Starting phenix.real_space_refine on Wed Mar 4 01:26:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cv2_27006/03_2026/8cv2_27006.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cv2_27006/03_2026/8cv2_27006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cv2_27006/03_2026/8cv2_27006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cv2_27006/03_2026/8cv2_27006.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cv2_27006/03_2026/8cv2_27006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cv2_27006/03_2026/8cv2_27006.map" } resolution = 2.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.111 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: 5 Type Number sf(0) Gaussians S 63 5.16 5 Na 6 4.78 5 C 6459 2.51 5 N 1578 2.21 5 O 1776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9882 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3292 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 12, 'TRANS': 420} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C Time building chain proxies: 2.40, per 1000 atoms: 0.24 Number of scatterers: 9882 At special positions: 0 Unit cell: (109.056, 105.648, 80.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 Na 6 11.00 O 1776 8.00 N 1578 7.00 C 6459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 310.9 milliseconds 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 3 sheets defined 84.3% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.739A pdb=" N ALA A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.839A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 117 Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.542A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.608A pdb=" N ALA A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 229 removed outlier: 3.597A pdb=" N LYS A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 273 removed outlier: 4.029A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.547A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 282 through 309 removed outlier: 4.898A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Proline residue: A 302 - end of helix Processing helix chain 'A' and resid 312 through 320 removed outlier: 4.053A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.703A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 390 through 408 Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 429 through 438 removed outlier: 3.542A pdb=" N THR A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 437 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA A 438 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 4.596A pdb=" N ARG A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 removed outlier: 3.803A pdb=" N LEU A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 42 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.738A pdb=" N ALA B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 66 through 82 removed outlier: 3.838A pdb=" N LEU B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 117 Processing helix chain 'B' and resid 137 through 150 removed outlier: 3.543A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 removed outlier: 3.608A pdb=" N ALA B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 229 removed outlier: 3.597A pdb=" N LYS B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 273 removed outlier: 4.028A pdb=" N TRP B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TYR B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.546A pdb=" N PHE B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL B 273 " --> pdb=" O CYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 282 Processing helix chain 'B' and resid 282 through 309 removed outlier: 4.897A pdb=" N LEU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Proline residue: B 302 - end of helix Processing helix chain 'B' and resid 312 through 320 removed outlier: 4.052A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 336 through 347 Processing helix chain 'B' and resid 351 through 366 removed outlier: 3.703A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Proline residue: B 360 - end of helix Processing helix chain 'B' and resid 367 through 385 Processing helix chain 'B' and resid 390 through 408 Processing helix chain 'B' and resid 413 through 427 Processing helix chain 'B' and resid 429 through 438 removed outlier: 3.542A pdb=" N THR B 434 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B 437 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA B 438 " --> pdb=" O LEU B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 466 removed outlier: 4.596A pdb=" N ARG B 445 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 476 removed outlier: 3.802A pdb=" N LEU