Starting phenix.real_space_refine on Thu Mar 5 04:07:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zfo_11184/03_2026/6zfo_11184_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zfo_11184/03_2026/6zfo_11184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zfo_11184/03_2026/6zfo_11184_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zfo_11184/03_2026/6zfo_11184_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zfo_11184/03_2026/6zfo_11184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zfo_11184/03_2026/6zfo_11184.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 38 5.16 5 C 6128 2.51 5 N 1612 2.21 5 O 1900 1.98 5 H 9310 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18988 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2986 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "H" Number of atoms: 3272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3272 Classifications: {'peptide': 218} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 206} Chain breaks: 1 Chain: "L" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3222 Classifications: {'peptide': 214} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203} Chain: "A" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2986 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "B" Number of atoms: 3272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3272 Classifications: {'peptide': 218} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 206} Chain breaks: 1 Chain: "C" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3222 Classifications: {'peptide': 214} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.62, per 1000 atoms: 0.19 Number of scatterers: 18988 At special positions: 0 Unit cell: (78.02, 137.78, 170.15, 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 38 16.00 O 1900 8.00 N 1612 7.00 C 6128 6.00 H 9310 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " distance=2.03 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " " NAG E 601 " - " ASN E 343 " Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 655.4 milliseconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 28 sheets defined 9.4% alpha, 40.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 371 removed outlier: 3.660A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 388 removed outlier: 3.974A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 408 removed outlier: 4.359A pdb=" N ARG E 408 " --> pdb=" O GLY E 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 404 through 408' Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.724A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.680A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 129 Processing helix chain 'L' and resid 184 through 189 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.660A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.976A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.361A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.725A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.679A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.801A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.017A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.846A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.846A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 159 through 162 removed outlier: 4.496A pdb=" N TYR H 202 " --> pdb=" O VAL H 219 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 6.024A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.818A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.588A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.534A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.944A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.944A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR L 98 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.864A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 154 through 156 removed outlier: 4.353A pdb=" N TRP L 149 " --> pdb=" O GLN L 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.801A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AC1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.017A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 128 through 132 removed outlier: 5.846A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 128 through 132 removed outlier: 5.846A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 159 through 162 removed outlier: 4.496A pdb=" N TYR B 202 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 4 through 7 removed outlier: 6.025A pdb=" N THR C 69 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 10.818A pdb=" N GLN C 27 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 10.070A pdb=" N SER C 67 " --> pdb=" O GLN C 27 " (cutoff:3.500A) removed outlier: 11.588A pdb=" N ILE C 29 " --> pdb=" O SER C 65 " (cutoff:3.500A) removed outlier: 11.535A pdb=" N SER