Starting phenix.real_space_refine (version: 1.19rc7) on Sun Dec 6 14:10:32 2020 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xpd_22285/12_2020/6xpd_22285.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xpd_22285/12_2020/6xpd_22285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xpd_22285/12_2020/6xpd_22285.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xpd_22285/12_2020/6xpd_22285.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xpd_22285/12_2020/6xpd_22285.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xpd_22285/12_2020/6xpd_22285.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 4622 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2309 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2309 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2325 SG CYS A 53 42.422 21.767 23.908 1.00 88.16 S ATOM 2246 SG CYS B 361 39.757 15.017 23.922 1.00 99.56 S ATOM 2271 SG CYS B 364 39.570 17.025 26.950 1.00 81.28 S ATOM 16 SG CYS B 53 33.976 39.660 23.918 1.00 89.15 S ATOM 4555 SG CYS A 361 36.712 46.426 23.890 1.00100.58 S ATOM 4580 SG CYS A 364 36.887 44.419 26.919 1.00 82.53 S Time building chain proxies: 2.84, per 1000 atoms: 0.61 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Number of scatterers: 4622 At special positions: 0 Unit cell: (77.19, 62.25, 102.92, 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) Zn 4 29.99 S 32 16.00 O 822 8.00 N 754 7.00 C 3010 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 - 3.50 Amimo acid : False - 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: 2.10 Conformation dependent library (CDL) restraints added in 652.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS B 53 " pdb="ZN ZN A 401 " - pdb=" ND1 HIS A 318 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 301 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 364 " pdb="ZN ZN A 402 " - pdb=" ND1 HIS B 54 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 361 " pdb="ZN ZN A 402 " - pdb=" NE2 HIS B 52 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" ND1 HIS B 318 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 301 " pdb="ZN ZN B 401 " - pdb=" SG CYS A 53 " pdb=" ZN B 402 " pdb="ZN ZN B 402 " - pdb=" NE2 HIS A 52 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 361 " pdb="ZN ZN B 402 " - pdb=" ND1 HIS A 54 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 364 " Number of angles added : 4 1188 Ramachandran restraints generated. 594 Oldfield and 0 Emsley and 594 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 69.0% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'B' and resid 63 through 94 removed outlier: 3.844A pdb=" N TYR B 67 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY B 92 " --> pdb=" O GLU B 88 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 126 removed outlier: 4.078A pdb=" N HIS B 106 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS B 126 " --> pdb=" O TRP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 168 Processing helix chain 'B' and resid 176 through 196 removed outlier: 3.637A pdb=" N ILE B 180 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 182 " --> pdb=" O MET B 178 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 241 removed outlier: 3.688A pdb=" N ASN B 224 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 275 removed outlier: 4.478A pdb=" N ILE B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 Processing helix chain 'B' and resid 326 through 342 removed outlier: 3.983A pdb=" N VAL B 330 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 365 removed outlier: 4.655A pdb=" N LEU B 362 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE B 363 " --> pdb=" O ASP B 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 94 removed outlier: 3.843A pdb=" N TYR A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 126 removed outlier: 4.036A pdb=" N HIS A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 168 Processing helix chain 'A' and resid 176 through 196 removed outlier: 3.637A pdb=" N ILE A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 182 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 241 removed outlier: 3.688A pdb=" N ASN A 224 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 275 removed outlier: 4.478A pdb=" N ILE A 250 " --> pdb=" O ILE A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 293 Processing helix chain 'A' and resid 326 through 342 removed outlier: 3.983A pdb=" N VAL A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 365 removed outlier: 4.655A pdb=" N LEU A 362 " --> pdb=" O PRO A 359 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE A 363 " --> pdb=" O ASP A 360 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 297 through 304 removed outlier: 5.680A pdb=" N VAL B 300 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ALA B 320 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER B 302 " --> pdb=" O HIS B 318 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS B 318 " --> pdb=" O SER B 302 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU B 315 " --> pdb=" O THR B 348 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 297 through 304 removed outlier: 5.679A pdb=" N VAL A 300 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ALA A 320 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER A 302 " --> pdb=" O HIS A 318 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS A 318 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU A 315 " --> pdb=" O THR A 348 " (cutoff:3.500A) 306 hydrogen bonds defined for protein. 