B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 42 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.738A pdb=" N ALA C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 65 Processing helix chain 'C' and resid 66 through 82 removed outlier: 3.839A pdb=" N LEU C 82 " --> pdb=" O GLY C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 117 Processing helix chain 'C' and resid 137 through 150 removed outlier: 3.543A pdb=" N PHE C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 removed outlier: 3.608A pdb=" N ALA C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 229 removed outlier: 3.596A pdb=" N LYS C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 273 removed outlier: 4.028A pdb=" N TRP C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TYR C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.546A pdb=" N PHE C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL C 273 " --> pdb=" O CYS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 282 Processing helix chain 'C' and resid 282 through 309 removed outlier: 4.897A pdb=" N LEU C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Proline residue: C 302 - end of helix Processing helix chain 'C' and resid 312 through 320 removed outlier: 4.052A pdb=" N PHE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'C' and resid 351 through 366 removed outlier: 3.703A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Proline residue: C 360 - end of helix Processing helix chain 'C' and resid 367 through 385 Processing helix chain 'C' and resid 390 through 408 Processing helix chain 'C' and resid 413 through 427 Processing helix chain 'C' and resid 429 through 438 removed outlier: 3.541A pdb=" N THR C 434 " --> pdb=" O GLU C 431 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C 437 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA C 438 " --> pdb=" O LEU C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 466 removed outlier: 4.596A pdb=" N ARG C 445 " --> pdb=" O CYS C 441 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 476 removed outlier: 3.802A pdb=" N LEU C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 167 Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 167 783 hydrogen bonds defined for protein. 2304 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3092 1.34 - 1.46: 1443 1.46 - 1.58: 5371 1.58 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 10023 Sorted by residual: bond pdb=" N GLU C 274 " pdb=" CA GLU C 274 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.26e-02 6.30e+03 6.20e+00 bond pdb=" N GLU B 274 " pdb=" CA GLU B 274 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.26e-02 6.30e+03 5.97e+00 bond pdb=" N GLU A 274 " pdb=" CA GLU A 274 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.26e-02 6.30e+03 5.79e+00 bond pdb=" N SER C 331 " pdb=" CA SER C 331 " ideal model delta sigma weight residual 1.460 1.489 -0.030 1.48e-02 4.57e+03 4.10e+00 bond pdb=" N SER A 331 " pdb=" CA SER A 331 " ideal model delta sigma weight residual 1.460 1.489 -0.030 1.48e-02 4.57e+03 4.09e+00 ... (remaining 10018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 13080 1.15 - 2.30: 413 2.30 - 3.45: 73 3.45 - 4.60: 27 4.60 - 5.74: 15 Bond angle restraints: 13608 Sorted by residual: angle pdb=" CB GLU C 471 " pdb=" CG GLU C 471 " pdb=" CD GLU C 471 " ideal model delta sigma weight residual 112.60 116.51 -3.91 1.70e+00 3.46e-01 5.29e+00 angle pdb=" CB GLU B 471 " pdb=" CG GLU B 471 " pdb=" CD GLU B 471 " ideal model delta sigma weight residual 112.60 116.51 -3.91 1.70e+00 3.46e-01 5.29e+00 angle pdb=" CB GLU A 471 " pdb=" CG GLU A 471 " pdb=" CD GLU A 471 " ideal model delta sigma weight residual 112.60 116.51 -3.91 1.70e+00 3.46e-01 5.28e+00 angle pdb=" CA GLU C 274 " pdb=" C GLU C 274 " pdb=" O GLU C 274 " ideal model delta sigma weight residual 120.24 117.74 2.50 1.11e+00 8.12e-01 5.06e+00 angle pdb=" CA SER A 331 " pdb=" C SER A 331 " pdb=" O SER A 331 " ideal model delta sigma weight residual 120.57 117.90 2.67 1.20e+00 6.94e-01 4.96e+00 ... (remaining 13603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.74: 5287 15.74 - 31.48: 512 31.48 - 47.22: 177 47.22 - 62.96: 21 62.96 - 78.70: 6 Dihedral angle restraints: 6003 sinusoidal: 2280 harmonic: 3723 Sorted by residual: dihedral pdb=" CA VAL C 299 " pdb=" C VAL C 299 " pdb=" N ILE C 300 " pdb=" CA ILE C 300 " ideal model delta harmonic sigma weight residual -180.00 -162.82 -17.18 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA VAL A 299 " pdb=" C VAL A 299 " pdb=" N ILE A 300 " pdb=" CA ILE A 300 " ideal model delta harmonic sigma weight residual -180.00 -162.85 -17.15 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA VAL B 299 " pdb=" C VAL B 299 " pdb=" N ILE