Starting phenix.real_space_refine on Sat Aug 23 02:23:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cii_16676/08_2025/8cii_16676.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cii_16676/08_2025/8cii_16676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cii_16676/08_2025/8cii_16676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cii_16676/08_2025/8cii_16676.map" model { file = "/net/cci-nas-00/data/ceres_data/8cii_16676/08_2025/8cii_16676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cii_16676/08_2025/8cii_16676.cif" } resolution = 2.7 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= 0.000 sd= 0.007 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 5696 2.51 5 N 1513 2.21 5 O 1784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9024 Number of models: 1 Model: "" Number of chains: 7 Chain: "E" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1482 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "H" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1657 Classifications: {'peptide': 217} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Chain: "L" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1622 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 200} Chain: "A" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1644 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 207} Chain breaks: 1 Chain: "B" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1614 Classifications: {'peptide': 211} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 199} Chain: "C" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 956 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.06, per 1000 atoms: 0.23 Number of scatterers: 9024 At special positions: 0 Unit cell: (78.8724, 127.802, 140.218, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1784 8.00 N 1513 7.00 C 5696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, 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 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " BETA1-6 " NAG D 1 " - " FUC D 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG D 1 " - " ASN E 343 " Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 260.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 26 sheets defined 11.3% alpha, 44.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 364 through 370 removed outlier: 3.958A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 Processing helix chain 'E' and resid 406 through 410 Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 502 through 506 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.958A pdb=" N TYR H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 86 through 90 removed outlier: 4.021A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 167 No H-bonds generated for 'chain 'H' and resid 165 through 167' Processing helix chain 'H' and resid 194 through 198 removed outlier: 3.520A pdb=" N SER H 197 " --> pdb=" O PRO H 194 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU H 198 " --> pdb=" O SER H 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 194 through 198' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.746A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.578A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.528A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.510A pdb=" N LEU A 202 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 removed outlier: 3.501A pdb=" N SER B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 107 through 111 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 452 through 454 Processing sheet with id=AA3, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.251A pdb=" N HIS H 33 " --> pdb=" O LEU H 98 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.898A pdb=" N CYS H 95 " --> pdb=" O TRP H 112 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TRP H 112 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG H 97 " --> pdb=" O ASP H 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 129 through 133 removed outlier: 3.649A pdb=" N SER H 189 " --> pdb=" O CYS H 149 