Starting phenix.real_space_refine on Fri Feb 14 05:49:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cv2_27006/02_2025/8cv2_27006.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cv2_27006/02_2025/8cv2_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cv2_27006/02_2025/8cv2_27006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cv2_27006/02_2025/8cv2_27006.map" model { file = "/net/cci-nas-00/data/ceres_data/8cv2_27006/02_2025/8cv2_27006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cv2_27006/02_2025/8cv2_27006.cif" } resolution = 2.44 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= 0.010 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: C, B Time building chain proxies: 6.11, per 1000 atoms: 0.62 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: 2.68 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.87 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: 2.74 Time building geometry restraints manager: 3.05 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.520 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.520 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.640 ------------------------------------------------------------------------------- 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= 0.196 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (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 TRP 0.007 0.001 TRP B 19 HIS 0.002 0.001 HIS C 41 PHE 0.011 0.001 PHE C 341 TYR 0.009 0.001 TYR B 373 ARG 0.005 0.001 ARG A 356 *********************** 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 : 1.076 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: 1.5063 time to fit residues: 213.7348 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 : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.169442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.111265 restraints weight = 10072.329| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.86 r_work: 0.3132 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10023 Z= 0.222 Angle : 0.525 5.635 13608 Z= 0.284 Chirality : 0.038 0.130 1725 Planarity : 0.004 0.033 1665 Dihedral : 3.792 18.012 1365 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.14 % Allowed : 15.60 % Favored : 81.26 % 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: 2.60 (0.23), residues: 1287 helix: 2.28 (0.16), residues: 1011 sheet: 1.62 (0.53), residues: 48 loop : -0.88 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 19 HIS 0.002 0.001 HIS B 296 PHE 0.012 0.002 PHE C 240 TYR 0.010 0.001 TYR A 373 ARG 0.004 0.001 ARG C 315 *********************** 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 164 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 1.109 Fit side-chains REVERT: A 274 GLU cc_start: 0.7329 (pm20) cc_final: 0.6970 (pm20) REVERT: A 330 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7607 (mt) REVERT: A 442 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7546 (tp) REVERT: B 274 GLU cc_start: 0.7412 (pm20) cc_final: 0.7059 (pm20) REVERT: B 330 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7593 (mt) REVERT: B 442 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7307 (tp) REVERT: C 274 GLU cc_start: 0.7263 (pm20) cc_final: 0.6928 (pm20) REVERT: C 449 MET cc_start: 0.8226 (ttp) cc_final: 0.7867 (tmt) outliers start: 34 outliers final: 12 residues processed: 153 average time/residue: 1.3426 time to fit residues: 219.8953 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 : 1.127 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.0970 chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.172426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.115068 restraints weight = 10269.969| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.86 r_work: 0.3185 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10023 Z= 0.161 Angle : 0.470 5.617 13608 Z= 0.253 Chirality : 0.037 0.155 1725 Planarity : 0.004 0.039 1665 Dihedral : 3.673 17.510 1365 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.31 % Allowed : 15.97 % Favored : 81.72 % 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: 2.90 (0.23), residues: 1287 helix: 2.50 (0.16), residues: 1011 sheet: 1.58 (0.55), residues: 48 loop : -0.78 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 256 HIS 0.001 0.000 HIS B 296 PHE 0.009 0.001 PHE A 240 TYR 0.007 0.001 TYR C 373 ARG 0.005 0.000 ARG A 315 *********************** 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 163 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 1.032 Fit side-chains REVERT: A 274 GLU cc_start: 0.7228 (pm20) cc_final: 0.6982 (pm20) REVERT: A 330 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7549 (mt) REVERT: B 205 MET cc_start: 0.8781 (ptm) cc_final: 0.8516 (ptm) REVERT: B 274 GLU cc_start: 0.7110 (pm20) cc_final: 0.6738 (pm20) REVERT: B 330 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7533 (mt) REVERT: B 442 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7177 (tp) REVERT: C 39 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.6992 (ttt90) REVERT: C 274 GLU cc_start: 0.7197 (pm20) cc_final: 0.6821 (pm20) outliers start: 25 outliers final: 10 residues processed: 154 average time/residue: 1.2938 time to fit residues: 213.1754 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 : 1.062 ------------------------------------------------------------------------------- 