C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.944A pdb=" N LEU C 11 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.944A pdb=" N LEU C 11 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR C 98 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 115 through 119 removed outlier: 5.864A pdb=" N TYR C 174 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 154 through 156 removed outlier: 4.354A pdb=" N TRP C 149 " --> pdb=" O GLN C 156 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 948 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: 4.77 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9310 1.03 - 1.23: 0 1.23 - 1.42: 4328 1.42 - 1.62: 5542 1.62 - 1.81: 44 Bond restraints: 19224 Sorted by residual: bond pdb=" C1 NAG E 601 " pdb=" O5 NAG E 601 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.80e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.77e+00 bond pdb=" C TYR A 505 " pdb=" N GLN A 506 " ideal model delta sigma weight residual 1.331 1.350 -0.019 1.48e-02 4.57e+03 1.73e+00 bond pdb=" C TYR E 505 " pdb=" N GLN E 506 " ideal model delta sigma weight residual 1.331 1.350 -0.019 1.48e-02 4.57e+03 1.71e+00 bond pdb=" C5 NAG E 601 " pdb=" O5 NAG E 601 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.31e+00 ... (remaining 19219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.90: 34537 10.90 - 21.80: 0 21.80 - 32.70: 0 32.70 - 43.61: 0 43.61 - 54.51: 2 Bond angle restraints: 34539 Sorted by residual: angle pdb=" C SER B 120 " pdb=" N SER B 121 " pdb=" H SER B 121 " ideal model delta sigma weight residual 123.52 69.02 54.51 3.00e+00 1.11e-01 3.30e+02 angle pdb=" CA SER B 121 " pdb=" N SER B 121 " pdb=" H SER B 121 " ideal model delta sigma weight residual 113.22 60.29 52.93 3.00e+00 1.11e-01 3.11e+02 angle pdb=" C SER H 120 " pdb=" N SER H 121 " pdb=" CA SER H 121 " ideal model delta sigma weight residual 123.25 129.32 -6.07 1.69e+00 3.50e-01 1.29e+01 angle pdb=" C SER B 120 " pdb=" N SER B 121 " pdb=" CA SER B 121 " ideal model delta sigma weight residual 123.25 129.31 -6.06 1.69e+00 3.50e-01 1.29e+01 angle pdb=" N ALA L 51 " pdb=" CA ALA L 51 " pdb=" C ALA L 51 " ideal model delta sigma weight residual 110.80 116.44 -5.64 2.13e+00 2.20e-01 7.01e+00 ... (remaining 34534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 8649 16.15 - 32.30: 435 32.30 - 48.45: 173 48.45 - 64.60: 53 64.60 - 80.75: 6 Dihedral angle restraints: 9316 sinusoidal: 4942 harmonic: 4374 Sorted by residual: dihedral pdb=" CA TRP B 111 " pdb=" C TRP B 111 " pdb=" N GLY B 112 " pdb=" CA GLY B 112 " ideal model delta harmonic sigma weight residual 180.00 163.74 16.26 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA TRP H 111 " pdb=" C TRP H 111 " pdb=" N GLY H 112 " pdb=" CA GLY H 112 " ideal model delta harmonic sigma weight residual 180.00 163.77 16.23 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ASP H 73 " pdb=" CB ASP H 73 " pdb=" CG ASP H 73 " pdb=" OD1 ASP H 73 " ideal model delta sinusoidal sigma weight residual -30.00 -83.26 53.26 1 2.00e+01 2.50e-03 9.64e+00 ... (remaining 9313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 848 0.029 - 0.059: 455 0.059 - 0.088: 60 0.088 - 0.117: 101 0.117 - 0.146: 28 Chirality restraints: 1492 Sorted by residual: chirality pdb=" CA ILE C 75 " pdb=" N ILE C 75 " pdb=" C ILE C 75 " pdb=" CB ILE C 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA VAL A 433 " pdb=" N VAL A 433 " pdb=" C VAL A 433 " pdb=" CB VAL A 433 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA VAL E 433 " pdb=" N VAL E 433 " pdb=" C VAL E 433 " pdb=" CB VAL E 433 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 1489 not shown) Planarity restraints: 2914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 156 " -0.027 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO H 157 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO H 157 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 157 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 156 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO B 157 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 402 " -0.006 2.00e-02 2.50e+03 1.21e-02 1.47e+00 pdb=" C ILE A 402 " 0.021 2.00e-02 2.50e+03 pdb=" O ILE A 402 " -0.008 2.00e-02 2.50e+03 pdb=" N ARG A 403 " -0.007 2.00e-02 2.50e+03 ... (remaining 2911 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.03: 213 2.03 - 2.67: 27339 2.67 - 3.31: 53693 3.31 - 3.96: 72610 3.96 - 4.60: 111007 Nonbonded interactions: 264862 Sorted by model distance: nonbonded pdb=" H SER B 121 " pdb=" HA SER B 121 " model vdw 1.382 1.816 nonbonded pdb="HE22 GLN L 6 " pdb=" O TYR L 86 " model vdw 1.548 2.450 nonbonded pdb="HE22 GLN C 6 " pdb=" O TYR C 86 " model vdw 1.553 2.450 nonbonded pdb="HE21 GLN L 90 " pdb=" OG1 THR L 98 " model vdw 1.619 2.450 nonbonded pdb="HE21 GLN C 90 " pdb=" OG1 THR C 98 " model vdw 1.621 2.450 ... (remaining 264857 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 333 