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 129 through 133 removed outlier: 3.649A pdb=" N SER H 189 " --> pdb=" O CYS H 149 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 160 through 163 removed outlier: 4.273A pdb=" N TYR H 203 " --> pdb=" O VAL H 220 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.875A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.353A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.620A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AB5, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.448A pdb=" N ILE A 34 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AB8, first strand: chain 'A' and resid 133 through 137 removed outlier: 3.564A pdb=" N SER A 193 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYR A 189 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 133 through 137 removed outlier: 3.564A pdb=" N SER A 193 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYR A 189 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 164 through 167 removed outlier: 4.402A pdb=" N TYR A 207 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.640A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.542A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 114 through 118 removed outlier: 3.523A pdb=" N VAL B 133 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AC6, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.797A pdb=" N SER C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.667A pdb=" N TYR C 113 " --> pdb=" O ALA C 98 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2868 1.34 - 1.46: 2166 1.46 - 1.58: 4176 1.58 - 1.70: 0 1.70 - 1.81: 37 Bond restraints: 9247 Sorted by residual: bond pdb=" C2 FUC D 4 " pdb=" C3 FUC D 4 " ideal model delta sigma weight residual 1.526 1.499 0.027 2.00e-02 2.50e+03 1.81e+00 bond pdb=" C3 FUC D 4 " pdb=" C4 FUC D 4 " ideal model delta sigma weight residual 1.529 1.502 0.027 2.00e-02 2.50e+03 1.78e+00 bond pdb=" CA VAL L 58 " pdb=" CB VAL L 58 " ideal model delta sigma weight residual 1.537 1.521 0.016 1.29e-02 6.01e+03 1.54e+00 bond pdb=" N ILE E 410 " pdb=" CA ILE E 410 " ideal model delta sigma weight residual 1.474 1.456 0.019 1.57e-02 4.06e+03 1.41e+00 bond pdb=" C GLN B 38 " pdb=" N LYS B 39 " ideal model delta sigma weight residual 1.339 1.273 0.066 5.57e-02 3.22e+02 1.41e+00 ... (remaining 9242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 12150 1.27 - 2.53: 337 2.53 - 3.80: 82 3.80 - 5.06: 12 5.06 - 6.33: 6 Bond angle restraints: 12587 Sorted by residual: angle pdb=" N LEU A 137 " pdb=" CA LEU A 137 " pdb=" C LEU A 137 " ideal model delta sigma weight residual 109.62 105.42 4.20 1.50e+00 4.44e-01 7.82e+00 angle pdb=" C PHE A 29 " pdb=" N SER A 30 " pdb=" CA SER A 30 " ideal model delta sigma weight residual 121.54 126.67 -5.13 1.91e+00 2.74e-01 7.23e+00 angle pdb=" N GLN A 62 " pdb=" CA GLN A 62 " pdb=" C GLN A 62 " ideal model delta sigma weight residual 113.20 109.64 3.56 1.36e+00 5.41e-01 6.85e+00 angle pdb=" N LEU H 133 " pdb=" CA LEU H 133 " pdb=" C LEU H 133 " ideal model delta sigma weight residual 109.62 105.70 3.92 1.50e+00 4.44e-01 6.84e+00 angle pdb=" N GLY C 103 " pdb=" CA GLY C 103 " pdb=" C GLY C 103 " ideal model delta sigma weight residual 110.58 114.07 -3.49 1.35e+00 5.49e-01 6.69e+00 ... (remaining 12582 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.17: 5364 21.17 - 42.34: 135 42.34 - 63.50: 22 63.50 - 84.67: 10 84.67 - 105.84: 5 Dihedral angle restraints: 5536 sinusoidal: 2161 harmonic: 3375 Sorted by residual: dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.13 105.84 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C3 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 47.62 -57.29 104.91 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" CA ILE A 52 " pdb=" C ILE A 52 " pdb=" N PRO A 53 " pdb=" CA PRO A 53 " ideal model delta harmonic sigma weight residual -180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 5533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1130 0.050 - 0.100: 214 0.100 - 0.150: 66 0.150 - 0.200: 0 0.200 - 0.250: 1 Chirality restraints: 