Starting phenix.real_space_refine on Mon Jul 28 00:05:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cv2_27006/07_2025/8cv2_27006.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cv2_27006/07_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_27006/07_2025/8cv2_27006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cv2_27006/07_2025/8cv2_27006.map" model { file = "/net/cci-nas-00/data/ceres_data/8cv2_27006/07_2025/8cv2_27006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cv2_27006/07_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.30, per 1000 atoms: 0.64 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: 2.69 Conformation dependent library (CDL) restraints added in 1.2 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: 1.05 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: 3.03 Time building geometry restraints manager: 3.13 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: 1.860 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.720 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:14.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.510 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.13649 ( 783) hydrogen bonds : angle 4.93005 ( 2304) covalent geometry : bond 0.00305 (10023) covalent geometry : angle 0.53311 (13608) *********************** 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 : 1.023 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: 1.4475 time to fit residues: 206.1224 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 : 1.018 ------------------------------------------------------------------------------- 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 = 0.3309 r_free = 0.3309 target = 0.111263 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: 3.85 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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= 0.164 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 Details of bonding type rmsd hydrogen bonds : bond 0.07010 ( 783) hydrogen bonds : angle 4.21735 ( 2304) covalent geometry : bond 0.00346 (10023) covalent geometry : angle 0.52523 (13608) *********************** 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 : 1.053 Fit side-chains REVERT: A 274 GLU cc_start: 0.7330 (pm20) cc_final: 0.6972 (pm20) REVERT: A 330 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7610 (mt) REVERT: A 442 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7541 (tp) REVERT: B 274 GLU cc_start: 0.7412 (pm20) cc_final: 0.7059 (pm20) REVERT: B 330 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7596 (mt) REVERT: B 442 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7299 (tp) REVERT: C 274 GLU cc_start: 0.7265 (pm20) cc_final: 0.6930 (pm20) REVERT: C 449 MET cc_start: 0.8228 (ttp) cc_final: 0.7870 (tmt) outliers start: 34 outliers final: 12 residues processed: 153 average time/residue: 1.3016 time to fit residues: 213.5963 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 : 1.027 ------------------------------------------------------------------------------- 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: 0.8980 chunk 40 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.172222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.114804 restraints weight = 10267.219| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.86 r_work: 0.3182 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10023 Z= 0.134 Angle : 0.472 5.706 13608 Z= 0.254 Chirality : 0.037 0.153 1725 Planarity : 0.004 0.038 1665 Dihedral : 3.681 17.512 1365 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.31 % Allowed : 16.07 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.23), residues: 1287 helix: 2.49 (0.16), residues: 1011 sheet: 1.56 (0.55), residues: 48 loop : -0.78 (0.40), 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 0.004 0.000 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.05771 ( 783) hydrogen bonds : angle 4.01333 ( 2304) covalent geometry : bond 0.00258 (10023) covalent geometry : angle 0.47175 (13608) *********************** 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 : 1.126 Fit side-chains REVERT: A 274 GLU cc_start: 0.7230 (pm20) cc_final: 0.6986 (pm20) REVERT: A 330 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7557 (mt) REVERT: B 205 MET cc_start: 0.8781 (ptm) cc_final: 0.8512 (ptm) REVERT: B 274 GLU cc_start: 0.7133 (pm20) cc_final: 0.6755 (pm20) REVERT: B 330 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7539 (mt) REVERT: B 442 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7177 (tp) REVERT: C 39 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.6977 (ttt90) REVERT: C 274 GLU cc_start: 0.7196 (pm20) cc_final: 0.6776 (pm20) outliers start: 25 outliers final: 11 residues processed: 153 average time/residue: 1.4668 time to fit residues: 241.1255 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 : 1.011 ------------------------------------------------------------------------------- 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 307 ILE 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: 0.9990 chunk 112 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.169642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.111523 restraints weight = 10116.232| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.87 r_work: 0.3137 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10023 Z= 0.148 Angle : 0.494 5.386 13608 Z= 0.267 Chirality : 0.038 0.146 1725 Planarity : 0.004 0.035 1665 Dihedral : 3.726 17.473 1365 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.14 % Allowed : 16.53 