through 465 or (resid 466 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name H \ G3 or name HD2 or name HD3 or name HE or name HH12 or name HH21)) or resid 467 t \ hrough 601)) selection = (chain 'E' and (resid 333 through 356 or (resid 357 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name H \ G3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH22)) o \ r resid 358 through 395 or (resid 396 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name C \ Z or name OH or name H or name HA or name HB2 or name HB3 or name HD1 or name HD \ 2 or name HE1 or name HE2)) or resid 397 through 601)) } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.980 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: 0.120 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.010 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5036 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 0.032 9932 Z= 0.145 Angle : 0.558 6.068 13520 Z= 0.318 Chirality : 0.043 0.146 1492 Planarity : 0.003 0.040 1730 Dihedral : 10.427 80.747 3552 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.30 % Allowed : 4.37 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.24), residues: 1236 helix: -1.91 (0.57), residues: 68 sheet: -0.18 (0.23), residues: 482 loop : -0.37 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.007 0.001 TYR L 49 PHE 0.009 0.001 PHE A 400 TRP 0.010 0.001 TRP E 353 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9914) covalent geometry : angle 0.55650 (13482) SS BOND : bond 0.00175 ( 16) SS BOND : angle 0.87187 ( 32) hydrogen bonds : bond 0.15784 ( 344) hydrogen bonds : angle 8.24060 ( 948) link_NAG-ASN : bond 0.00190 ( 2) link_NAG-ASN : angle 0.85506 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 241 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7275 (p0) cc_final: 0.5739 (t0) REVERT: L 95 LEU cc_start: 0.6508 (mt) cc_final: 0.5295 (tt) REVERT: L 123 ASP cc_start: 0.8255 (m-30) cc_final: 0.7599 (p0) REVERT: A 429 PHE cc_start: 0.7414 (t80) cc_final: 0.6942 (t80) REVERT: A 505 TYR cc_start: 0.6490 (m-80) cc_final: 0.6054 (m-10) REVERT: B 34 MET cc_start: 0.5530 (mmm) cc_final: 0.5005 (mmt) REVERT: B 38 ARG cc_start: 0.5186 (ptt180) cc_final: 0.4882 (ptt90) REVERT: C 54 LEU cc_start: 0.7889 (tp) cc_final: 0.7650 (mm) outliers start: 14 outliers final: 4 residues processed: 253 average time/residue: 0.2778 time to fit residues: 90.1493 Evaluate side-chains 162 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 158 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 55 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN C 156 GLN ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5078 r_free = 0.5078 target = 0.229540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.202519 restraints weight = 48679.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.201594 restraints weight = 51099.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.205436 restraints weight = 41054.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.206624 restraints weight = 26656.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.207393 restraints weight = 24610.743| |-----------------------------------------------------------------------------| r_work (final): 0.4873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5186 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9932 Z= 0.175 Angle : 0.589 16.017 13520 Z= 0.322 Chirality : 0.045 0.162 1492 Planarity : 0.005 0.080 1730 Dihedral : 4.810 29.927 1406 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.19 % Allowed : 2.88 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.23), residues: 1236 helix: -2.19 (0.51), residues: 70 sheet: -0.16 (0.22), residues: 476 loop : -0.56 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 357 TYR 0.019 0.002 TYR H 107 PHE 0.019 0.001 PHE E 377 TRP 0.014 0.002 TRP B 47 HIS 0.005 0.001 HIS C 190 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 9914) covalent geometry : angle 0.58846 (13482) SS BOND : bond 0.00574 ( 16) SS BOND : angle 0.71645 ( 32) hydrogen bonds : bond 0.04317 ( 344) hydrogen bonds : angle 6.46443 ( 948) link_NAG-ASN : bond 0.00103 ( 2) link_NAG-ASN : angle 1.17689 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 192 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 389 ASP cc_start: 0.6719 (p0) cc_final: 0.5251 (t0) REVERT: L 29 ILE cc_start: 0.6801 (pt) cc_final: 0.5627 (pt) REVERT: L 90 GLN cc_start: 0.5855 (pp30) cc_final: 0.5019 (tt0) REVERT: L 95 LEU cc_start: 0.7308 (mt) cc_final: 0.5778 (tt) REVERT: L 123 ASP cc_start: 0.7448 (m-30) cc_final: 0.7182 (p0) REVERT: A 408 ARG cc_start: 0.7544 (tpm170) cc_final: 0.7189 (tpm170) REVERT: A 429 PHE cc_start: 0.7993 (t80) cc_final: 0.7442 (t80) REVERT: A 505 TYR cc_start: 0.6439 (m-80) cc_final: 0.6085 (m-10) REVERT: B 38 ARG cc_start: 0.4895 (ptt180) cc_final: 0.4624 (ptp-170) REVERT: B 116 LEU cc_start: 0.5460 (tp) cc_final: 0.4904 (tt) REVERT: B 192 VAL cc_start: 0.5838 (m) cc_final: 0.5610 (m) REVERT: C 54 LEU cc_start: 0.7843 (tp) cc_final: 0.7602 (tt) outliers start: 2 outliers final: 2 residues processed: 194 average time/residue: 0.2732 time to fit residues: 68.6582 Evaluate side-chains 152 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 53 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 77 optimal weight: 0.0670 chunk 9 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN A 439 ASN ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.227879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.196456 restraints weight = 49187.