1411 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.17e+00 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.15e+00 ... (remaining 1408 not shown) Planarity restraints: 1606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 157 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO H 158 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO H 158 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 158 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 161 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 162 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 162 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 162 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 155 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO H 156 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO H 156 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 156 " -0.020 5.00e-02 4.00e+02 ... (remaining 1603 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1967 2.78 - 3.31: 7769 3.31 - 3.84: 14911 3.84 - 4.37: 17688 4.37 - 4.90: 31191 Nonbonded interactions: 73526 Sorted by model distance: nonbonded pdb=" O GLN B 124 " pdb=" OG SER B 127 " model vdw 2.253 3.040 nonbonded pdb=" OG SER E 438 " pdb=" OD2 ASP E 442 " model vdw 2.268 3.040 nonbonded pdb=" O GLN L 124 " pdb=" OG SER L 127 " model vdw 2.289 3.040 nonbonded pdb=" OG SER B 30 " pdb=" N SER B 31 " model vdw 2.298 3.120 nonbonded pdb=" O LEU A 111 " pdb=" ND2 ASN B 34 " model vdw 2.317 3.120 ... (remaining 73521 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 'B' and (resid 1 through 2 or resid 5 through 9 or resid 11 through 29 or \ resid 33 or resid 35 through 45 or resid 47 through 49 or resid 52 through 54 o \ r resid 56 through 69 or resid 71 through 76 or resid 78 through 80 or resid 82 \ through 90 or resid 93 or resid 98 through 211)) selection = (chain 'L' and (resid 1 through 2 or resid 5 through 9 or resid 11 through 29 or \ resid 33 or resid 35 through 45 or resid 47 through 49 or resid 52 through 54 o \ r resid 56 through 69 or resid 71 through 76 or resid 78 through 80 or resid 82 \ through 90 or resid 93 or resid 98 through 211)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.410 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 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 : 0.005 0.066 9263 Z= 0.239 Angle : 0.571 6.326 12623 Z= 0.306 Chirality : 0.043 0.250 1411 Planarity : 0.004 0.043 1605 Dihedral : 10.814 105.840 3344 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.40 % Allowed : 3.36 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % 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 aren not related in a simple way. whole: 0.69 (0.26), residues: 1152 helix: -1.61 (0.61), residues: 55 sheet: 1.04 (0.25), residues: 497 loop : 0.25 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 509 TYR 0.016 0.001 TYR H 50 PHE 0.012 0.001 PHE E 456 TRP 0.012 0.001 TRP A 116 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 9247) covalent geometry : angle 0.56649 (12587) SS BOND : bond 0.00208 ( 12) SS BOND : angle 0.72261 ( 24) hydrogen bonds : bond 0.22344 ( 365) hydrogen bonds : angle 9.89855 ( 996) link_BETA1-4 : bond 0.00076 ( 2) link_BETA1-4 : angle 1.73484 ( 6) link_BETA1-6 : bond 0.00333 ( 1) link_BETA1-6 : angle 2.43485 ( 3) link_NAG-ASN : bond 0.00706 ( 1) link_NAG-ASN : angle 2.71944 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 232 time to evaluate : 0.318 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: E 340 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8325 (tp30) REVERT: E 356 LYS cc_start: 0.8809 (tttp) cc_final: 0.8594 (tttt) REVERT: E 357 ARG cc_start: 0.8819 (ttp80) cc_final: 0.8558 (ttm-80) REVERT: E 386 LYS cc_start: 0.9333 (mttt) cc_final: 0.9120 (mmmm) REVERT: E 390 LEU cc_start: 0.8855 (mt) cc_final: 0.8578 (mp) REVERT: E 462 LYS cc_start: 0.8431 (mttp) cc_final: 0.8172 (mtpm) REVERT: H 3 GLN cc_start: 0.9127 (mt0) cc_final: 0.8734 (mp10) REVERT: H 16 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8121 (mm-30) REVERT: H 75 LYS cc_start: 0.9619 (mttp) cc_final: 0.9136 (mtmm) REVERT: H 129 SER cc_start: 0.8912 (m) cc_final: 0.8634 (p) REVERT: H 185 TYR cc_start: 0.8764 (m-80) cc_final: 0.8364 (m-10) REVERT: L 81 ASP cc_start: 0.9057 (m-30) cc_final: 0.8683 (t0) REVERT: L 90 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8955 (pp30) REVERT: L 106 ILE cc_start: 0.9027 (mt) cc_final: 0.8737 (mt) REVERT: L 134 CYS cc_start: 0.7835 (t) cc_final: 0.7490 (t) REVERT: L 167 ASP cc_start: 0.7287 (t70) cc_final: 0.6790 (t0) REVERT: L 170 ASP cc_start: 0.8873 (p0) cc_final: 0.8605 (p0) REVERT: A 10 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7483 (mp0) REVERT: A 12 LYS cc_start: 0.9142 (mmtt) cc_final: 0.8826 (mptp) REVERT: A 23 LYS cc_start: 0.9337 (tttm) cc_final: 0.9093 (tttm) REVERT: A 43 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7578 (mp10) REVERT: A 65 GLN cc_start: 0.8930 (tp40) cc_final: 0.8646 (pm20) REVERT: A 82 GLU cc_start: 0.9050 (tt0) cc_final: 0.8485 (tm-30) REVERT: A 130 LYS cc_start: 0.8541 (tttm) cc_final: 0.7915 (mmtp) REVERT: A 156 LYS cc_start: 0.8794 (tttp) cc_final: 0.8469 (mtpp) REVERT: A 157 ASP cc_start: 0.8617 (m-30) cc_final: 0.8301 (m-30) REVERT: A 219 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8931 (mptt) REVERT: B 82 ASP cc_start: 0.8222 (m-30) cc_final: 0.7791 (m-30) REVERT: B 106 ILE cc_start: 0.9291 (mt) cc_final: 0.9038 (mp) REVERT: B 140 TYR cc_start: 0.9133 (t80) cc_final: 0.8633 (t80) REVERT: B 164 THR cc_start: 0.8991 (p) cc_final: 0.8785 (t) REVERT: C 65 LYS cc_start: 0.9076 (tttt) cc_final: 0.8826 (tppp) REVERT: C 76 ASN cc_start: 0.9224 (p0) cc_final: 0.8711 (p0) REVERT: C 77 ASN cc_start: 0.9152 (t0) cc_final: 0.8907 (p0) REVERT: C 83 MET cc_start: 0.9249 (mtm) cc_final: 0.8990 (mmm) REVERT: C 93 ILE cc_start: 0.9330 (mt) cc_final: 0.9056 (mm) outliers start: 4 outliers final: 2 residues processed: 236 average time/residue: 0.6027 time to fit residues: 149.9757 Evaluate side-chains 166 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 163 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 474 GLN L 147 GLN A 59 ASN A 205 GLN B 6 GLN B 124 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.096219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.055649 restraints weight = 21093.414| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.72 r_work: 0.2712 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9263 Z= 0.142 Angle : 0.627 9.884 12623 Z= 0.322 Chirality : 0.045 0.145 1411 Planarity : 0.005 0.060 1605 Dihedral : 6.915 66.628 1346 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.48 % Allowed : 12.27 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % 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 aren not related in a simple way. whole: 0.81 (0.26), residues: 1152 helix: -2.33 (0.56), residues: 59 sheet: 1.22 (0.24), residues: 504 loop : 0.33 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 24 TYR 0.021 0.001 TYR L 173 PHE 0.015 0.001 PHE L 139 TRP 0.013 0.001 TRP A 167 HIS 0.005 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9247) covalent geometry : angle 0.62386 (12587) SS BOND : bond 0.00318 ( 12) SS BOND : angle 0.87867 ( 24) hydrogen bonds : bond 0.03950 ( 365) hydrogen bonds : angle 6.89696 ( 996) link_BETA1-4 : bond 0.00416 ( 2) link_BETA1-4 : angle 2.11527 ( 6) link_BETA1-6 : bond 0.00024 ( 1) link_BETA1-6 : angle 1.38285 ( 3) link_NAG-ASN : bond 0.00037 ( 1) link_NAG-ASN : angle 1.86404 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.245 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: E 340 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8328 (tp30) REVERT: E 462 LYS cc_start: 0.8224 (mttp) cc_final: 0.7975 (mtpm) REVERT: H 3 GLN cc_start: 0.8965 (mt0) cc_final: 0.8570 (mp10) REVERT: H 16 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8045 (mm-30) REVERT: H 72 ASP cc_start: 0.7080 (t0) cc_final: 0.6203 (t0) REVERT: H 75 LYS cc_start: 0.9486 (mttp) cc_final: 0.9268 (mtmm) REVERT: H 129 SER cc_start: 0.7935 (m) cc_final: 0.7648 (p) REVERT: L 17 ASP cc_start: 0.8825 (t0) cc_final: 0.7907 (m-30) REVERT: L 70 