Starting phenix.real_space_refine on Sat Jan 18 16:08:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9axa_43931/01_2025/9axa_43931.cif Found real_map, /net/cci-nas-00/data/ceres_data/9axa_43931/01_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_43931/01_2025/9axa_43931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9axa_43931/01_2025/9axa_43931.map" model { file = "/net/cci-nas-00/data/ceres_data/9axa_43931/01_2025/9axa_43931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9axa_43931/01_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 7.20, 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: 3.05 Conformation dependent library (CDL) restraints added in 1.6 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: 1.15 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: 3.82 Time building geometry restraints manager: 3.53 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: 0.350 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: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 28.780 Find NCS groups from input model: 0.530 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: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.490 ------------------------------------------------------------------------------- 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= 0.287 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 *********************** 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 : 1.357 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: 0.2418 time to fit residues: 81.8711 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 : 1.603 ------------------------------------------------------------------------------- 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 = 48)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.055835 restraints weight = 63034.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.057503 restraints weight = 39653.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.058636 restraints weight = 28674.278| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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= 0.260 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 *********************** 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 : 1.480 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: 0.9110 (tt0) cc_final: 0.8647 (tt0) REVERT: A 447 ASP cc_start: 0.9356 (m-30) cc_final: 0.9021 (m-30) REVERT: A 469 MET cc_start: 0.8891 (ppp) cc_final: 0.8248 (ppp) REVERT: A 486 ASP cc_start: 0.8519 (t0) cc_final: 0.7914 (t0) REVERT: A 534 TYR cc_start: 0.9258 (t80) cc_final: 0.8605 (t80) REVERT: B 341 CYS cc_start: 0.8740 (m) cc_final: 0.8460 (m) REVERT: C 350 MET cc_start: 0.4937 (ppp) cc_final: 0.4560 (ppp) REVERT: C 412 MET cc_start: 0.6410 (ppp) cc_final: 0.5824 (ppp) REVERT: C 442 MET cc_start: 0.7975 (tpt) cc_final: 0.7749 (tmm) REVERT: C 446 ILE cc_start: 0.9527 (mt) cc_final: 0.8318 (mt) REVERT: C 447 ASP cc_start: 0.9107 (t0) cc_final: 0.8579 (t0) REVERT: C 552 ASN cc_start: 0.8994 (p0) cc_final: 0.8348 (p0) REVERT: D 143 MET cc_start: 0.8369 (tpp) cc_final: 0.8049 (tpp) REVERT: D 249 MET cc_start: 0.9363 (tmm) cc_final: 0.8975 (tmm) REVERT: D 256 MET cc_start: 0.9330 (pmm) cc_final: 0.9073 (pmm) REVERT: E 181 TYR cc_start: 0.8668 (t80) cc_final: 0.8308 (t80) REVERT: E 220 MET cc_start: 0.7258 (ptp) cc_final: 0.7054 (ptp) REVERT: F 1 MET cc_start: 0.3598 (tpt) cc_final: 0.3257 (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: 0.2306 time to fit residues: 71.5654 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 : 1.382 ------------------------------------------------------------------------------- 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: 0.5980 chunk 145 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 0.0970 chunk 50 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.076498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.056835 restraints weight = 62010.