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 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 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 4 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.171891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.114704 restraints weight = 10204.800| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.84 r_work: 0.3186 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10023 Z= 0.158 Angle : 0.464 5.772 13608 Z= 0.250 Chirality : 0.037 0.146 1725 Planarity : 0.004 0.037 1665 Dihedral : 3.620 17.200 1365 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.86 % Allowed : 16.90 % Favored : 80.24 % 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: 2.94 (0.23), residues: 1287 helix: 2.57 (0.16), residues: 1011 sheet: 1.40 (0.55), residues: 48 loop : -0.93 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 256 HIS 0.001 0.000 HIS A 296 PHE 0.010 0.001 PHE C 240 TYR 0.008 0.001 TYR A 373 ARG 0.006 0.000 ARG B 315 *********************** 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 162 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 1.058 Fit side-chains REVERT: A 274 GLU cc_start: 0.7350 (pm20) cc_final: 0.7101 (pm20) REVERT: A 330 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7550 (mt) REVERT: A 367 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.6847 (mpm) REVERT: A 442 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7409 (tp) REVERT: B 39 ARG cc_start: 0.7325 (ttt90) cc_final: 0.6929 (ptm160) REVERT: B 167 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7297 (pp20) REVERT: B 205 MET cc_start: 0.8766 (ptm) cc_final: 0.8493 (ptm) REVERT: B 274 GLU cc_start: 0.7054 (pm20) cc_final: 0.6757 (pm20) REVERT: B 330 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7535 (mt) REVERT: B 442 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7161 (tp) REVERT: C 39 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6922 (ttt90) REVERT: C 274 GLU cc_start: 0.7196 (pm20) cc_final: 0.6750 (pm20) outliers start: 31 outliers final: 13 residues processed: 145 average time/residue: 1.3362 time to fit residues: 207.8241 Evaluate side-chains 149 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG 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 442 LEU 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 58 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.171134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.113730 restraints weight = 10152.470| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.84 r_work: 0.3172 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10023 Z= 0.171 Angle : 0.474 6.391 13608 Z= 0.255 Chirality : 0.037 0.141 1725 Planarity : 0.004 0.035 1665 Dihedral : 3.639 17.230 1365 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.49 % Allowed : 18.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.23), residues: 1287 helix: 2.56 (0.16), residues: 1011 sheet: 1.28 (0.55), residues: 48 loop : -1.01 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 256 HIS 0.001 0.001 HIS B 296 PHE 0.011 0.001 PHE C 240 TYR 0.010 0.001 TYR A 373 ARG 0.006 0.000 ARG A 315 *********************** 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 161 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 1.023 Fit side-chains REVERT: A 274 GLU cc_start: 0.7383 (pm20) cc_final: 0.7073 (pm20) REVERT: A 330 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7490 (mt) REVERT: A 367 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.6845 (mpm) REVERT: B 39 ARG cc_start: 0.7329 (ttt90) cc_final: 0.6903 (ptm160) REVERT: B 167 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7312 (pp20) REVERT: B 205 MET cc_start: 0.8759 (ptm) cc_final: 0.8513 (ptm) REVERT: B 274 GLU cc_start: 0.7246 (pm20) cc_final: 0.6907 (pm20) REVERT: B 330 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7547 (mt) REVERT: B 442 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7191 (tp) REVERT: C 39 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.6955 (ttt90) REVERT: C 274 GLU cc_start: 0.7195 (pm20) cc_final: 0.6773 (pm20) outliers start: 27 outliers final: 13 residues processed: 150 average time/residue: 1.3308 time to fit residues: 213.3425 Evaluate side-chains 149 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 B 322 GLN C 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.171002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113124 restraints weight = 10210.666| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.90 r_work: 0.3160 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10023 Z= 0.173 Angle : 0.479 6.917 13608 Z= 0.258 Chirality : 0.037 0.142 1725 Planarity : 0.004 0.035 1665 Dihedral : 3.654 17.232 1365 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.59 % Allowed : 18.84 % Favored : 78.58 % 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: 2.88 (0.23), residues: 1287 helix: 2.56 (0.16), residues: 1011 sheet: 1.23 (0.55), residues: 48 loop : -1.10 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 256 HIS 0.001 0.000 HIS B 296 PHE 0.011 0.001 PHE C 240 TYR 0.010 0.001 TYR A 373 ARG 0.006 0.000 ARG A 315 *********************** 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 163 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.093 Fit side-chains REVERT: A 274 GLU cc_start: 0.7385 (pm20) cc_final: 0.7098 (pm20) REVERT: A 330 