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.198551 restraints weight = 58007.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.202253 restraints weight = 39174.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.203417 restraints weight = 25336.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.203661 restraints weight = 26109.774| |-----------------------------------------------------------------------------| r_work (final): 0.4835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5275 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9932 Z= 0.134 Angle : 0.522 15.373 13520 Z= 0.283 Chirality : 0.044 0.152 1492 Planarity : 0.005 0.083 1730 Dihedral : 4.527 24.531 1406 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.24), residues: 1236 helix: -2.00 (0.56), residues: 68 sheet: -0.06 (0.23), residues: 476 loop : -0.59 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 408 TYR 0.014 0.001 TYR H 60 PHE 0.008 0.001 PHE A 490 TRP 0.016 0.002 TRP B 162 HIS 0.003 0.001 HIS B 172 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9914) covalent geometry : angle 0.52012 (13482) SS BOND : bond 0.00351 ( 16) SS BOND : angle 0.95556 ( 32) hydrogen bonds : bond 0.03945 ( 344) hydrogen bonds : angle 6.16826 ( 948) link_NAG-ASN : bond 0.00174 ( 2) link_NAG-ASN : angle 1.01804 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 389 ASP cc_start: 0.6749 (p0) cc_final: 0.5278 (t0) REVERT: A 408 ARG cc_start: 0.7691 (tpm170) cc_final: 0.7460 (tpm170) REVERT: A 429 PHE cc_start: 0.7906 (t80) cc_final: 0.7307 (t80) REVERT: A 505 TYR cc_start: 0.6420 (m-80) cc_final: 0.6063 (m-10) REVERT: B 34 MET cc_start: 0.6051 (mmt) cc_final: 0.5793 (mmt) REVERT: B 38 ARG cc_start: 0.4951 (ptt180) cc_final: 0.4733 (ptt180) REVERT: B 116 LEU cc_start: 0.5609 (tp) cc_final: 0.5180 (tt) REVERT: C 54 LEU cc_start: 0.7828 (tp) cc_final: 0.7617 (tt) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2827 time to fit residues: 64.3900 Evaluate side-chains 143 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 85 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 HIS ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN A 450 ASN B 57 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.214497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.188761 restraints weight = 49449.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.189499 restraints weight = 63031.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.191250 restraints weight = 47197.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.191284 restraints weight = 35678.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.192291 restraints weight = 30352.319| |-----------------------------------------------------------------------------| r_work (final): 0.4725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5647 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 9932 Z= 0.304 Angle : 0.737 15.646 13520 Z= 0.406 Chirality : 0.048 0.179 1492 Planarity : 0.006 0.078 1730 Dihedral : 5.458 31.627 1406 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.28 % Allowed : 2.60 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.23), residues: 1236 helix: -1.99 (0.52), residues: 68 sheet: -0.32 (0.23), residues: 468 loop : -1.23 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 67 TYR 0.033 0.003 TYR C 36 PHE 0.027 0.003 PHE E 377 TRP 0.024 0.004 TRP H 47 HIS 0.008 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00684 ( 9914) covalent geometry : angle 0.73497 (13482) SS BOND : bond 0.00402 ( 16) SS BOND : angle 1.36708 ( 32) hydrogen bonds : bond 0.05653 ( 344) hydrogen bonds : angle 6.76050 ( 948) link_NAG-ASN : bond 0.00428 ( 2) link_NAG-ASN : angle 0.99923 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 167 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 176 LEU cc_start: 0.7682 (tt) cc_final: 0.7363 (tp) REVERT: A 429 PHE cc_start: 0.8246 (t80) cc_final: 0.7847 (t80) REVERT: A 495 TYR cc_start: 0.7751 (m-80) cc_final: 0.7541 (m-10) REVERT: B 116 LEU cc_start: 0.5924 (tp) cc_final: 0.5468 (tt) outliers start: 3 outliers final: 3 residues processed: 170 average time/residue: 0.2675 time to fit residues: 58.8029 Evaluate side-chains 134 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 131 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 22 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 0.0870 chunk 39 optimal weight: 0.1980 chunk 14 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 414 GLN L 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5012 r_free = 0.5012 target = 0.222278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.190135 restraints weight = 49228.