B 300 " pdb=" CA ILE B 300 " ideal model delta harmonic sigma weight residual -180.00 -162.86 -17.14 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 6000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1130 0.029 - 0.058: 378 0.058 - 0.087: 156 0.087 - 0.116: 46 0.116 - 0.145: 15 Chirality restraints: 1725 Sorted by residual: chirality pdb=" CA VAL B 411 " pdb=" N VAL B 411 " pdb=" C VAL B 411 " pdb=" CB VAL B 411 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA VAL A 411 " pdb=" N VAL A 411 " pdb=" C VAL A 411 " pdb=" CB VAL A 411 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA VAL C 411 " pdb=" N VAL C 411 " pdb=" C VAL C 411 " pdb=" CB VAL C 411 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1722 not shown) Planarity restraints: 1665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 401 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C ALA C 401 " -0.033 2.00e-02 2.50e+03 pdb=" O ALA C 401 " 0.012 2.00e-02 2.50e+03 pdb=" N THR C 402 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 296 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.48e+00 pdb=" C HIS C 296 " 0.032 2.00e-02 2.50e+03 pdb=" O HIS C 296 " -0.012 2.00e-02 2.50e+03 pdb=" N SER C 297 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 401 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C ALA A 401 " -0.032 2.00e-02 2.50e+03 pdb=" O ALA A 401 " 0.012 2.00e-02 2.50e+03 pdb=" N THR A 402 " 0.011 2.00e-02 2.50e+03 ... (remaining 1662 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2453 2.80 - 3.33: 9997 3.33 - 3.85: 16120 3.85 - 4.38: 18160 4.38 - 4.90: 32528 Nonbonded interactions: 79258 Sorted by model distance: nonbonded pdb=" NH2 ARG C 39 " pdb=" O VAL C 273 " model vdw 2.281 3.120 nonbonded pdb=" NH2 ARG A 39 " pdb=" O VAL A 273 " model vdw 2.281 3.120 nonbonded pdb=" NH2 ARG B 39 " pdb=" O VAL B 273 " model vdw 2.282 3.120 nonbonded pdb=" OD1 ASP C 368 " pdb="NA NA C 602 " model vdw 2.321 2.470 nonbonded pdb=" OD1 ASP A 368 " pdb="NA NA A 602 " model vdw 2.322 2.470 ... (remaining 79253 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 individual isotropic 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: 2.390 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.380 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 : 0.003 0.045 10023 Z= 0.161 Angle : 0.533 5.744 13608 Z= 0.297 Chirality : 0.037 0.145 1725 Planarity : 0.004 0.033 1665 Dihedral : 14.128 78.698 3603 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 19.11 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.23), residues: 1287 helix: 1.83 (0.16), residues: 1029 sheet: 1.73 (0.53), residues: 48 loop : -1.87 (0.31), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 356 TYR 0.009 0.001 TYR B 373 PHE 0.011 0.001 PHE C 341 TRP 0.007 0.001 TRP B 19 HIS 0.002 0.001 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00305 (10023) covalent geometry : angle 0.53311 (13608) hydrogen bonds : bond 0.13649 ( 783) hydrogen bonds : angle 4.93005 ( 2304) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.366 Fit side-chains REVERT: A 274 GLU cc_start: 0.7289 (pm20) cc_final: 0.6901 (pm20) REVERT: B 205 MET cc_start: 0.8442 (ptm) cc_final: 0.8216 (ptm) REVERT: B 258 MET cc_start: 0.8659 (ttm) cc_final: 0.8437 (ttp) REVERT: B 274 GLU cc_start: 0.7284 (pm20) cc_final: 0.6752 (pm20) REVERT: B 473 MET cc_start: 0.7174 (ttp) cc_final: 0.6904 (ttm) REVERT: C 274 GLU cc_start: 0.7233 (pm20) cc_final: 0.6833 (pm20) REVERT: C 449 MET cc_start: 0.8214 (ttp) cc_final: 0.7898 (tmt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.6170 time to fit residues: 87.6111 Evaluate side-chains 125 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN C 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.169623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.111428 restraints weight = 10202.575| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.87 r_work: 0.3135 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10023 Z= 0.162 Angle : 0.521 5.714 13608 Z= 0.281 Chirality : 0.038 0.130 1725 Planarity : 0.004 0.032 1665 Dihedral : 3.780 17.983 1365 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.86 % Allowed : 15.79 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.23), residues: 1287 helix: 2.29 (0.16), residues: 1011 sheet: 1.62 (0.53), residues: 48 loop : -0.91 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 315 TYR 0.010 0.001 TYR A 373 PHE 0.012 0.002 PHE C 240 TRP 0.003 0.001 TRP C 19 HIS 0.002 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00339 (10023) covalent geometry : angle 0.52123 (13608) hydrogen bonds : bond 0.06959 ( 783) hydrogen bonds : angle 4.21378 ( 2304) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.386 