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.058484 restraints weight = 39582.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.059605 restraints weight = 28790.587| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12657 Z= 0.168 Angle : 0.586 6.433 17062 Z= 0.307 Chirality : 0.043 0.142 1882 Planarity : 0.004 0.050 2171 Dihedral : 5.316 62.596 1734 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.96 % Favored : 95.91 % Rotamer: Outliers : 0.07 % Allowed : 3.34 % Favored : 96.59 % 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: 1.06 (0.18), residues: 861 sheet: -0.34 (0.60), residues: 76 loop : -0.94 (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 0.017 0.001 PHE F 176 TYR 0.023 0.001 TYR F 48 ARG 0.006 0.000 ARG E 148 *********************** 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 212 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 1.486 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: 0.9118 (tt0) cc_final: 0.8625 (tt0) REVERT: A 447 ASP cc_start: 0.9287 (m-30) cc_final: 0.8920 (m-30) REVERT: A 469 MET cc_start: 0.8707 (ppp) cc_final: 0.8079 (ppp) REVERT: A 486 ASP cc_start: 0.8756 (t0) cc_final: 0.7967 (t0) REVERT: A 534 TYR cc_start: 0.9318 (t80) cc_final: 0.8526 (t80) REVERT: B 341 CYS cc_start: 0.8837 (m) cc_final: 0.8575 (m) REVERT: C 350 MET cc_start: 0.4998 (ppp) cc_final: 0.4602 (ppp) REVERT: C 412 MET cc_start: 0.6297 (ppp) cc_final: 0.5674 (ppp) REVERT: C 442 MET cc_start: 0.7967 (tpt) cc_final: 0.7747 (tmm) REVERT: C 446 ILE cc_start: 0.9515 (mt) cc_final: 0.8128 (mt) REVERT: C 447 ASP cc_start: 0.9180 (t0) cc_final: 0.8633 (t0) REVERT: C 552 ASN cc_start: 0.9003 (p0) cc_final: 0.8269 (p0) REVERT: D 125 TYR cc_start: 0.9077 (m-10) cc_final: 0.8874 (m-10) REVERT: D 143 MET cc_start: 0.8420 (tpp) cc_final: 0.7958 (tpp) REVERT: D 146 MET cc_start: 0.7800 (tpt) cc_final: 0.7267 (tpp) REVERT: D 249 MET cc_start: 0.9447 (tmm) cc_final: 0.9031 (tmm) REVERT: E 1 MET cc_start: 0.6011 (tpp) cc_final: 0.5532 (tmm) REVERT: E 162 MET cc_start: 0.2812 (mtt) cc_final: 0.2403 (mtp) REVERT: E 220 MET cc_start: 0.7214 (ptp) cc_final: 0.6809 (ptp) REVERT: F 1 MET cc_start: 0.3762 (tpt) cc_final: 0.3518 (tpp) REVERT: F 124 LYS cc_start: 0.8938 (pptt) cc_final: 0.8520 (pptt) REVERT: F 155 MET cc_start: 0.7683 (ptp) cc_final: 0.7282 (ptp) REVERT: F 220 MET cc_start: 0.8041 (mmp) cc_final: 0.7839 (mmp) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.2273 time to fit residues: 71.5479 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 : 1.416 ------------------------------------------------------------------------------- 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: 2.9990 chunk 74 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 49 optimal weight: 0.1980 chunk 46 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.076635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.056760 restraints weight = 62190.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.058475 restraints weight = 38992.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.059674 restraints weight = 28081.972| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12657 Z= 0.160 Angle : 0.582 6.666 17062 Z= 0.301 Chirality : 0.042 0.142 1882 Planarity : 0.004 0.057 2171 Dihedral : 5.133 63.165 1734 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % 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: 0.47 (0.21), residues: 1515 helix: 1.17 (0.18), residues: 862 sheet: -0.41 (0.56), residues: 81 loop : -0.86 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 247 HIS 0.005 0.001 HIS C 460 PHE 0.021 0.001 PHE F 176 TYR 0.018 0.001 TYR F 48 ARG 0.004 0.000 ARG F 148 *********************** 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 215 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.392 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: 0.9077 (tt0) cc_final: 0.8518 (tt0) REVERT: A 447 ASP cc_start: 0.9242 (m-30) cc_final: 0.8889 (m-30) REVERT: A 469 MET cc_start: 0.8648 (ppp) cc_final: 0.8043 (ppp) REVERT: A 