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7465 (mt) REVERT: A 367 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.6795 (mpm) REVERT: B 167 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7272 (pp20) REVERT: B 205 MET cc_start: 0.8748 (ptm) cc_final: 0.8493 (ptm) REVERT: B 274 GLU cc_start: 0.7237 (pm20) cc_final: 0.6883 (pm20) REVERT: B 330 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7569 (mt) REVERT: B 356 ARG cc_start: 0.7900 (mmt180) cc_final: 0.7679 (mmt90) REVERT: B 442 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7131 (tp) REVERT: C 39 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6834 (ttt90) REVERT: C 229 MET cc_start: 0.8784 (mtp) cc_final: 0.8560 (mtp) REVERT: C 274 GLU cc_start: 0.7207 (pm20) cc_final: 0.6768 (pm20) REVERT: C 432 ASP cc_start: 0.7128 (m-30) cc_final: 0.6629 (m-30) outliers start: 28 outliers final: 15 residues processed: 151 average time/residue: 1.3228 time to fit residues: 213.7363 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 : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 367 MET 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 62 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 1.9990 chunk 120 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.169198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111462 restraints weight = 10210.198| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.84 r_work: 0.3138 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1274 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= 0.204 Angle : 0.505 5.899 13608 Z= 0.273 Chirality : 0.038 0.165 1725 Planarity : 0.004 0.034 1665 Dihedral : 3.727 17.212 1365 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.59 % Allowed : 18.56 % Favored : 78.86 % 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: 2.75 (0.23), residues: 1287 helix: 2.47 (0.16), residues: 1011 sheet: 1.20 (0.55), residues: 48 loop : -1.17 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 PHE 0.013 0.001 PHE C 240 TYR 0.013 0.001 TYR A 373 ARG 0.006 0.001 ARG A 315 *********************** 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 160 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.146 Fit side-chains REVERT: A 231 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: A 274 GLU cc_start: 0.7380 (pm20) cc_final: 0.7081 (pm20) REVERT: A 330 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7558 (mt) REVERT: A 367 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.6448 (mpt) REVERT: B 39 ARG cc_start: 0.7221 (ttt90) cc_final: 0.6865 (ptm160) REVERT: B 167 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7348 (pp20) REVERT: B 258 MET cc_start: 0.8716 (ttm) cc_final: 0.8232 (ttm) REVERT: B 274 GLU cc_start: 0.7171 (pm20) cc_final: 0.6903 (pm20) REVERT: B 330 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7603 (mt) REVERT: B 442 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7235 (tp) REVERT: C 39 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.6533 (ttm-80) REVERT: C 274 GLU cc_start: 0.7217 (pm20) cc_final: 0.6785 (pm20) REVERT: C 432 ASP cc_start: 0.7199 (m-30) cc_final: 0.6639 (m-30) outliers start: 28 outliers final: 14 residues processed: 146 average time/residue: 1.3039 time to fit residues: 203.9838 Evaluate side-chains 152 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 367 MET 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 58 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.166942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.108952 restraints weight = 10196.406| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.83 r_work: 0.3099 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10023 Z= 0.263 Angle : 0.555 6.317 13608 Z= 0.300 Chirality : 0.040 0.172 1725 Planarity : 0.004 0.032 1665 Dihedral : 3.916 17.923 1365 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.40 % Allowed : 18.93 % Favored : 78.67 % 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: 2.47 (0.23), residues: 1287 helix: 2.27 (0.16), residues: 1011 sheet: 1.14 (0.55), residues: 48 loop : -1.25 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 PHE 0.014 0.002 PHE A 240 TYR 0.015 0.002 TYR A 373 ARG 0.006 0.001 ARG A 315 *********************** 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 159 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 1.060 Fit side-chains REVERT: A 274 GLU cc_start: 0.7355 (pm20) cc_final: 0.7040 (pm20) REVERT: A 330 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7581 (mt) REVERT: A 367 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7068 (mpm) REVERT: B 167 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7336 (pp20) REVERT: B 330 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7594 (mt) REVERT: B 442 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7401 (tp) REVERT: C 39 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6537 (ttm-80) REVERT: C 258 MET cc_start: 0.8801 (ttm) cc_final: 0.8598 (ttp) REVERT: C 274 GLU cc_start: 0.7227 (pm20) cc_final: 0.6767 (pm20) REVERT: C 432 ASP cc_start: 0.7182 (m-30) cc_final: 0.6633 (m-30) outliers start: 26 outliers final: 16 residues processed: 148 average time/residue: 1.2947 time to fit residues: 205.2806 Evaluate side-chains 153 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 367 MET Chi-restraints excluded: chain A residue 437 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 