894 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1432 1.34 - 1.46: 1103 1.46 - 1.58: 2135 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 4714 Sorted by residual: bond pdb=" CA THR A 348 " pdb=" CB THR A 348 " ideal model delta sigma weight residual 1.527 1.498 0.029 2.48e-02 1.63e+03 1.38e+00 bond pdb=" C SER B 262 " pdb=" O SER B 262 " ideal model delta sigma weight residual 1.237 1.250 -0.014 1.17e-02 7.31e+03 1.36e+00 bond pdb=" CA THR B 348 " pdb=" CB THR B 348 " ideal model delta sigma weight residual 1.527 1.499 0.029 2.48e-02 1.63e+03 1.33e+00 bond pdb=" CG LEU B 308 " pdb=" CD1 LEU B 308 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CG LEU A 308 " pdb=" CD1 LEU A 308 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.16e+00 ... (remaining 4709 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.04: 81 106.04 - 113.03: 2838 113.03 - 120.02: 1512 120.02 - 127.00: 1929 127.00 - 133.99: 62 Bond angle restraints: 6422 Sorted by residual: angle pdb=" C SER B 353 " pdb=" N PRO B 354 " pdb=" CA PRO B 354 " ideal model delta sigma weight residual 119.05 122.88 -3.83 1.11e+00 8.12e-01 1.19e+01 angle pdb=" C SER A 353 " pdb=" N PRO A 354 " pdb=" CA PRO A 354 " ideal model delta sigma weight residual 119.05 122.56 -3.51 1.11e+00 8.12e-01 9.98e+00 angle pdb=" C ASP B 356 " pdb=" N GLN B 357 " pdb=" CA GLN B 357 " ideal model delta sigma weight residual 122.41 117.98 4.43 1.41e+00 5.03e-01 9.86e+00 angle pdb=" C ASP A 356 " pdb=" N GLN A 357 " pdb=" CA GLN A 357 " ideal model delta sigma weight residual 122.16 118.05 4.11 1.50e+00 4.44e-01 7.51e+00 angle pdb=" N PRO B 354 " pdb=" CA PRO B 354 " pdb=" C PRO B 354 " ideal model delta sigma weight residual 113.53 110.13 3.40 1.39e+00 5.18e-01 6.00e+00 ... (remaining 6417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.92: 2330 12.92 - 25.83: 325 25.83 - 38.75: 94 38.75 - 51.67: 28 51.67 - 64.58: 11 Dihedral angle restraints: 2788 sinusoidal: 1008 harmonic: 1780 Sorted by residual: dihedral pdb=" CA LEU B 308 " pdb=" C LEU B 308 " pdb=" N THR B 309 " pdb=" CA THR B 309 " ideal model delta harmonic sigma weight residual -180.00 -157.52 -22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LEU A 308 " pdb=" C LEU A 308 " pdb=" N THR A 309 " pdb=" CA THR A 309 " ideal model delta harmonic sigma weight residual -180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA GLU A 88 " pdb=" C GLU A 88 " pdb=" N VAL A 89 " pdb=" CA VAL A 89 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 2785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 520 0.039 - 0.078: 232 0.078 - 0.118: 41 0.118 - 0.157: 5 0.157 - 0.196: 2 Chirality restraints: 800 Sorted by residual: chirality pdb=" CA ASP A 356 " pdb=" N ASP A 356 " pdb=" C ASP A 356 " pdb=" CB ASP A 356 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.61e-01 chirality pdb=" CA ASP B 356 " pdb=" N ASP B 356 " pdb=" C ASP B 356 " pdb=" CB ASP B 356 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.38e-01 chirality pdb=" CB ILE A 305 " pdb=" CA ILE A 305 " pdb=" CG1 ILE A 305 " pdb=" CG2 ILE A 305 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 797 not shown) Planarity restraints: 776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 220 " -0.010 2.00e-02 2.50e+03 1.21e-02 2.18e+00 pdb=" CG HIS B 220 " 0.026 2.00e-02 2.50e+03 pdb=" ND1 HIS B 220 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 220 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS B 220 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS B 220 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 220 " 0.011 2.00e-02 2.50e+03 1.20e-02 2.16e+00 pdb=" CG HIS A 220 " -0.026 2.00e-02 2.50e+03 pdb=" ND1 HIS A 220 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS A 220 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS A 220 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 220 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 365 " 0.006 2.00e-02 2.50e+03 1.22e-02 1.49e+00 pdb=" C GLU B 365 " -0.021 2.00e-02 2.50e+03 pdb=" O GLU B 365 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP B 366 " 0.007 2.00e-02 2.50e+03 ... (remaining 773 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 3 2.15 - 2.84: 1695 2.84 - 3.52: 7055 3.52 - 4.21: 10088 4.21 - 4.90: 17725 Nonbonded interactions: 36566 Sorted by model distance: nonbonded pdb=" OE2 GLU A 352 " pdb="ZN ZN A 401 " model vdw 1.461 2.260 nonbonded pdb=" OE2 GLU B 352 " pdb="ZN ZN B 401 " model vdw 1.781 2.260 nonbonded pdb=" OG1 THR B 348 " pdb=" OG1 THR A 348 " model vdw 2.140 2.440 nonbonded pdb=" O GLN B 227 " pdb=" OG SER B 230 " model vdw 2.184 2.440 nonbonded pdb=" O GLN A 227 " pdb=" OG SER A 230 " model vdw 2.185 2.440 ... (remaining 36561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 4622 4622 False True No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 32 5.16 5 C 3010 2.51 5 N 754 2.21 5 O 822 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.230 Set model interpretation parameters: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.810 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.020 Process input model: 18.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 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:2.230 Internal consistency checks: 0.000 Total: 22.