486 ASP cc_start: 0.8745 (t0) cc_final: 0.7944 (t0) REVERT: A 534 TYR cc_start: 0.9435 (t80) cc_final: 0.8725 (t80) REVERT: A 607 GLU cc_start: 0.9457 (pm20) cc_final: 0.9251 (pm20) REVERT: C 350 MET cc_start: 0.5161 (ppp) cc_final: 0.4677 (ppp) REVERT: C 412 MET cc_start: 0.6259 (ppp) cc_final: 0.5633 (ppp) REVERT: C 442 MET cc_start: 0.7955 (tpt) cc_final: 0.7753 (tmm) REVERT: C 446 ILE cc_start: 0.9524 (mt) cc_final: 0.8191 (mt) REVERT: C 447 ASP cc_start: 0.9146 (t0) cc_final: 0.8593 (t0) REVERT: C 552 ASN cc_start: 0.9024 (p0) cc_final: 0.8298 (p0) REVERT: D 146 MET cc_start: 0.7662 (tpt) cc_final: 0.7150 (tpp) REVERT: D 249 MET cc_start: 0.9419 (tmm) cc_final: 0.8961 (tmm) REVERT: E 162 MET cc_start: 0.2296 (mtt) cc_final: 0.1926 (mtp) REVERT: E 220 MET cc_start: 0.7428 (ptp) cc_final: 0.7070 (ptp) REVERT: F 15 GLN cc_start: 0.8688 (mt0) cc_final: 0.8429 (mp10) REVERT: F 124 LYS cc_start: 0.8964 (pptt) cc_final: 0.8506 (pptt) REVERT: F 155 MET cc_start: 0.7678 (ptp) cc_final: 0.7381 (ptp) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2165 time to fit residues: 70.1276 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 : 1.384 ------------------------------------------------------------------------------- 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: 1.9990 chunk 84 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 141 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 115 optimal weight: 0.3980 chunk 86 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.074611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.055053 restraints weight = 63891.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.056670 restraints weight = 40837.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.057792 restraints weight = 29876.161| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12657 Z= 0.245 Angle : 0.632 8.439 17062 Z= 0.330 Chirality : 0.044 0.166 1882 Planarity : 0.004 0.048 2171 Dihedral : 5.219 63.048 1734 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.88 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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: 0.49 (0.21), residues: 1515 helix: 1.21 (0.18), residues: 860 sheet: -0.43 (0.55), residues: 81 loop : -0.88 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 230 HIS 0.004 0.001 HIS C 460 PHE 0.024 0.002 PHE E 25 TYR 0.024 0.002 TYR F 181 ARG 0.006 0.000 ARG E 148 *********************** 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 209 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 1.500 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: 0.9170 (tt0) cc_final: 0.8750 (tt0) REVERT: A 447 ASP cc_start: 0.9326 (m-30) cc_final: 0.9009 (m-30) REVERT: A 469 MET cc_start: 0.8575 (ppp) cc_final: 0.7939 (ppp) REVERT: A 486 ASP cc_start: 0.8483 (t0) cc_final: 0.7831 (t0) REVERT: B 190 ASP cc_start: 0.8597 (m-30) cc_final: 0.8311 (m-30) REVERT: C 350 MET cc_start: 0.5245 (ppp) cc_final: 0.4851 (ppp) REVERT: C 412 MET cc_start: 0.6361 (ppp) cc_final: 0.5903 (ppp) REVERT: C 446 ILE cc_start: 0.9545 (mt) cc_final: 0.8322 (mt) REVERT: C 447 ASP cc_start: 0.9241 (t0) cc_final: 0.8694 (t0) REVERT: C 552 ASN cc_start: 0.9074 (p0) cc_final: 0.8333 (p0) REVERT: D 146 MET cc_start: 0.7880 (tpt) cc_final: 0.7346 (tpp) REVERT: D 249 MET cc_start: 0.9451 (tmm) cc_final: 0.9027 (tmm) REVERT: E 1 MET cc_start: 0.5425 (tpp) cc_final: 0.4823 (tmm) REVERT: E 22 MET cc_start: 0.8121 (ppp) cc_final: 0.7881 (ppp) REVERT: E 144 ILE cc_start: 0.8935 (pt) cc_final: 0.8505 (tt) REVERT: E 220 MET cc_start: 0.7911 (ptp) cc_final: 0.7481 (ptp) REVERT: F 124 LYS cc_start: 0.8882 (pptt) cc_final: 0.8647 (pptt) REVERT: F 155 MET cc_start: 0.7817 (ptp) cc_final: 0.7443 (ptp) REVERT: F 181 TYR cc_start: 0.8119 (t80) cc_final: 0.7510 (t80) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2253 time to fit residues: 70.5933 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 : 1.457 ------------------------------------------------------------------------------- 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: 2.