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.189686 restraints weight = 43668.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.191673 restraints weight = 35500.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.192597 restraints weight = 29885.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.192954 restraints weight = 25946.448| |-----------------------------------------------------------------------------| r_work (final): 0.4711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5638 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9932 Z= 0.116 Angle : 0.533 15.569 13520 Z= 0.288 Chirality : 0.044 0.147 1492 Planarity : 0.004 0.070 1730 Dihedral : 4.697 24.099 1406 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.24), residues: 1236 helix: -1.68 (0.57), residues: 68 sheet: -0.20 (0.23), residues: 484 loop : -0.97 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 61 TYR 0.022 0.001 TYR H 60 PHE 0.016 0.001 PHE E 377 TRP 0.014 0.002 TRP A 436 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9914) covalent geometry : angle 0.53232 (13482) SS BOND : bond 0.00183 ( 16) SS BOND : angle 0.62321 ( 32) hydrogen bonds : bond 0.03534 ( 344) hydrogen bonds : angle 6.00632 ( 948) link_NAG-ASN : bond 0.00190 ( 2) link_NAG-ASN : angle 1.33424 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.5069 (mmm) cc_final: 0.4661 (mmm) REVERT: A 429 PHE cc_start: 0.7874 (t80) cc_final: 0.7563 (t80) REVERT: A 505 TYR cc_start: 0.6686 (m-80) cc_final: 0.6455 (m-10) REVERT: B 38 ARG cc_start: 0.5085 (ptt180) cc_final: 0.4525 (ptt180) REVERT: B 116 LEU cc_start: 0.5842 (tp) cc_final: 0.5372 (tt) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2513 time to fit residues: 56.1517 Evaluate side-chains 136 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 0.0050 chunk 117 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN L 34 ASN B 57 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.218887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.191466 restraints weight = 48963.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.194278 restraints weight = 51436.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.196367 restraints weight = 33413.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.196588 restraints weight = 25837.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.196843 restraints weight = 23976.062| |-----------------------------------------------------------------------------| r_work (final): 0.4771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5474 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9932 Z= 0.148 Angle : 0.535 15.571 13520 Z= 0.290 Chirality : 0.044 0.151 1492 Planarity : 0.004 0.066 1730 Dihedral : 4.677 24.204 1406 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.24), residues: 1236 helix: -1.55 (0.58), residues: 68 sheet: -0.18 (0.23), residues: 484 loop : -1.03 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 67 TYR 0.019 0.002 TYR H 60 PHE 0.018 0.001 PHE E 377 TRP 0.011 0.002 TRP B 162 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9914) covalent geometry : angle 0.53424 (13482) SS BOND : bond 0.00190 ( 16) SS BOND : angle 0.71560 ( 32) hydrogen bonds : bond 0.03750 ( 344) hydrogen bonds : angle 5.94506 ( 948) link_NAG-ASN : bond 0.00209 ( 2) link_NAG-ASN : angle 0.96514 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 PHE cc_start: 0.6224 (m-10) cc_final: 0.5715 (m-10) REVERT: A 429 PHE cc_start: 0.7991 (t80) cc_final: 0.7645 (t80) REVERT: A 505 TYR cc_start: 0.6729 (m-80) cc_final: 0.6473 (m-10) REVERT: B 38 ARG cc_start: 0.5133 (ptt180) cc_final: 0.4522 (ptt180) REVERT: B 116 LEU cc_start: 0.5643 (tp) cc_final: 0.5241 (tt) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2673 time to fit residues: 56.0348 Evaluate side-chains 131 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 93 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4976 r_free = 0.4976 target = 0.218487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.189692 restraints weight = 49503.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.192525 restraints weight = 56300.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.192222 restraints weight = 34044.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.192773 restraints weight = 31623.