Fit side-chains REVERT: A 274 GLU cc_start: 0.7328 (pm20) cc_final: 0.6970 (pm20) REVERT: A 330 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7596 (mt) REVERT: A 442 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7542 (tp) REVERT: B 205 MET cc_start: 0.8777 (ptm) cc_final: 0.8546 (ptm) REVERT: B 274 GLU cc_start: 0.7389 (pm20) cc_final: 0.7033 (pm20) REVERT: B 330 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7591 (mt) REVERT: B 442 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7282 (tp) REVERT: C 274 GLU cc_start: 0.7292 (pm20) cc_final: 0.6954 (pm20) REVERT: C 449 MET cc_start: 0.8226 (ttp) cc_final: 0.7866 (tmt) outliers start: 31 outliers final: 12 residues processed: 151 average time/residue: 0.5714 time to fit residues: 92.2180 Evaluate side-chains 139 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 57 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 82 optimal weight: 0.0270 chunk 35 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN C 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.172968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.115735 restraints weight = 10230.485| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.86 r_work: 0.3196 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10023 Z= 0.130 Angle : 0.464 5.702 13608 Z= 0.250 Chirality : 0.037 0.154 1725 Planarity : 0.004 0.039 1665 Dihedral : 3.648 17.416 1365 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.49 % Allowed : 15.60 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.23), residues: 1287 helix: 2.52 (0.16), residues: 1011 sheet: 1.57 (0.55), residues: 48 loop : -0.78 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 315 TYR 0.007 0.001 TYR C 373 PHE 0.009 0.001 PHE B 240 TRP 0.005 0.001 TRP A 256 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00245 (10023) covalent geometry : angle 0.46389 (13608) hydrogen bonds : bond 0.05554 ( 783) hydrogen bonds : angle 3.99064 ( 2304) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.381 Fit side-chains REVERT: A 274 GLU cc_start: 0.7245 (pm20) cc_final: 0.7005 (pm20) REVERT: A 330 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7537 (mt) REVERT: B 205 MET cc_start: 0.8700 (ptm) cc_final: 0.8488 (ptm) REVERT: B 274 GLU cc_start: 0.7132 (pm20) cc_final: 0.6756 (pm20) REVERT: B 442 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7187 (tp) REVERT: C 39 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6992 (ttt90) REVERT: C 274 GLU cc_start: 0.7188 (pm20) cc_final: 0.6810 (pm20) outliers start: 27 outliers final: 11 residues processed: 153 average time/residue: 0.5793 time to fit residues: 94.8546 Evaluate side-chains 147 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 58 optimal weight: 0.0570 chunk 79 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 overall best weight: 1.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN C 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.168094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.110159 restraints weight = 10168.983| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.83 r_work: 0.3116 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10023 Z= 0.166 Angle : 0.524 5.804 13608 Z= 0.283 Chirality : 0.038 0.147 1725 Planarity : 0.004 0.035 1665 Dihedral : 3.812 17.789 1365 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.14 % Allowed : 16.44 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.23), residues: 1287 helix: 2.35 (0.16), residues: 1011 sheet: 1.33 (0.54), residues: 48 loop : -0.93 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 315 TYR 0.009 0.001 TYR A 373 PHE 0.013 0.002 PHE A 240 TRP 0.004 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00352 (10023) covalent geometry : angle 0.52373 (13608) hydrogen bonds : bond 0.07089 ( 783) hydrogen bonds : angle 4.11533 ( 2304) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.286 Fit side-chains REVERT: A 231 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: A 274 GLU cc_start: 0.7382 (pm20) cc_final: 0.7125 (pm20) REVERT: A 330 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7598 (mt) REVERT: B 39 ARG cc_start: 0.7383 (ttt90) cc_final: 0.6999 (ptm160) REVERT: B 167 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7305 (pp20) REVERT: B 274 GLU cc_start: 0.7147 (pm20) cc_final: 0.6820 (pm20) REVERT: B 330 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7548 (mp) REVERT: B 442 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7333 (tp) REVERT: C 39 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.6618 (ttm-80) REVERT: C 274 GLU cc_start: 0.7142 (pm20) cc_final: 0.6711 (pm20) outliers start: 34 outliers final: 15 residues processed: 148 average time/residue: 