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7521 (mp0) REVERT: L 81 ASP cc_start: 0.9287 (m-30) cc_final: 0.8699 (t0) REVERT: L 90 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8544 (pp30) REVERT: A 12 LYS cc_start: 0.8872 (mmtt) cc_final: 0.8659 (mptp) REVERT: A 23 LYS cc_start: 0.9184 (tttm) cc_final: 0.8950 (tttm) REVERT: A 62 GLN cc_start: 0.9092 (tp40) cc_final: 0.8880 (tp40) REVERT: A 80 TYR cc_start: 0.8776 (m-80) cc_final: 0.8501 (m-10) REVERT: A 82 GLU cc_start: 0.9203 (tt0) cc_final: 0.8471 (tm-30) REVERT: A 130 LYS cc_start: 0.8088 (tttm) cc_final: 0.7816 (tptm) REVERT: A 167 TRP cc_start: 0.8116 (m100) cc_final: 0.7879 (m100) REVERT: A 207 TYR cc_start: 0.8612 (m-80) cc_final: 0.8068 (m-80) REVERT: A 219 LYS cc_start: 0.9212 (mtpt) cc_final: 0.8829 (mmtt) REVERT: B 70 ASP cc_start: 0.8224 (m-30) cc_final: 0.7883 (t0) REVERT: B 82 ASP cc_start: 0.8259 (m-30) cc_final: 0.7409 (m-30) REVERT: B 143 GLU cc_start: 0.7674 (pm20) cc_final: 0.5435 (pm20) REVERT: C 39 GLN cc_start: 0.9301 (tt0) cc_final: 0.8814 (tp40) REVERT: C 43 LYS cc_start: 0.9334 (mmmm) cc_final: 0.8943 (mptt) REVERT: C 65 LYS cc_start: 0.9089 (tttt) cc_final: 0.8789 (tppp) REVERT: C 76 ASN cc_start: 0.9332 (p0) cc_final: 0.8793 (p0) REVERT: C 77 ASN cc_start: 0.9148 (t0) cc_final: 0.8852 (p0) REVERT: C 80 TYR cc_start: 0.8657 (m-80) cc_final: 0.8139 (m-80) REVERT: C 83 MET cc_start: 0.9277 (mtm) cc_final: 0.8992 (mtm) REVERT: C 85 MET cc_start: 0.9160 (mpp) cc_final: 0.8872 (mpp) REVERT: C 93 ILE cc_start: 0.8729 (mt) cc_final: 0.8472 (mm) REVERT: C 105 ASP cc_start: 0.8717 (t0) cc_final: 0.8475 (t0) outliers start: 15 outliers final: 6 residues processed: 190 average time/residue: 0.6115 time to fit residues: 122.6014 Evaluate side-chains 167 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 160 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 72 optimal weight: 4.9990 chunk 39 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.0040 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.096174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.055886 restraints weight = 21011.848| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.73 r_work: 0.2722 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9263 Z= 0.138 Angle : 0.612 10.057 12623 Z= 0.309 Chirality : 0.045 0.154 1411 Planarity : 0.005 0.058 1605 Dihedral : 5.690 52.028 1344 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.18 % Allowed : 13.95 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % 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 aren not related in a simple way. whole: 0.75 (0.25), residues: 1152 helix: -2.35 (0.57), residues: 58 sheet: 1.08 (0.22), residues: 521 loop : 0.38 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 24 TYR 0.027 0.001 TYR B 140 PHE 0.026 0.001 PHE H 131 TRP 0.009 0.001 TRP L 148 HIS 0.006 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9247) covalent geometry : angle 0.60869 (12587) SS BOND : bond 0.00317 ( 12) SS BOND : angle 0.81071 ( 24) hydrogen bonds : bond 0.03415 ( 365) hydrogen bonds : angle 6.26651 ( 996) link_BETA1-4 : bond 0.00358 ( 2) link_BETA1-4 : angle 2.15749 ( 6) link_BETA1-6 : bond 0.00161 ( 1) link_BETA1-6 : angle 1.42463 ( 3) link_NAG-ASN : bond 0.00094 ( 1) link_NAG-ASN : angle 1.85615 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.343 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: E 340 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8345 (tp30) REVERT: E 462 LYS cc_start: 0.8220 (mttp) cc_final: 0.7965 (mtpp) REVERT: H 3 GLN cc_start: 0.8899 (mt0) cc_final: 0.8514 (mp10) REVERT: H 16 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8064 (mm-30) REVERT: H 43 LYS cc_start: 0.8817 (mmmm) cc_final: 0.8606 (mmmm) REVERT: H 46 GLU cc_start: 0.8862 (tt0) cc_final: 0.8563 (tt0) REVERT: H 72 ASP cc_start: 0.7198 (t0) cc_final: 0.6129 (t0) REVERT: H 75 LYS cc_start: 0.9517 (mttp) cc_final: 0.9279 (mtmm) REVERT: H 219 ARG cc_start: 0.9113 (ttt180) cc_final: 0.8820 (tpt170) REVERT: L 17 ASP cc_start: 0.8866 (t0) cc_final: 0.7856 (m-30) REVERT: L 70 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7555 (mp0) REVERT: L 81 ASP cc_start: 0.9293 (m-30) cc_final: 0.8709 (t0) REVERT: L 90 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8542 (pp30) REVERT: L 142 ARG cc_start: 0.8442 (mmm-85) cc_final: 0.8173 (mmm160) REVERT: A 23 LYS cc_start: 0.9168 (tttm) cc_final: 0.8909 (tttm) REVERT: A 62 GLN cc_start: 0.9127 (tp40) cc_final: 0.8880 (tp40) REVERT: A 80 TYR cc_start: 0.8780 (m-80) cc_final: 0.8507 (m-10) REVERT: A 82 GLU cc_start: 0.9156 (tt0) cc_final: 0.8421 (tm-30) REVERT: A 98 ARG cc_start: 0.8294 (ttp-110) cc_final: 0.7981 (ttp-110) REVERT: A 130 LYS cc_start: 0.8080 (tttm) cc_final: 0.7809 (tptm) REVERT: A 207 TYR cc_start: 0.8751 (m-80) cc_final: 0.8122 (m-80) REVERT: B 82 ASP cc_start: 0.8249 (m-30) cc_final: 0.7285 (m-30) REVERT: C 65 LYS cc_start: 0.9117 (tttt) cc_final: 0.8829 (tppp) REVERT: C 76 ASN cc_start: 0.9288 (p0) cc_final: 0.8793 (p0) REVERT: C 77 ASN cc_start: 0.9157 (t0) cc_final: 0.8860 (p0) REVERT: C 80 TYR cc_start: 0.8720 (m-80) cc_final: 0.8198 (m-80) REVERT: C 83 MET cc_start: 0.9309 (mtm) cc_final: 0.9027 (mtm) REVERT: C 85 MET cc_start: 0.9208 (mpp) cc_final: 0.8915 (mpp) REVERT: C 93 ILE cc_start: 0.8692 (mt) cc_final: 0.8466 (mm) outliers start: 22 outliers final: 7 residues processed: 180 average time/residue: 0.5997 time to fit residues: 114.1016 Evaluate side-chains 158 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 5 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 147 GLN B 79 GLN B 92 HIS B 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.092721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.052591 restraints weight = 21599.090| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.70 r_work: 0.2640 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 9263 Z= 0.367 Angle : 0.688 7.403 12623 Z= 0.356 Chirality : 0.048 0.182 1411 Planarity : 0.005 0.064 1605 Dihedral : 5.353 52.379 1344 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.66 % Allowed : 13.85 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % 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 aren not related in a simple way. whole: 0.49 (0.25), residues: 1152 helix: -2.68 (0.54), residues: 59 sheet: 0.89 (0.22), residues: 526 loop : 0.24 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 77 TYR 0.041 0.002 TYR B 140 PHE 0.026 0.002 PHE H 131 TRP 0.037 0.002 TRP A 167 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00839 ( 9247) covalent geometry : angle 0.68434 (12587) SS BOND : bond 0.00388 ( 12) SS BOND : angle 1.00195 ( 24) hydrogen bonds : bond 0.03699 ( 365) hydrogen bonds : angle 6.19168 ( 996) link_BETA1-4 : bond 0.00335 ( 2) link_BETA1-4 : angle 2.38992 ( 6) link_BETA1-6 : bond 0.00221 ( 1) link_BETA1-6 : angle 1.70800 ( 3) link_NAG-ASN : bond 0.00709 ( 1) link_NAG-ASN : angle 2.40471 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.286 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: E 340 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8433 (tp30) REVERT: E 386 LYS cc_start: 0.9249 (mmmm) cc_final: 0.8923 (mmmm) REVERT: E 390 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8539 (mp) REVERT: E 462 LYS cc_start: 0.8235 (mttp) cc_final: 0.7969 (mtpm) REVERT: H 3 GLN cc_start: 0.8906 (mt0) cc_final: 0.8497 (mp10) REVERT: H 16 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8077 (mm-30) REVERT: H 27 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8811 (m-30) REVERT: H 43 LYS cc_start: 0.8818 (mmmm) cc_final: 0.8607 (mmmm) REVERT: H 72 ASP cc_start: 0.7539 (t0) cc_final: 0.6456 (t0) REVERT: H 75 LYS cc_start: 0.9460 (mttp) cc_final: 0.9169 (mtmm) REVERT: L 17 ASP cc_start: 0.8890 (t0) cc_final: 0.7888 (m-30) REVERT: L 70 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7619 (mp0) REVERT: L 81 ASP cc_start: 0.9307 (m-30) cc_final: 0.8686 (t0) REVERT: L 90 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8675 (pp30) REVERT: L 142 ARG cc_start: 0.8508 (mmm-85) cc_final: 0.8286 (mmm-85) REVERT: A 62 GLN cc_start: 0.9254 (tp40) cc_final: 0.8998 (tp40) REVERT: A 82 GLU cc_start: 0.9181 (tt0) cc_final: 0.8477 (tm-30) REVERT: A 