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.007 0.036 4714 Angle : 0.770 6.410 6422 Chirality : 0.043 0.196 800 Planarity : 0.003 0.022 776 Dihedral : 14.372 64.582 1624 Min Nonbonded Distance : 1.461 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer Outliers : 0.20 % 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: -3.83 (0.30), residues: 594 helix: -1.82 (0.22), residues: 384 sheet: -3.84 (0.69), residues: 46 loop : -3.48 (0.46), residues: 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield and 0 Emsley and 594 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield and 0 Emsley and 594 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 518 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.569 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.2102 time to fit residues: 29.0252 Evaluate side-chains 85 residues out of total 518 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.590 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 0.0270 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN B 211 ASN A 172 GLN ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.021 4714 Angle : 0.536 5.223 6422 Chirality : 0.038 0.187 800 Planarity : 0.004 0.042 776 Dihedral : 4.494 20.473 630 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.35), residues: 594 helix: 1.10 (0.26), residues: 384 sheet: -3.80 (0.66), residues: 46 loop : -2.30 (0.50), residues: 164 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield and 0 Emsley and 594 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield and 0 Emsley and 594 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 518 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.580 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1436 time to fit residues: 19.5988 Evaluate side-chains 78 residues out of total 518 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 30.0000 chunk 16 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 0.0370 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.022 4714 Angle : 0.553 6.322 6422 Chirality : 0.039 0.201 800 Planarity : 0.004 0.041 776 Dihedral : 4.316 18.657 630 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.37), residues: 594 helix: 1.77 (0.26), residues: 390 sheet: -3.69 (0.65), residues: 46 loop : -1.79 (0.54), residues: 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield and 0 Emsley and 594 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield and 0 Emsley and 594 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 518 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.513 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1217 time to fit residues: 15.5848 Evaluate side-chains 89 residues out of total 518 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.569 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 0.1980 chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 32 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.017 4714 Angle : 0.508 6.121 6422 Chirality : 0.038 0.204 800 Planarity : 0.003 0.040 776 Dihedral : 3.831 16.385 630 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.00 % 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: 1.10 (0.37), residues: 594 helix: 2.22 (0.26), residues: 382 sheet: -3.29 (0.70), residues: 46 loop : -1.69 (0.53), residues: 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield and 0 Emsley and 594 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield and 0 Emsley and 594 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 518 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.540 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1262 time to fit residues: 16.5320 Evaluate side-chains 83 residues out of total 518 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 40.0000 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 0.0370 chunk 14 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 34 optimal weight: 0.3980 overall best weight: 1.6864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.019 4714 Angle : 0.524 5.719 6422 Chirality : 0.038 0.225 800 Planarity : 0.003 0.039 776 Dihedral : 3.899 20.144 630 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.00 % 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: 1.20 (0.37), residues: 594 helix: 2.25 (0.26), residues: 382 sheet: -3.26 (0.68), residues: 46 loop : -1.52 (0.53), residues: 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield and 0 Emsley and 594 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield and 0 Emsley and 594 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 518 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.536 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1250 time to fit residues: 15.1762 Evaluate side-chains 80 residues out of total 518 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.612 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 30.0000 chunk 55 optimal weight: 0.3980 chunk 6 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.018 4714 Angle : 0.517 6.150 6422 Chirality : 0.038 0.239 800 Planarity : 0.003 0.038 776 Dihedral : 3.783 20.694 630 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.00 % 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: 1.26 (0.37), residues: 594 helix: 2.27 (0.26), residues: 382 sheet: -3.17 (0.66), residues: 46 loop : -1.42 (0.52), residues: 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield and 0 Emsley and 594 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield and 0 Emsley and 594 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 518 