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.23), residues: 1287 helix: 2.44 (0.16), residues: 1011 sheet: 1.34 (0.54), residues: 48 loop : -0.94 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 PHE 0.012 0.001 PHE C 240 TYR 0.008 0.001 TYR A 373 ARG 0.005 0.000 ARG B 315 Details of bonding type rmsd hydrogen bonds : bond 0.06439 ( 783) hydrogen bonds : angle 4.03604 ( 2304) covalent geometry : bond 0.00299 (10023) covalent geometry : angle 0.49441 (13608) *********************** 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 : 1.018 Fit side-chains REVERT: A 274 GLU cc_start: 0.7395 (pm20) cc_final: 0.7145 (pm20) REVERT: A 330 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7497 (mt) REVERT: A 367 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.6878 (mpm) REVERT: B 39 ARG cc_start: 0.7323 (ttt90) cc_final: 0.6929 (ptm160) REVERT: B 167 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7307 (pp20) REVERT: B 274 GLU cc_start: 0.7059 (pm20) cc_final: 0.6752 (pm20) REVERT: B 330 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7554 (mt) REVERT: B 442 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7183 (tp) REVERT: C 39 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6573 (ttm-80) REVERT: C 229 MET cc_start: 0.8850 (mtp) cc_final: 0.8610 (mtp) REVERT: C 274 GLU cc_start: 0.7175 (pm20) cc_final: 0.6777 (pm20) outliers start: 34 outliers final: 15 residues processed: 146 average time/residue: 1.2409 time to fit residues: 194.4824 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 : 1.286 ------------------------------------------------------------------------------- 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 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 262 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.170820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.113305 restraints weight = 10129.975| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.84 r_work: 0.3165 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10023 Z= 0.138 Angle : 0.478 6.666 13608 Z= 0.258 Chirality : 0.037 0.140 1725 Planarity : 0.004 0.032 1665 Dihedral : 3.690 17.341 1365 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.49 % Allowed : 18.19 % Favored : 79.32 % 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: 2.84 (0.23), residues: 1287 helix: 2.52 (0.16), residues: 1011 sheet: 1.33 (0.55), residues: 48 loop : -1.08 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 256 HIS 0.001 0.001 HIS B 296 PHE 0.010 0.001 PHE C 240 TYR 0.010 0.001 TYR A 373 ARG 0.006 0.000 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.05963 ( 783) hydrogen bonds : angle 3.97398 ( 2304) covalent geometry : bond 0.00268 (10023) covalent geometry : angle 0.47820 (13608) *********************** 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 : 1.006 Fit side-chains REVERT: A 274 GLU cc_start: 0.7382 (pm20) cc_final: 0.7071 (pm20) REVERT: A 330 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7452 (mt) REVERT: A 367 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.6833 (mpm) REVERT: B 39 ARG cc_start: 0.7330 (ttt90) cc_final: 0.6925 (ptm160) REVERT: B 274 GLU cc_start: 0.7237 (pm20) cc_final: 0.6895 (pm20) REVERT: B 330 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7543 (mt) REVERT: B 442 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7225 (tp) REVERT: C 39 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.6975 (ttt90) REVERT: C 229 MET cc_start: 0.8909 (mtp) cc_final: 0.8654 (mtp) REVERT: C 274 GLU cc_start: 0.7167 (pm20) cc_final: 0.6746 (pm20) outliers start: 27 outliers final: 15 residues processed: 150 average time/residue: 1.2556 time to fit residues: 202.2287 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 : 1.002 ------------------------------------------------------------------------------- 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 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 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 307 ILE 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: 6.9990 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 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 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 = 0.3973 r_free = 0.3973 target = 0.170634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113215 restraints weight = 10224.966| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.84 r_work: 0.3161 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10023 Z= 0.138 Angle : 0.481 7.188 13608 Z= 0.259 Chirality : 0.037 0.163 1725 Planarity : 0.004 0.037 1665 Dihedral : 3.679 17.358 1365 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.59 % Allowed : 18.28 % 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: 2.85 (0.23), residues: 1287 helix: 2.54 (0.16), residues: 1011 sheet: 1.32 (0.55), residues: 48 loop : -1.18 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 Details of bonding type rmsd hydrogen bonds : bond 0.05964 ( 783) hydrogen bonds : angle 3.94217 ( 2304) covalent geometry : bond 0.00271 (10023) covalent geometry : angle 0.48087 (13608) *********************** 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 158 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 1.140 Fit side-chains REVERT: A 274 GLU cc_start: 0.7383 (pm20) cc_final: 0.7065 (pm20) REVERT: A 330 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7513 (mt) REVERT: A 367 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.6840 (mpm) REVERT: B 167 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7355 (pp20) REVERT: B 274 GLU cc_start: 0.7211 (pm20) cc_final: 0.6846 (pm20) REVERT: B 330 