98 ARG cc_start: 0.8203 (ttp-110) cc_final: 0.7564 (ttm-80) REVERT: A 207 TYR cc_start: 0.8693 (m-80) cc_final: 0.8261 (m-80) REVERT: A 219 LYS cc_start: 0.9269 (mtpt) cc_final: 0.8907 (mptt) REVERT: A 222 LYS cc_start: 0.7905 (tptp) cc_final: 0.7451 (tmtt) REVERT: B 82 ASP cc_start: 0.8442 (m-30) cc_final: 0.7916 (m-30) REVERT: B 105 GLU cc_start: 0.7958 (pp20) cc_final: 0.7735 (pp20) REVERT: B 201 LEU cc_start: 0.9205 (mt) cc_final: 0.8906 (mt) REVERT: C 30 ASP cc_start: 0.8005 (p0) cc_final: 0.7645 (p0) REVERT: C 39 GLN cc_start: 0.9030 (tt0) cc_final: 0.8696 (tp40) REVERT: C 65 LYS cc_start: 0.9199 (tttt) cc_final: 0.8861 (tppp) REVERT: C 76 ASN cc_start: 0.9224 (p0) cc_final: 0.8995 (p0) REVERT: C 77 ASN cc_start: 0.9176 (t0) cc_final: 0.8892 (t0) REVERT: C 80 TYR cc_start: 0.8864 (m-80) cc_final: 0.8273 (m-80) REVERT: C 93 ILE cc_start: 0.8919 (mt) cc_final: 0.8635 (mm) REVERT: C 105 ASP cc_start: 0.9064 (t0) cc_final: 0.8822 (t0) outliers start: 37 outliers final: 12 residues processed: 175 average time/residue: 0.6713 time to fit residues: 124.0674 Evaluate side-chains 159 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 28 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 83 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 74 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.094240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.053913 restraints weight = 21366.387| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.73 r_work: 0.2673 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9263 Z= 0.198 Angle : 0.626 8.875 12623 Z= 0.320 Chirality : 0.046 0.195 1411 Planarity : 0.005 0.057 1605 Dihedral : 5.035 46.411 1344 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.57 % Allowed : 15.43 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % 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 aren not related in a simple way. whole: 0.50 (0.25), residues: 1152 helix: -2.84 (0.52), residues: 59 sheet: 0.88 (0.22), residues: 535 loop : 0.26 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 100 TYR 0.029 0.001 TYR B 140 PHE 0.016 0.001 PHE H 131 TRP 0.049 0.002 TRP A 167 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 9247) covalent geometry : angle 0.62355 (12587) SS BOND : bond 0.00274 ( 12) SS BOND : angle 0.78097 ( 24) hydrogen bonds : bond 0.03148 ( 365) hydrogen bonds : angle 5.82395 ( 996) link_BETA1-4 : bond 0.00122 ( 2) link_BETA1-4 : angle 1.80788 ( 6) link_BETA1-6 : bond 0.00040 ( 1) link_BETA1-6 : angle 1.44210 ( 3) link_NAG-ASN : bond 0.00139 ( 1) link_NAG-ASN : angle 1.76039 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.470 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: E 340 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8395 (tp30) REVERT: E 386 LYS cc_start: 0.9218 (mmmm) cc_final: 0.8878 (mmmm) REVERT: E 390 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8614 (mp) REVERT: E 420 ASP cc_start: 0.8817 (m-30) cc_final: 0.8560 (m-30) REVERT: E 462 LYS cc_start: 0.8237 (mttp) cc_final: 0.7983 (mtpm) REVERT: H 3 GLN cc_start: 0.8879 (mt0) cc_final: 0.8491 (mp10) REVERT: H 43 LYS cc_start: 0.8834 (mmmm) cc_final: 0.8622 (mmmm) REVERT: H 72 ASP cc_start: 0.7525 (t0) cc_final: 0.6344 (t0) REVERT: H 75 LYS cc_start: 0.9456 (mttp) cc_final: 0.9148 (mtmm) REVERT: H 219 ARG cc_start: 0.9149 (ttt180) cc_final: 0.8848 (tpt170) REVERT: L 17 ASP cc_start: 0.8908 (t0) cc_final: 0.7933 (m-30) REVERT: L 70 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7568 (mp0) REVERT: L 81 ASP cc_start: 0.9293 (m-30) cc_final: 0.8696 (t0) REVERT: L 90 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8607 (pp30) REVERT: L 142 ARG cc_start: 0.8490 (mmm-85) cc_final: 0.8267 (mmm-85) REVERT: A 62 GLN cc_start: 0.9274 (tp40) cc_final: 0.8947 (tp40) REVERT: A 82 GLU cc_start: 0.9124 (tt0) cc_final: 0.8436 (tm-30) REVERT: A 89 ASP cc_start: 0.9150 (m-30) cc_final: 0.8572 (p0) REVERT: A 205 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.8045 (tm-30) REVERT: A 219 LYS cc_start: 0.9271 (mtpt) cc_final: 0.8870 (mmtt) REVERT: A 222 LYS cc_start: 0.7875 (tptp) cc_final: 