62 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 118 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 58 optimal weight: 0.5980 chunk 81 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 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 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 = 0.3976 r_free = 0.3976 target = 0.170959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113597 restraints weight = 10234.662| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.86 r_work: 0.3172 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1317 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= 0.167 Angle : 0.490 6.206 13608 Z= 0.263 Chirality : 0.037 0.167 1725 Planarity : 0.004 0.033 1665 Dihedral : 3.744 17.265 1365 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.12 % Allowed : 19.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.23), residues: 1287 helix: 2.50 (0.16), residues: 1011 sheet: 1.13 (0.55), residues: 48 loop : -1.25 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 256 HIS 0.001 0.000 HIS B 296 PHE 0.010 0.001 PHE A 240 TYR 0.012 0.001 TYR A 373 ARG 0.007 0.000 ARG A 315 *********************** 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 154 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.112 Fit side-chains REVERT: A 274 GLU cc_start: 0.7422 (pm20) cc_final: 0.7153 (pm20) REVERT: A 330 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7526 (mt) REVERT: B 258 MET cc_start: 0.8684 (ttm) cc_final: 0.8220 (ttm) REVERT: B 330 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7520 (mt) REVERT: B 442 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7300 (tp) REVERT: C 39 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6520 (ttm-80) REVERT: C 229 MET cc_start: 0.8852 (mtp) cc_final: 0.8584 (mtp) REVERT: C 258 MET cc_start: 0.8672 (ttm) cc_final: 0.8467 (ttp) REVERT: C 274 GLU cc_start: 0.7177 (pm20) cc_final: 0.6752 (pm20) REVERT: C 432 ASP cc_start: 0.7116 (m-30) cc_final: 0.6572 (m-30) outliers start: 23 outliers final: 11 residues processed: 144 average time/residue: 1.3584 time to fit residues: 209.5084 Evaluate side-chains 144 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE 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 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 53 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.170136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.111943 restraints weight = 10231.628| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.89 r_work: 0.3162 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1329 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= 0.179 Angle : 0.505 7.331 13608 Z= 0.269 Chirality : 0.037 0.165 1725 Planarity : 0.004 0.033 1665 Dihedral : 3.709 17.116 1365 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.75 % Allowed : 20.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.23), residues: 1287 helix: 2.52 (0.16), residues: 1011 sheet: 1.17 (0.55), residues: 48 loop : -1.31 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 256 HIS 0.001 0.001 HIS B 296 PHE 0.010 0.001 PHE C 240 TYR 0.012 0.001 TYR A 373 ARG 0.007 0.000 ARG B 315 ********************** 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 150 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.092 Fit side-chains REVERT: A 274 GLU cc_start: 0.7375 (pm20) cc_final: 0.7090 (pm20) REVERT: A 330 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7399 (mt) REVERT: B 258 MET cc_start: 0.8696 (ttm) cc_final: 0.8213 (ttm) REVERT: B 330 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7518 (mt) REVERT: B 442 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7221 (tp) REVERT: C 39 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6506 (ttm-80) REVERT: C 229 MET cc_start: 0.8858 (mtp) cc_final: 0.8596 (mtp) REVERT: C 274 GLU cc_start: 0.7241 (pm20) cc_final: 0.6802 (pm20) REVERT: C 432 ASP cc_start: 0.7108 (m-30) cc_final: 0.6582 (m-30) outliers start: 19 outliers final: 11 residues processed: 141 average time/residue: 1.3764 time to fit residues: 207.9304 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 : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE 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 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 19 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 92 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.171307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113698 restraints weight = 10278.819| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.86 r_work: 0.3186 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1394 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= 0.166 Angle : 0.496 7.992 13608 Z= 0.262 Chirality : 0.037 0.163 1725 Planarity : 0.004 0.034 1665 Dihedral : 3.654 16.843 1365 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.85 % Allowed : 20.31 % Favored : 77.84 % 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: 2.87 (0.23), residues: 1287 helix: 2.60 (0.16), residues: 1011 sheet: 1.15 (0.55), residues: 48 loop : -1.32 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 256 HIS 0.001 0.000 HIS B 296 PHE 0.009 0.001 PHE A 240 TYR 0.013 0.001 TYR A 373 ARG 0.007 0.000 ARG B 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8474.74 seconds wall clock time: 149 minutes 49.66 seconds (8989.66 seconds total)