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7616 (mt) REVERT: B 442 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7211 (tp) REVERT: C 39 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.6871 (ttt90) REVERT: C 229 MET cc_start: 0.8925 (mtp) cc_final: 0.8723 (mtp) REVERT: C 274 GLU cc_start: 0.7173 (pm20) cc_final: 0.6711 (pm20) REVERT: C 432 ASP cc_start: 0.7201 (m-30) cc_final: 0.6679 (m-30) outliers start: 28 outliers final: 15 residues processed: 144 average time/residue: 1.3328 time to fit residues: 206.5177 Evaluate side-chains 150 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 1.788 ------------------------------------------------------------------------------- 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 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 262 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 110 optimal weight: 0.3980 chunk 33 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.169248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111466 restraints weight = 10192.440| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.83 r_work: 0.3135 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10023 Z= 0.153 Angle : 0.509 9.040 13608 Z= 0.273 Chirality : 0.038 0.167 1725 Planarity : 0.004 0.035 1665 Dihedral : 3.740 17.268 1365 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.59 % Allowed : 18.28 % 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: 2.73 (0.23), residues: 1287 helix: 2.46 (0.16), residues: 1011 sheet: 1.27 (0.54), residues: 48 loop : -1.23 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 PHE 0.013 0.001 PHE C 240 TYR 0.011 0.001 TYR A 373 ARG 0.006 0.000 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.06543 ( 783) hydrogen bonds : angle 3.99682 ( 2304) covalent geometry : bond 0.00317 (10023) covalent geometry : angle 0.50897 (13608) *********************** 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 158 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 1.119 Fit side-chains REVERT: A 274 GLU cc_start: 0.7381 (pm20) cc_final: 0.7079 (pm20) REVERT: A 330 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7531 (mt) REVERT: A 367 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.6861 (mpm) REVERT: B 39 ARG cc_start: 0.7211 (ttt90) cc_final: 0.6910 (ptm160) REVERT: B 167 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7366 (pp20) REVERT: B 258 MET cc_start: 0.8775 (ttm) cc_final: 0.8315 (ttm) REVERT: B 274 GLU cc_start: 0.7187 (pm20) cc_final: 0.6902 (pm20) REVERT: B 330 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7538 (mt) REVERT: B 442 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7254 (tp) REVERT: C 39 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6588 (ttm-80) REVERT: C 274 GLU cc_start: 0.7201 (pm20) cc_final: 0.6763 (pm20) REVERT: C 432 ASP cc_start: 0.7213 (m-30) cc_final: 0.6665 (m-30) outliers start: 28 outliers final: 15 residues processed: 146 average time/residue: 1.2607 time to fit residues: 197.5143 Evaluate side-chains 149 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 58 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 66 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 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 = 0.3954 r_free = 0.3954 target = 0.168805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111007 restraints weight = 10222.683| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.84 r_work: 0.3131 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1292 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= 0.157 Angle : 0.523 8.933 13608 Z= 0.280 Chirality : 0.038 0.164 1725 Planarity : 0.004 0.032 1665 Dihedral : 3.807 17.440 1365 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.68 % Allowed : 18.84 % Favored : 78.49 % 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: 2.67 (0.23), residues: 1287 helix: 2.42 (0.16), residues: 1011 sheet: 1.27 (0.55), residues: 48 loop : -1.29 (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 0.012 0.002 PHE C 240 TYR 0.012 0.001 TYR A 373 ARG 0.006 0.000 ARG B 315 Details of bonding type rmsd hydrogen bonds : bond 0.06667 ( 783) hydrogen bonds : angle 4.00090 ( 2304) covalent geometry : bond 0.00329 (10023) covalent geometry : angle 0.52263 (13608) *********************** 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 162 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 1.091 Fit side-chains REVERT: A 274 GLU cc_start: 0.7374 (pm20) cc_final: 0.7081 (pm20) REVERT: A 367 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.6791 (mpm) REVERT: B 39 ARG cc_start: 0.7245 (ttt90) cc_final: 0.6903 (ptm160) REVERT: B 167 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7347 (pp20) REVERT: B 258 MET cc_start: 0.8743 (ttm) cc_final: 0.8276 (ttm) REVERT: B 274 GLU cc_start: 0.7252 (pm20) cc_final: 0.6957 (pm20) REVERT: B 330 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7507 (mt) REVERT: B 442 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7358 (tp) REVERT: C 39 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.6510 (ttm-80) REVERT: C 274 GLU cc_start: 0.7208 (pm20) cc_final: 0.6757 (pm20) REVERT: C 432 ASP cc_start: 0.7170 (m-30) cc_final: 0.6638 (m-30) outliers start: 29 outliers final: 16 residues processed: 146 average time/residue: 1.2754 time to fit residues: 199.5515 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 : 0.965 ------------------------------------------------------------------------------- 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 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 167 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 