MET cc_start: 0.7146 (tpt) cc_final: 0.6914 (tpt) REVERT: B 308 MET cc_start: 0.7099 (tmm) cc_final: 0.5627 (mmp) REVERT: C 350 MET cc_start: 0.6095 (ppp) cc_final: 0.5542 (ppp) REVERT: C 412 MET cc_start: 0.6332 (ppp) cc_final: 0.5730 (ppp) REVERT: C 446 ILE cc_start: 0.9494 (mt) cc_final: 0.9007 (mm) REVERT: C 447 ASP cc_start: 0.9286 (t0) cc_final: 0.8813 (t0) REVERT: D 94 MET cc_start: 0.4197 (tpt) cc_final: 0.3524 (tpt) REVERT: D 146 MET cc_start: 0.7892 (tpt) cc_final: 0.7583 (tpp) REVERT: D 219 MET cc_start: 0.8955 (ptp) cc_final: 0.8439 (ptp) REVERT: D 249 MET cc_start: 0.9515 (tmm) cc_final: 0.9073 (tmm) REVERT: E 144 ILE cc_start: 0.8858 (pt) cc_final: 0.8344 (tt) REVERT: F 1 MET cc_start: 0.4219 (tpt) cc_final: 0.3576 (tmm) REVERT: F 26 MET cc_start: 0.9131 (mtp) cc_final: 0.8872 (mtp) REVERT: F 153 GLU cc_start: 0.8016 (mp0) cc_final: 0.7808 (mp0) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2108 time to fit residues: 61.6183 Evaluate side-chains 141 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 102 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.073891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.054079 restraints weight = 64591.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.055770 restraints weight = 40266.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.056942 restraints weight = 29025.777| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12657 Z= 0.142 Angle : 0.686 10.658 17062 Z= 0.352 Chirality : 0.045 0.211 1882 Planarity : 0.004 0.069 2171 Dihedral : 5.311 69.174 1734 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.08 % Favored : 94.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1515 helix: 0.99 (0.18), residues: 857 sheet: -0.80 (0.51), residues: 90 loop : -0.97 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 511 HIS 0.004 0.001 HIS E 180 PHE 0.022 0.002 PHE F 176 TYR 0.026 0.002 TYR B 240 ARG 0.008 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 709) hydrogen bonds : angle 4.93268 ( 2085) covalent geometry : bond 0.00304 (12657) covalent geometry : angle 0.68646 (17062) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3809.66 seconds wall clock time: 66 minutes 32.77 seconds (3992.77 seconds total)