0.5883 time to fit residues: 92.9436 Evaluate side-chains 151 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 44 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 57 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN A 322 GLN B 312 ASN B 322 GLN C 312 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.168743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.110231 restraints weight = 10202.785| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.04 r_work: 0.3134 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10023 Z= 0.150 Angle : 0.499 6.708 13608 Z= 0.270 Chirality : 0.038 0.141 1725 Planarity : 0.004 0.032 1665 Dihedral : 3.779 17.799 1365 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.95 % Allowed : 17.91 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.23), residues: 1287 helix: 2.42 (0.16), residues: 1011 sheet: 1.28 (0.55), residues: 48 loop : -1.11 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 315 TYR 0.009 0.001 TYR A 373 PHE 0.012 0.001 PHE C 240 TRP 0.005 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00305 (10023) covalent geometry : angle 0.49888 (13608) hydrogen bonds : bond 0.06485 ( 783) hydrogen bonds : angle 4.04262 ( 2304) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.292 Fit side-chains REVERT: A 274 GLU cc_start: 0.7424 (pm20) cc_final: 0.7165 (pm20) REVERT: A 330 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7569 (mt) REVERT: B 39 ARG cc_start: 0.7337 (ttt90) cc_final: 0.6928 (ptm160) REVERT: B 274 GLU cc_start: 0.7174 (pm20) cc_final: 0.6836 (pm20) REVERT: B 330 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7524 (mp) REVERT: B 442 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7312 (tp) REVERT: C 39 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6891 (ttt90) REVERT: C 229 MET cc_start: 0.8905 (mtp) cc_final: 0.8629 (mtp) REVERT: C 274 GLU cc_start: 0.7193 (pm20) cc_final: 0.6729 (pm20) outliers start: 32 outliers final: 16 residues processed: 147 average time/residue: 0.5611 time to fit residues: 88.2043 Evaluate side-chains 150 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 449 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 89 optimal weight: 0.0000 chunk 4 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 115 optimal weight: 0.0470 chunk 47 optimal weight: 1.9990 overall best weight: 0.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN A 322 GLN B 312 ASN C 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.173943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117380 restraints weight = 10274.545| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.86 r_work: 0.3222 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10023 Z= 0.119 Angle : 0.451 7.159 13608 Z= 0.242 Chirality : 0.036 0.159 1725 Planarity : 0.003 0.038 1665 Dihedral : 3.579 17.012 1365 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.77 % Allowed : 18.28 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.02 (0.23), residues: 1287 helix: 2.68 (0.16), residues: 1011 sheet: 1.28 (0.55), residues: 48 loop : -1.19 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 315 TYR 0.009 0.001 TYR A 373 PHE 0.009 0.001 PHE A 218 TRP 0.005 0.001 TRP A 256 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00217 (10023) covalent geometry : angle 0.45150 (13608) hydrogen bonds : bond 0.04898 ( 783) hydrogen bonds : angle 3.82951 ( 2304) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.302 Fit side-chains REVERT: A 274 GLU cc_start: 0.7373 (pm20) cc_final: 0.7079 (pm20) REVERT: A 330 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7553 (mt) REVERT: B 205 MET cc_start: 0.8720 (ptm) cc_final: 0.8458 (ptm) REVERT: B 274 GLU cc_start: 0.7222 (pm20) cc_final: 0.6879 (pm20) REVERT: B 330 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7465 (mp) REVERT: B 442 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7152 (tp) REVERT: C 39 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6790 (ttt90) REVERT: C 274 GLU cc_start: 0.7164 (pm20) cc_final: 0.6733 (pm20) REVERT: C 432 ASP cc_start: 0.7159 (m-30) cc_final: 0.6691 (m-30) outliers start: 30 outliers final: 11 residues processed: 151 average time/residue: 0.6101 time to fit residues: 98.1519 Evaluate side-chains 145 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 72 optimal weight: 0.0980 chunk 54 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 0.0980 chunk 16 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.174192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.117691 restraints weight = 10250.916| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.84 r_work: 0.3213 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10023 Z= 0.118 Angle : 0.458 