262 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 118 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 115 optimal weight: 0.0040 chunk 84 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.170023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.112384 restraints weight = 10190.745| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.84 r_work: 0.3153 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10023 Z= 0.145 Angle : 0.506 9.382 13608 Z= 0.270 Chirality : 0.038 0.160 1725 Planarity : 0.004 0.033 1665 Dihedral : 3.758 17.281 1365 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.40 % Allowed : 19.11 % Favored : 78.49 % 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: 2.73 (0.23), residues: 1287 helix: 2.47 (0.16), residues: 1011 sheet: 1.30 (0.55), residues: 48 loop : -1.30 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 256 HIS 0.001 0.001 HIS B 296 PHE 0.011 0.001 PHE C 240 TYR 0.014 0.001 TYR A 373 ARG 0.007 0.000 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.06193 ( 783) hydrogen bonds : angle 3.95072 ( 2304) covalent geometry : bond 0.00293 (10023) covalent geometry : angle 0.50556 (13608) *********************** 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 157 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.027 Fit side-chains REVERT: A 274 GLU cc_start: 0.7413 (pm20) cc_final: 0.7139 (pm20) REVERT: A 367 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.6841 (mpm) REVERT: B 167 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7348 (pp20) REVERT: B 258 MET cc_start: 0.8737 (ttm) cc_final: 0.8327 (ttm) REVERT: B 330 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7536 (mt) REVERT: B 442 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7274 (tp) REVERT: C 39 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6529 (ttm-80) REVERT: C 274 GLU cc_start: 0.7211 (pm20) cc_final: 0.6766 (pm20) REVERT: C 432 ASP cc_start: 0.7157 (m-30) cc_final: 0.6626 (m-30) outliers start: 26 outliers final: 15 residues processed: 144 average time/residue: 1.2877 time to fit residues: 198.4473 Evaluate side-chains 148 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 307 ILE Chi-restraints excluded: chain A residue 309 VAL 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 307 ILE 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: 3.9990 chunk 9 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.169499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.111735 restraints weight = 10186.592| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.86 r_work: 0.3145 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10023 Z= 0.151 Angle : 0.526 9.203 13608 Z= 0.280 Chirality : 0.038 0.161 1725 Planarity : 0.004 0.033 1665 Dihedral : 3.770 17.353 1365 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.22 % Allowed : 19.21 % 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: 2.70 (0.23), residues: 1287 helix: 2.45 (0.16), residues: 1011 sheet: 1.30 (0.55), residues: 48 loop : -1.31 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 PHE 0.012 0.001 PHE C 240 TYR 0.014 0.001 TYR A 373 ARG 0.007 0.000 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.06367 ( 783) hydrogen bonds : angle 3.94734 ( 2304) covalent geometry : bond 0.00315 (10023) covalent geometry : angle 0.52590 (13608) ********************** 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: 24 poor density : 130 time to evaluate : 0.980 Fit side-chains REVERT: A 274 GLU cc_start: 0.7422 (pm20) cc_final: 0.7133 (pm20) REVERT: A 367 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.6860 (mpm) REVERT: B 167 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7345 (pp20) REVERT: B 258 MET cc_start: 0.8745 (ttm) cc_final: 0.8335 (ttm) REVERT: B 330 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7590 (mt) REVERT: B 442 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7276 (tp) REVERT: C 39 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6521 (ttm-80) REVERT: C 274 GLU cc_start: 0.7230 (pm20) cc_final: 0.6787 (pm20) REVERT: C 432 ASP cc_start: 0.7146 (m-30) cc_final: 0.6614 (m-30) outliers start: 24 outliers final: 16 residues processed: 141 average time/residue: 1.3591 time to fit residues: 205.3001 Evaluate side-chains 150 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 307 ILE Chi-restraints excluded: chain A residue 309 VAL 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 307 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 19 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.171282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.113919 restraints weight = 10236.279| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.85 r_work: 0.3177 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10023 Z= 0.135 Angle : 0.502 8.890 13608 Z= 0.266 Chirality : 0.037 0.159 1725 Planarity : 0.004 0.032 1665 Dihedral : 3.696 17.153 1365 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.12 % Allowed : 19.58 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.23), residues: 1287 helix: 2.56 (0.16), residues: 1011 sheet: 1.31 (0.55), residues: 48 loop : -1.33 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 256 HIS 0.001 0.000 HIS B 296 PHE 0.010 0.001 PHE C 240 TYR 0.015 0.001 TYR A 373 ARG 0.007 0.000 ARG B 315 Details of bonding type rmsd hydrogen bonds : bond 0.05694 ( 783) hydrogen bonds : angle 3.85489 ( 2304) covalent geometry : bond 0.00268 (10023) covalent geometry : angle 0.50218 (13608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9362.33 seconds wall clock time: 165 minutes 51.33 seconds (9951.33 seconds total)