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 135 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 0.0010 chunk 75 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 = 0.076009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.056171 restraints weight = 64395.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.057894 restraints weight = 40297.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.059084 restraints weight = 29032.498| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2224 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= 0.161 Angle : 0.605 6.779 17062 Z= 0.315 Chirality : 0.043 0.187 1882 Planarity : 0.004 0.047 2171 Dihedral : 5.093 64.014 1734 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.55 % Favored : 95.38 % Rotamer: Outliers : 0.07 % Allowed : 1.19 % Favored : 98.74 % 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: 0.54 (0.21), residues: 1515 helix: 1.28 (0.18), residues: 855 sheet: -0.52 (0.55), residues: 82 loop : -0.88 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 247 HIS 0.008 0.001 HIS F 180 PHE 0.061 0.002 PHE F 176 TYR 0.021 0.001 TYR B 240 ARG 0.005 0.000 ARG A 554 *********************** 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 212 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 1.529 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: 0.9120 (tt0) cc_final: 0.8642 (tt0) REVERT: A 447 ASP cc_start: 0.9291 (m-30) cc_final: 0.8975 (m-30) REVERT: A 456 MET cc_start: 0.8883 (mmt) cc_final: 0.8624 (mmt) REVERT: A 469 MET cc_start: 0.8593 (ppp) cc_final: 0.7979 (ppp) REVERT: A 486 ASP cc_start: 0.8438 (t0) cc_final: 0.7789 (t0) REVERT: B 196 ILE cc_start: 0.9404 (pt) cc_final: 0.9050 (tp) REVERT: B 204 ILE cc_start: 0.8939 (mp) cc_final: 0.8491 (mp) REVERT: C 350 MET cc_start: 0.5819 (ppp) cc_final: 0.5127 (ppp) REVERT: C 412 MET cc_start: 0.6159 (ppp) cc_final: 0.5521 (ppp) REVERT: C 447 ASP cc_start: 0.9190 (t0) cc_final: 0.8620 (t0) REVERT: D 192 LYS cc_start: 0.8735 (mmmt) cc_final: 0.8506 (mmmt) REVERT: D 249 MET cc_start: 0.9397 (tmm) cc_final: 0.9034 (tmm) REVERT: D 256 MET cc_start: 0.9305 (pmm) cc_final: 0.9008 (pmm) REVERT: E 144 ILE cc_start: 0.8919 (pt) cc_final: 0.8495 (tt) REVERT: E 153 GLU cc_start: 0.9377 (mp0) cc_final: 0.9137 (mp0) REVERT: E 220 MET cc_start: 0.7907 (ptp) cc_final: 0.7707 (ptp) REVERT: F 1 MET cc_start: 0.4217 (tpt) cc_final: 0.3832 (tpp) REVERT: F 124 LYS cc_start: 0.8886 (pptt) cc_final: 0.8465 (pptt) REVERT: F 181 TYR cc_start: 0.8192 (t80) cc_final: 0.7822 (t80) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.2287 time to fit residues: 71.5853 Evaluate side-chains 160 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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: 0.7980 chunk 112 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 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 = 0.3597 r_free = 0.3597 target = 0.075485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.055830 restraints weight = 63895.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.057554 restraints weight = 39837.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.058750 restraints weight = 28562.738| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.003 0.031 12657 Z= 0.177 Angle : 0.606 7.831 17062 Z= 0.312 Chirality : 0.043 0.154 1882 Planarity : 0.004 0.045 2171 Dihedral : 5.065 65.047 1734 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.82 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: 0.56 (0.22), residues: 1515 helix: 1.27 (0.18), residues: 858 sheet: -0.52 (0.55), residues: 81 loop : -0.81 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 247 HIS 0.009 0.001 HIS D 184 PHE 0.016 0.001 PHE A 599 TYR 0.014 0.001 TYR F 127 ARG 0.007 0.000 ARG E 148 *********************** 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 216 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.442 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: 