8.842 13608 Z= 0.243 Chirality : 0.036 0.155 1725 Planarity : 0.003 0.038 1665 Dihedral : 3.525 16.802 1365 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.94 % Allowed : 19.67 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.12 (0.23), residues: 1287 helix: 2.77 (0.16), residues: 1011 sheet: 1.24 (0.55), residues: 48 loop : -1.23 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 315 TYR 0.011 0.001 TYR A 373 PHE 0.008 0.001 PHE A 239 TRP 0.006 0.001 TRP A 256 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00216 (10023) covalent geometry : angle 0.45811 (13608) hydrogen bonds : bond 0.04842 ( 783) hydrogen bonds : angle 3.80306 ( 2304) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.324 Fit side-chains REVERT: A 274 GLU cc_start: 0.7425 (pm20) cc_final: 0.7090 (pm20) REVERT: A 330 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7520 (mt) REVERT: B 205 MET cc_start: 0.8739 (ptm) cc_final: 0.8483 (ptm) REVERT: B 274 GLU cc_start: 0.7156 (pm20) cc_final: 0.6834 (pm20) REVERT: B 330 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7445 (mp) REVERT: B 442 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7130 (tp) REVERT: C 39 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6856 (ttt90) REVERT: C 274 GLU cc_start: 0.7185 (pm20) cc_final: 0.6730 (pm20) outliers start: 21 outliers final: 9 residues processed: 144 average time/residue: 0.5998 time to fit residues: 92.1472 Evaluate side-chains 141 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 19 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 53 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN C 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.171436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.114061 restraints weight = 10189.562| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.88 r_work: 0.3178 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10023 Z= 0.131 Angle : 0.483 8.823 13608 Z= 0.256 Chirality : 0.037 0.158 1725 Planarity : 0.004 0.037 1665 Dihedral : 3.579 17.066 1365 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.75 % Allowed : 20.13 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.23), residues: 1287 helix: 2.68 (0.16), residues: 1011 sheet: 1.23 (0.55), residues: 48 loop : -1.25 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 315 TYR 0.013 0.001 TYR A 373 PHE 0.010 0.001 PHE C 240 TRP 0.008 0.001 TRP A 256 HIS 0.001 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00254 (10023) covalent geometry : angle 0.48300 (13608) hydrogen bonds : bond 0.05587 ( 783) hydrogen bonds : angle 3.85949 ( 2304) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.393 Fit side-chains REVERT: A 274 GLU cc_start: 0.7403 (pm20) cc_final: 0.7059 (pm20) REVERT: A 330 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7473 (mt) REVERT: B 167 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7194 (pp20) REVERT: B 205 MET cc_start: 0.8762 (ptm) cc_final: 0.8490 (ptm) REVERT: B 274 GLU cc_start: 0.7070 (pm20) cc_final: 0.6768 (pm20) REVERT: B 330 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7450 (mp) REVERT: B 442 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7088 (tp) REVERT: C 39 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6780 (ttt90) REVERT: C 229 MET cc_start: 0.8888 (mtp) cc_final: 0.8602 (mtp) REVERT: C 258 MET cc_start: 0.8723 (ttm) cc_final: 0.8489 (ttp) REVERT: C 274 GLU cc_start: 0.7202 (pm20) cc_final: 0.6746 (pm20) outliers start: 19 outliers final: 11 residues processed: 146 average time/residue: 0.6019 time to fit residues: 93.5883 Evaluate side-chains 147 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 0.2980 chunk 37 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 99 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN C 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.171820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.114760 restraints weight = 10233.267| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.84 r_work: 0.3188 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10023 Z= 0.131 Angle : 0.488 8.290 13608 Z= 0.258 Chirality : 0.037 0.156 1725 Planarity : 0.004 0.037 1665 Dihedral : 3.600 17.068 1365 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.85 % Allowed : 20.04 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.23), residues: 1287 helix: 2.68 (0.16), residues: 1011 sheet: 1.23 (0.55), residues: 48 loop : -1.26 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 315 TYR 0.014 0.001 TYR A 373 PHE 0.010 0.001 PHE C 240 TRP 0.008 0.001 TRP A 256 HIS 0.001 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00256 (10023) covalent geometry : angle 0.48818 (13608) hydrogen bonds : bond 0.05549 ( 783) hydrogen