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.600 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1190 time to fit residues: 14.9724 Evaluate side-chains 85 residues out of total 518 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.569 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.021 4714 Angle : 0.559 7.472 6422 Chirality : 0.040 0.256 800 Planarity : 0.003 0.038 776 Dihedral : 4.056 20.898 630 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 0.00 % 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: 1.29 (0.37), residues: 594 helix: 2.22 (0.26), residues: 384 sheet: -2.81 (0.71), residues: 42 loop : -1.43 (0.52), residues: 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield and 0 Emsley and 594 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield and 0 Emsley and 594 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 518 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.660 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1125 time to fit residues: 14.4696 Evaluate side-chains 87 residues out of total 518 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.518 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 55 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.016 4714 Angle : 0.548 7.887 6422 Chirality : 0.040 0.295 800 Planarity : 0.003 0.038 776 Dihedral : 3.795 17.946 630 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.00 % 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: 1.49 (0.37), residues: 594 helix: 2.40 (0.26), residues: 382 sheet: -2.74 (0.78), residues: 40 loop : -1.39 (0.51), residues: 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield and 0 Emsley and 594 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield and 0 Emsley and 594 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 518 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.615 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1208 time to fit residues: 14.7982 Evaluate side-chains 89 residues out of total 518 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.533 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 0.2980 chunk 34 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 0.0870 chunk 55 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.017 4714 Angle : 0.583 8.061 6422 Chirality : 0.040 0.280 800 Planarity : 0.003 0.038 776 Dihedral : 3.758 15.326 630 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.00 % 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: 1.82 (0.37), residues: 594 helix: 2.59 (0.26), residues: 390 sheet: -2.49 (0.80), residues: 40 loop : -1.33 (0.52), residues: 164 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield and 0 Emsley and 594 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield and 0 Emsley and 594 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 518 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.562 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1105 time to fit residues: 14.6026 Evaluate side-chains 88 residues out of total 518 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.575 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 47 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.063 4714 Angle : 0.616 9.354 6422 Chirality : 0.042 0.325 800 Planarity : 0.006 0.127 776 Dihedral : 3.911 17.626 630 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.00 % 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: 1.63 (0.36), residues: 594 helix: 2.45 (0.26), residues: 390 sheet: -2.47 (0.73), residues: 42 loop : -1.43 (0.52), residues: 162 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield and 0 Emsley and 594 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield and 0 Emsley and 594 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 518 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.538 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1161 time to fit residues: 14.3476 Evaluate side-chains 86 residues out of total 518 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.153381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.133332 restraints weight = 8486.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.135971 restraints weight = 5216.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.137706 restraints weight = 3722.344| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.004 0.025 4714 ANGLE : 0.648 8.361 6422 CHIRALITY : 0.041 0.252 800 PLANARITY : 0.004 0.037 776 DIHEDRAL : 4.127 19.778 630 MIN NONBONDED DISTANCE : 2.047 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 9.83 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 5.39 % FAVORED : 94.61 % ROTAMER OUTLIERS : 0.00 % 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: 1.45 (0.36), RESIDUES: 594 HELIX: 2.35 (0.26), RESIDUES: 382 SHEET: -2.94 (0.69), RESIDUES: 46 LOOP : -1.23 (0.52), RESIDUES: 166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.025 4714 Angle : 0.648 8.361 6422 Chirality : 0.041 0.252 800 Planarity : 0.004 0.037 776 Dihedral : 4.127 19.778 630 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 0.00 % 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: 1.45 (0.36), residues: 594 helix: 2.35 (0.26), residues: 382 sheet: -2.94 (0.69), residues: 46 loop : -1.23 (0.52), residues: 166 =============================================================================== Job complete usr+sys time: 1175.02 seconds wall clock time: 21 minutes 54.06 seconds (1314.06 seconds total)