0.9105 (tt0) cc_final: 0.8610 (tt0) REVERT: A 442 MET cc_start: 0.8280 (ppp) cc_final: 0.8041 (ppp) REVERT: A 447 ASP cc_start: 0.9301 (m-30) cc_final: 0.8973 (m-30) REVERT: A 456 MET cc_start: 0.8894 (mmt) cc_final: 0.8563 (mmt) REVERT: A 469 MET cc_start: 0.8753 (ppp) cc_final: 0.8024 (ppp) REVERT: A 486 ASP cc_start: 0.8452 (t0) cc_final: 0.7824 (t0) REVERT: A 581 MET cc_start: 0.6790 (ptt) cc_final: 0.6546 (ptt) REVERT: C 350 MET cc_start: 0.5878 (ppp) cc_final: 0.5187 (ppp) REVERT: C 412 MET cc_start: 0.6099 (ppp) cc_final: 0.5480 (ppp) REVERT: C 442 MET cc_start: 0.7930 (tpt) cc_final: 0.7365 (tmm) REVERT: C 446 ILE cc_start: 0.9543 (mt) cc_final: 0.8639 (mt) REVERT: C 447 ASP cc_start: 0.9225 (t0) cc_final: 0.8663 (t0) REVERT: D 94 MET cc_start: 0.3479 (tpt) cc_final: 0.2525 (mmm) REVERT: D 146 MET cc_start: 0.7892 (tpt) cc_final: 0.7305 (tpp) REVERT: D 219 MET cc_start: 0.9124 (ptp) cc_final: 0.8847 (ptp) REVERT: D 249 MET cc_start: 0.9418 (tmm) cc_final: 0.9028 (tmm) REVERT: E 1 MET cc_start: 0.5735 (tpp) cc_final: 0.5226 (tmm) REVERT: E 144 ILE cc_start: 0.8937 (pt) cc_final: 0.8497 (tt) REVERT: E 153 GLU cc_start: 0.9363 (mp0) cc_final: 0.9116 (mp0) REVERT: E 220 MET cc_start: 0.7940 (ptp) cc_final: 0.7711 (ptp) REVERT: F 119 PHE cc_start: 0.8613 (t80) cc_final: 0.8348 (t80) REVERT: F 124 LYS cc_start: 0.8899 (pptt) cc_final: 0.8472 (pptt) REVERT: F 181 TYR cc_start: 0.8583 (t80) cc_final: 0.8137 (t80) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2171 time to fit residues: 70.1416 Evaluate side-chains 152 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.534 ------------------------------------------------------------------------------- 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: 6.9990 chunk 7 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 chunk 119 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 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 = 0.3599 r_free = 0.3599 target = 0.075460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.055646 restraints weight = 64711.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.057385 restraints weight = 40150.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.058586 restraints weight = 28768.986| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2468 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= 0.188 Angle : 0.631 7.522 17062 Z= 0.323 Chirality : 0.044 0.177 1882 Planarity : 0.004 0.044 2171 Dihedral : 5.071 65.812 1734 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.62 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % 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: 0.54 (0.22), residues: 1515 helix: 1.24 (0.18), residues: 859 sheet: -0.64 (0.55), residues: 82 loop : -0.79 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 511 HIS 0.006 0.001 HIS E 180 PHE 0.029 0.001 PHE F 176 TYR 0.020 0.001 TYR A 534 ARG 0.005 0.000 ARG F 56 *********************** 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 214 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.372 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: 0.9122 (tt0) cc_final: 0.8613 (tt0) REVERT: A 447 ASP cc_start: 0.9301 (m-30) cc_final: 0.8989 (m-30) REVERT: A 469 MET cc_start: 0.8708 (ppp) cc_final: 0.8030 (ppp) REVERT: A 486 ASP cc_start: 0.8497 (t0) cc_final: 0.7836 (t0) REVERT: C 350 MET cc_start: 0.5918 (ppp) cc_final: 0.5223 (ppp) REVERT: C 412 MET cc_start: 0.6082 (ppp) cc_final: 0.5465 (ppp) REVERT: C 442 MET cc_start: 0.7999 (tpt) cc_final: 0.7661 (tmm) REVERT: C 446 ILE cc_start: 0.9523 (mt) cc_final: 0.8991 (mm) REVERT: C 447 ASP cc_start: 0.9208 (t0) cc_final: 0.8677 (t0) REVERT: D 94 MET cc_start: 0.3378 (tpt) cc_final: 0.2554 (mmm) REVERT: D 146 MET cc_start: 0.7907 (tpt) cc_final: 0.7335 (tpp) REVERT: D 219 MET cc_start: 0.9135 (ptp) cc_final: 0.8766 (ptp) REVERT: D 249 MET cc_start: 0.9452 (tmm) cc_final: 0.9025 (tmm) REVERT: E 144 ILE cc_start: 0.8925 (pt) cc_final: 0.8498 (tt) REVERT: E 220 MET