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.193621 restraints weight = 25824.044| |-----------------------------------------------------------------------------| r_work (final): 0.4736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9932 Z= 0.151 Angle : 0.534 15.641 13520 Z= 0.290 Chirality : 0.044 0.150 1492 Planarity : 0.004 0.064 1730 Dihedral : 4.640 24.678 1406 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.23), residues: 1236 helix: -2.12 (0.50), residues: 84 sheet: -0.08 (0.23), residues: 474 loop : -1.05 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 67 TYR 0.017 0.002 TYR B 110 PHE 0.018 0.001 PHE E 377 TRP 0.009 0.002 TRP A 436 HIS 0.012 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9914) covalent geometry : angle 0.53382 (13482) SS BOND : bond 0.00248 ( 16) SS BOND : angle 0.57852 ( 32) hydrogen bonds : bond 0.03731 ( 344) hydrogen bonds : angle 5.98242 ( 948) link_NAG-ASN : bond 0.00186 ( 2) link_NAG-ASN : angle 1.17139 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 83 MET cc_start: -0.1471 (mtm) cc_final: -0.1994 (mtm) REVERT: H 150 VAL cc_start: 0.7252 (t) cc_final: 0.6901 (t) REVERT: A 374 PHE cc_start: 0.6087 (m-10) cc_final: 0.5523 (m-10) REVERT: A 429 PHE cc_start: 0.8038 (t80) cc_final: 0.7702 (t80) REVERT: B 38 ARG cc_start: 0.5294 (ptt180) cc_final: 0.4499 (ptt180) REVERT: B 116 LEU cc_start: 0.5861 (tp) cc_final: 0.5483 (tt) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2437 time to fit residues: 51.2187 Evaluate side-chains 130 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 100 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN L 156 GLN L 199 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4972 r_free = 0.4972 target = 0.218104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.189769 restraints weight = 49032.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.192164 restraints weight = 55719.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.194174 restraints weight = 34985.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.194098 restraints weight = 25682.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.195167 restraints weight = 23609.667| |-----------------------------------------------------------------------------| r_work (final): 0.4750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5545 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9932 Z= 0.147 Angle : 0.533 15.686 13520 Z= 0.288 Chirality : 0.044 0.149 1492 Planarity : 0.004 0.064 1730 Dihedral : 4.617 24.970 1406 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.23), residues: 1236 helix: -2.06 (0.51), residues: 84 sheet: -0.08 (0.23), residues: 472 loop : -1.05 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 67 TYR 0.019 0.002 TYR A 351 PHE 0.017 0.001 PHE E 377 TRP 0.015 0.002 TRP E 436 HIS 0.005 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9914) covalent geometry : angle 0.53258 (13482) SS BOND : bond 0.00192 ( 16) SS BOND : angle 0.55297 ( 32) hydrogen bonds : bond 0.03696 ( 344) hydrogen bonds : angle 5.89943 ( 948) link_NAG-ASN : bond 0.00201 ( 2) link_NAG-ASN : angle 1.12795 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 355 ARG cc_start: 0.5958 (ttm170) cc_final: 0.5750 (ttp-170) REVERT: H 34 MET cc_start: 0.5518 (mmm) cc_final: 0.5043 (mmm) REVERT: H 83 MET cc_start: -0.1560 (mtm) cc_final: -0.2131 (mtm) REVERT: A 374 PHE cc_start: 0.6155 (m-10) cc_final: 0.5547 (m-10) REVERT: A 429 PHE cc_start: 0.8018 (t80) cc_final: 0.7685 (t80) REVERT: A 508 TYR cc_start: 0.4627 (m-80) cc_final: 0.4393 (m-80) REVERT: B 38 ARG cc_start: 0.5340 (ptt180) cc_final: 0.4545 (ptt180) REVERT: B 116 LEU cc_start: 0.5884 (tp) cc_final: 0.5502 (tt) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2636 time to fit residues: 57.3128 Evaluate side-chains 131 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 31 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 81 optimal weight: 0.0070 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 0.0980 chunk 74 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN A 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4975 r_free = 0.4975 target = 0.218689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.183165 restraints weight = 49662.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.185295 restraints weight = 38382.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.187279 restraints weight = 30912.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.189261 restraints weight = 24829.