bonds : angle 3.85016 ( 2304) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.239 Fit side-chains REVERT: A 274 GLU cc_start: 0.7371 (pm20) cc_final: 0.7078 (pm20) REVERT: A 330 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7418 (mt) REVERT: A 367 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.6081 (mpt) REVERT: B 167 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7199 (pp20) REVERT: B 205 MET cc_start: 0.8765 (ptm) cc_final: 0.8510 (ptm) REVERT: B 274 GLU cc_start: 0.7090 (pm20) cc_final: 0.6807 (pm20) REVERT: B 330 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7495 (mp) REVERT: B 442 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7168 (tp) REVERT: C 39 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6946 (ttt90) REVERT: C 229 MET cc_start: 0.8903 (mtp) cc_final: 0.8698 (mtp) REVERT: C 258 MET cc_start: 0.8680 (ttm) cc_final: 0.8464 (ttp) REVERT: C 274 GLU cc_start: 0.7198 (pm20) cc_final: 0.6786 (pm20) REVERT: C 432 ASP cc_start: 0.7175 (m-30) cc_final: 0.6675 (m-30) outliers start: 20 outliers final: 14 residues processed: 144 average time/residue: 0.5797 time to fit residues: 89.2698 Evaluate side-chains 151 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 83 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN C 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.168174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.109718 restraints weight = 10114.800| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.87 r_work: 0.3127 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10023 Z= 0.160 Angle : 0.534 8.230 13608 Z= 0.285 Chirality : 0.038 0.157 1725 Planarity : 0.004 0.031 1665 Dihedral : 3.780 17.598 1365 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.12 % Allowed : 19.94 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.23), residues: 1287 helix: 2.51 (0.16), residues: 1011 sheet: 1.24 (0.56), residues: 48 loop : -1.33 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 315 TYR 0.015 0.001 TYR A 373 PHE 0.013 0.002 PHE C 240 TRP 0.011 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00339 (10023) covalent geometry : angle 0.53390 (13608) hydrogen bonds : bond 0.06794 ( 783) hydrogen bonds : angle 3.99627 ( 2304) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2574 Ramachandran restraints generated. 1287 Oldfield, 0 Emsley, 1287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.360 Fit side-chains REVERT: A 274 GLU cc_start: 0.7321 (pm20) cc_final: 0.6983 (pm20) REVERT: A 330 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7396 (mt) REVERT: B 167 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7188 (pp20) REVERT: B 258 MET cc_start: 0.8780 (ttm) cc_final: 0.8348 (ttm) REVERT: B 274 GLU cc_start: 0.7056 (pm20) cc_final: 0.6814 (pm20) REVERT: B 330 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7466 (mp) REVERT: B 431 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6848 (mp0) REVERT: B 442 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7265 (tp) REVERT: C 39 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6539 (ttm-80) REVERT: C 229 MET cc_start: 0.8930 (mtp) cc_final: 0.8690 (mtp) REVERT: C 258 MET cc_start: 0.8733 (ttm) cc_final: 0.8521 (ttp) REVERT: C 274 GLU cc_start: 0.7229 (pm20) cc_final: 0.6781 (pm20) REVERT: C 432 ASP cc_start: 0.7136 (m-30) cc_final: 0.6572 (m-30) outliers start: 23 outliers final: 14 residues processed: 144 average time/residue: 0.5800 time to fit residues: 89.2157 Evaluate side-chains 148 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 441 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 312 ASN C 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.171016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.113789 restraints weight = 10290.828| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.85 r_work: 0.3174 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10023 Z= 0.136 Angle : 0.501 8.230 13608 Z= 0.265 Chirality : 0.037 0.157 1725 Planarity : 0.004 0.032 1665 Dihedral : 3.708 17.169 1365 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.40 % Allowed : 19.67 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.23), residues: 1287 helix: 2.59 (0.16), residues: 1011 sheet: 1.18 (0.56), residues: 48 loop : -1.34 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 315 TYR 0.015 0.001 TYR A 373 PHE 0.010 0.001 PHE A 240 TRP 0.010 0.001 TRP A 256 HIS 0.001 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00268 (10023) covalent geometry : angle 0.50121 (13608) hydrogen bonds : bond 0.05801 ( 783) hydrogen bonds : angle 3.88596 ( 2304) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4235.18 seconds wall clock time: 72 minutes 29.44 seconds (4349.44 seconds total)