cc_start: 0.7931 (ptp) cc_final: 0.7705 (ptp) REVERT: F 1 MET cc_start: 0.4881 (tpp) cc_final: 0.4224 (tmm) REVERT: F 124 LYS cc_start: 0.8911 (pptt) cc_final: 0.8506 (pptt) REVERT: F 155 MET cc_start: 0.7730 (ptp) cc_final: 0.7343 (ptp) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.2263 time to fit residues: 71.4646 Evaluate side-chains 153 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.387 ------------------------------------------------------------------------------- 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: 7.9990 chunk 55 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 123 optimal weight: 20.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.072141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.052819 restraints weight = 65878.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.054436 restraints weight = 41590.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.055555 restraints weight = 30074.026| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12657 Z= 0.356 Angle : 0.736 7.635 17062 Z= 0.384 Chirality : 0.047 0.184 1882 Planarity : 0.005 0.087 2171 Dihedral : 5.546 66.979 1734 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.41 % Favored : 94.52 % 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 (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: 0.13 (0.21), residues: 1515 helix: 0.92 (0.17), residues: 858 sheet: -0.78 (0.50), residues: 90 loop : -0.97 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 511 HIS 0.010 0.002 HIS C 460 PHE 0.029 0.002 PHE E 176 TYR 0.019 0.002 TYR F 181 ARG 0.006 0.001 ARG E 148 *********************** 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 197 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 GLU cc_start: 0.9215 (tt0) cc_final: 0.8805 (tt0) REVERT: A 447 ASP cc_start: 0.9320 (m-30) cc_final: 0.9040 (m-30) REVERT: A 469 MET cc_start: 0.8902 (ppp) cc_final: 0.7958 (ppp) REVERT: A 486 ASP cc_start: 0.8561 (t0) cc_final: 0.7915 (t0) REVERT: B 110 GLN cc_start: 0.8793 (tp-100) cc_final: 0.8459 (tp-100) REVERT: B 190 ASP cc_start: 0.8087 (m-30) cc_final: 0.7811 (m-30) REVERT: B 341 CYS cc_start: 0.8848 (m) cc_final: 0.8629 (m) REVERT: C 350 MET cc_start: 0.5950 (ppp) cc_final: 0.5398 (ppp) REVERT: C 412 MET cc_start: 0.6250 (ppp) cc_final: 0.5518 (ppp) REVERT: C 442 MET cc_start: 0.8060 (tpt) cc_final: 0.7485 (tmm) REVERT: C 446 ILE cc_start: 0.9502 (mt) cc_final: 0.8522 (mt) REVERT: C 447 ASP cc_start: 0.9258 (t0) cc_final: 0.8778 (t0) REVERT: C 462 LYS cc_start: 0.9153 (tttt) cc_final: 0.8942 (tttt) REVERT: D 146 MET cc_start: 0.8176 (tpt) cc_final: 0.7711 (tpp) REVERT: D 219 MET cc_start: 0.8978 (ptp) cc_final: 0.8417 (ptp) REVERT: D 249 MET cc_start: 0.9521 (tmm) cc_final: 0.9079 (tmm) REVERT: D 256 MET cc_start: 0.9385 (pmm) cc_final: 0.9137 (pmm) REVERT: E 1 MET cc_start: 0.5199 (tpp) cc_final: 0.4854 (tmm) REVERT: E 144 ILE cc_start: 0.8961 (pt) cc_final: 0.8505 (tt) REVERT: E 180 HIS cc_start: 0.7439 (m170) cc_final: 0.6717 (m170) REVERT: F 26 MET cc_start: 0.9227 (mtp) cc_final: 0.8772 (ptt) REVERT: F 155 MET cc_start: 0.7693 (ptp) cc_final: 0.7461 (ptp) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2199 time to fit residues: 65.8302 Evaluate side-chains 143 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.612 ------------------------------------------------------------------------------- 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: 5.9990 chunk 125 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 60 optimal weight: 0.0050 chunk 15 optimal weight: 2.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.072966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.053565 restraints weight = 64438.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.055229 restraints weight = 40399.