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.189757 restraints weight = 22275.570| |-----------------------------------------------------------------------------| r_work (final): 0.4668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5739 moved from start: 0.6058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9932 Z= 0.128 Angle : 0.507 15.613 13520 Z= 0.275 Chirality : 0.043 0.147 1492 Planarity : 0.004 0.063 1730 Dihedral : 4.493 24.095 1406 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.24), residues: 1236 helix: -2.02 (0.51), residues: 84 sheet: -0.05 (0.23), residues: 478 loop : -0.95 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 67 TYR 0.021 0.002 TYR H 60 PHE 0.015 0.001 PHE E 377 TRP 0.016 0.002 TRP E 436 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9914) covalent geometry : angle 0.50650 (13482) SS BOND : bond 0.00185 ( 16) SS BOND : angle 0.49491 ( 32) hydrogen bonds : bond 0.03419 ( 344) hydrogen bonds : angle 5.74338 ( 948) link_NAG-ASN : bond 0.00186 ( 2) link_NAG-ASN : angle 1.07162 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 355 ARG cc_start: 0.6218 (ttm170) cc_final: 0.5956 (ttp-170) REVERT: H 34 MET cc_start: 0.5516 (mmm) cc_final: 0.5149 (mmm) REVERT: H 83 MET cc_start: -0.1548 (mtm) cc_final: -0.2087 (mtm) REVERT: A 429 PHE cc_start: 0.8051 (t80) cc_final: 0.7719 (t80) REVERT: B 38 ARG cc_start: 0.5415 (ptt180) cc_final: 0.4618 (ptt180) REVERT: B 116 LEU cc_start: 0.5977 (tp) cc_final: 0.5599 (tt) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2691 time to fit residues: 58.6309 Evaluate side-chains 137 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 110 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN L 156 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4955 r_free = 0.4955 target = 0.216272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.189823 restraints weight = 48894.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.192110 restraints weight = 58239.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.194369 restraints weight = 39230.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.194149 restraints weight = 27947.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.194880 restraints weight = 26119.529| |-----------------------------------------------------------------------------| r_work (final): 0.4749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5530 moved from start: 0.6320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9932 Z= 0.171 Angle : 0.548 15.650 13520 Z= 0.296 Chirality : 0.044 0.154 1492 Planarity : 0.005 0.085 1730 Dihedral : 4.673 25.487 1406 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.24), residues: 1236 helix: -2.01 (0.51), residues: 84 sheet: -0.09 (0.23), residues: 478 loop : -1.03 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG H 67 TYR 0.018 0.002 TYR A 351 PHE 0.014 0.001 PHE E 377 TRP 0.022 0.002 TRP E 436 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 9914) covalent geometry : angle 0.54727 (13482) SS BOND : bond 0.00224 ( 16) SS BOND : angle 0.61930 ( 32) hydrogen bonds : bond 0.03811 ( 344) hydrogen bonds : angle 5.84410 ( 948) link_NAG-ASN : bond 0.00204 ( 2) link_NAG-ASN : angle 1.12757 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 355 ARG cc_start: 0.6208 (ttm170) cc_final: 0.5796 (ttp-170) REVERT: H 34 MET cc_start: 0.5576 (mmm) cc_final: 0.4972 (mmm) REVERT: H 83 MET cc_start: -0.1562 (mtm) cc_final: -0.2097 (mtm) REVERT: H 150 VAL cc_start: 0.6752 (t) cc_final: 0.6376 (t) REVERT: L 4 MET cc_start: 0.6705 (mmm) cc_final: 0.6503 (mmm) REVERT: B 116 LEU cc_start: 0.5882 (tp) cc_final: 0.5587 (tt) REVERT: C 4 MET cc_start: 0.5258 (mmm) cc_final: 0.5006 (mmm) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2578 time to fit residues: 55.4802 Evaluate side-chains 143 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 54 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 98 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 84 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4975 r_free = 0.4975 target = 0.218187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.181087 restraints weight = 49106.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.183054 restraints weight = 37344.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.184216 restraints weight = 31324.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.185754 restraints weight = 28329.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.186631 restraints weight = 24297.660| |-----------------------------------------------------------------------------| r_work (final): 0.4624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5839 moved from start: 0.6409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9932 Z= 0.128 Angle : 0.516 15.582 13520 Z= 0.280 Chirality : 0.044 0.145 1492 Planarity : 0.004 0.063 1730 Dihedral : 4.550 24.160 1406 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.24), residues: 1236 helix: -1.96 (0.51), residues: 84 sheet: -0.02 (0.23), residues: 478 loop : -1.03 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 67 TYR 0.016 0.001 TYR A 351 PHE 0.011 0.001 PHE A 490 TRP 0.011 0.002 TRP E 436 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9914) covalent geometry : angle 0.51575 (13482) SS BOND : bond 0.00428 ( 16) SS BOND : angle 0.63411 ( 32) hydrogen bonds : bond 0.03383 ( 344) hydrogen bonds : angle 5.69526 ( 948) link_NAG-ASN : bond 0.00175 ( 2) link_NAG-ASN : angle 1.08811 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3452.76 seconds wall clock time: 60 minutes 34.11 seconds (3634.11 seconds total)