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.056359 restraints weight = 29117.075| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12657 Z= 0.245 Angle : 0.682 7.962 17062 Z= 0.353 Chirality : 0.045 0.156 1882 Planarity : 0.004 0.075 2171 Dihedral : 5.322 67.891 1734 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.35 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: 0.16 (0.21), residues: 1515 helix: 0.95 (0.18), residues: 858 sheet: -0.86 (0.50), residues: 90 loop : -0.97 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 511 HIS 0.005 0.001 HIS A 466 PHE 0.021 0.002 PHE F 176 TYR 0.027 0.002 TYR B 240 ARG 0.007 0.001 ARG E 148 ********************** 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 201 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 1.453 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: 0.9174 (tt0) cc_final: 0.8753 (tt0) REVERT: A 436 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8541 (mm-40) REVERT: A 442 MET cc_start: 0.8348 (ppp) cc_final: 0.8138 (ppp) REVERT: A 447 ASP cc_start: 0.9299 (m-30) cc_final: 0.9000 (m-30) REVERT: A 456 MET cc_start: 0.8965 (mmt) cc_final: 0.8762 (mmt) REVERT: A 469 MET cc_start: 0.8836 (ppp) cc_final: 0.8113 (ppp) REVERT: A 486 ASP cc_start: 0.8476 (t0) cc_final: 0.7841 (t0) REVERT: A 512 MET cc_start: 0.7651 (ptp) cc_final: 0.7429 (ptp) REVERT: B 110 GLN cc_start: 0.8798 (tp-100) cc_final: 0.8462 (tp-100) REVERT: B 190 ASP cc_start: 0.8131 (m-30) cc_final: 0.7845 (m-30) REVERT: B 308 MET cc_start: 0.5906 (tmm) cc_final: 0.5606 (mmp) REVERT: C 350 MET cc_start: 0.5948 (ppp) cc_final: 0.5468 (ppp) REVERT: C 412 MET cc_start: 0.6164 (ppp) cc_final: 0.5431 (ppp) REVERT: C 447 ASP cc_start: 0.9210 (t0) cc_final: 0.8713 (t0) REVERT: C 462 LYS cc_start: 0.9051 (tttt) cc_final: 0.8761 (tttt) REVERT: C 464 ILE cc_start: 0.9052 (mm) cc_final: 0.8639 (mp) REVERT: D 125 TYR cc_start: 0.8960 (m-10) cc_final: 0.8758 (m-10) REVERT: D 146 MET cc_start: 0.7805 (tpt) cc_final: 0.7500 (tpp) REVERT: D 219 MET cc_start: 0.8949 (ptp) cc_final: 0.8298 (ptp) REVERT: D 249 MET cc_start: 0.9462 (tmm) cc_final: 0.9022 (tmm) REVERT: D 256 MET cc_start: 0.9346 (pmm) cc_final: 0.9135 (pmm) REVERT: E 144 ILE cc_start: 0.8928 (pt) cc_final: 0.8429 (tt) REVERT: E 180 HIS cc_start: 0.7779 (m170) cc_final: 0.7558 (m170) REVERT: E 220 MET cc_start: 0.7965 (ptm) cc_final: 0.7644 (ptm) REVERT: F 1 MET cc_start: 0.4006 (tpp) cc_final: 0.3358 (tmm) REVERT: F 26 MET cc_start: 0.9225 (mtp) cc_final: 0.8646 (ptt) REVERT: F 48 TYR cc_start: 0.8225 (m-80) cc_final: 0.7383 (m-80) REVERT: F 155 MET cc_start: 0.7678 (ptp) cc_final: 0.7447 (ptp) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.2196 time to fit residues: 66.7810 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 : 1.476 ------------------------------------------------------------------------------- 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: 0.0670 chunk 49 optimal weight: 0.0570 chunk 103 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 55 optimal weight: 0.3980 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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 = 0.075183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.055605 restraints weight = 63586.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.057304 restraints weight = 39580.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.058490 restraints weight = 28490.619| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3024 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= 0.166 Angle : 0.671 8.061 17062 Z= 0.343 Chirality : 0.045 0.155 1882 Planarity : 0.004 0.068 2171 Dihedral : 5.132 69.744 1734 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.42 % Favored : 95.51 % 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: 0.28 (0.21), residues: 1515 helix: 1.06 (0.18), residues: 856 sheet: -0.80 (0.54), residues: 82 loop : -0.94 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 511 HIS 0.005 0.001 HIS E 180 PHE 0.024 0.002 PHE E 25 TYR 0.017 0.001 TYR E 84 ARG 0.004 0.000 ARG D 96 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3517.63 seconds wall clock time: 63 minutes 54.04 seconds (3834.04 seconds total)