0.7396 (tmtt) REVERT: B 75 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8378 (mm) REVERT: B 82 ASP cc_start: 0.8526 (m-30) cc_final: 0.7892 (m-30) REVERT: B 201 LEU cc_start: 0.9239 (mt) cc_final: 0.8947 (mt) REVERT: C 18 LEU cc_start: 0.8684 (tp) cc_final: 0.8455 (tt) REVERT: C 39 GLN cc_start: 0.8972 (tt0) cc_final: 0.8621 (tp40) REVERT: C 65 LYS cc_start: 0.9207 (tttt) cc_final: 0.8917 (tppp) REVERT: C 77 ASN cc_start: 0.9175 (t0) cc_final: 0.8885 (t0) REVERT: C 80 TYR cc_start: 0.8866 (m-80) cc_final: 0.8570 (m-80) REVERT: C 87 LYS cc_start: 0.8441 (ttpp) cc_final: 0.8217 (tmtt) REVERT: C 93 ILE cc_start: 0.8798 (mt) cc_final: 0.8500 (mm) REVERT: C 105 ASP cc_start: 0.8999 (t0) cc_final: 0.8785 (t0) outliers start: 26 outliers final: 9 residues processed: 177 average time/residue: 0.6927 time to fit residues: 129.5315 Evaluate side-chains 161 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 50 optimal weight: 40.0000 chunk 87 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 40 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.094581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.054278 restraints weight = 21319.342| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.73 r_work: 0.2667 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9263 Z= 0.174 Angle : 0.629 9.302 12623 Z= 0.321 Chirality : 0.046 0.191 1411 Planarity : 0.005 0.057 1605 Dihedral : 4.912 42.685 1344 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.18 % Allowed : 16.91 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % 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 aren not related in a simple way. whole: 0.61 (0.25), residues: 1152 helix: -2.85 (0.53), residues: 59 sheet: 1.02 (0.23), residues: 518 loop : 0.30 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 98 TYR 0.023 0.001 TYR B 140 PHE 0.030 0.001 PHE B 118 TRP 0.036 0.001 TRP A 167 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 9247) covalent geometry : angle 0.62678 (12587) SS BOND : bond 0.00248 ( 12) SS BOND : angle 0.79359 ( 24) hydrogen bonds : bond 0.02980 ( 365) hydrogen bonds : angle 5.64506 ( 996) link_BETA1-4 : bond 0.00324 ( 2) link_BETA1-4 : angle 1.73844 ( 6) link_BETA1-6 : bond 0.00018 ( 1) link_BETA1-6 : angle 1.46492 ( 3) link_NAG-ASN : bond 0.00144 ( 1) link_NAG-ASN : angle 1.67940 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.323 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: E 340 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8435 (tp30) REVERT: E 386 LYS cc_start: 0.9213 (mmmm) cc_final: 0.8838 (mmmm) REVERT: E 389 ASP cc_start: 0.9334 (m-30) cc_final: 0.9035 (m-30) REVERT: E 420 ASP cc_start: 0.8816 (m-30) cc_final: 0.8586 (m-30) REVERT: E 462 LYS cc_start: 0.8237 (mttp) cc_final: 0.7976 (mtpm) REVERT: H 3 GLN cc_start: 0.8867 (mt0) cc_final: 0.8494 (mp10) REVERT: H 43 LYS cc_start: 0.8833 (mmmm) cc_final: 0.8618 (mmmm) REVERT: H 72 ASP cc_start: 0.7549 (t0) cc_final: 0.6351 (t0) REVERT: H 75 LYS cc_start: 0.9455 (mttp) cc_final: 0.9146 (mtmm) REVERT: H 219 ARG cc_start: 0.9144 (ttt180) cc_final: 0.8836 (tpt170) REVERT: L 17 ASP cc_start: 0.8943 (t0) cc_final: 0.7960 (m-30) REVERT: L 70 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7563 (mp0) REVERT: L 81 ASP cc_start: 0.9286 (m-30) cc_final: 0.8675 (t0) REVERT: L 90 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8575 (pp30) REVERT: L 142 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.8292 (mmm160) REVERT: A 62 GLN cc_start: 0.9289 (tp40) cc_final: 0.8939 (tp40) REVERT: A 73 ASP cc_start: 0.8428 (t0) cc_final: 0.7893 (t0) REVERT: A 82 GLU cc_start: 0.9077 (tt0) cc_final: 0.8400 (tm-30) REVERT: A 89 ASP cc_start: 0.9170 (m-30) cc_final: 0.8610 (p0) REVERT: A 205 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8133 (tm-30) REVERT: A 219 LYS cc_start: 0.9284 (mtpt) cc_final: 0.8880 (mmtt) REVERT: B 70 ASP cc_start: 0.8267 (m-30) cc_final: 0.7895 (t0) REVERT: B 82 ASP cc_start: 0.8589 (m-30) cc_final: 0.7836 (m-30) REVERT: B 105 GLU cc_start: 0.7782 (pp20) cc_final: 0.7565 (pp20) REVERT: B 201 LEU cc_start: 0.9243 (mt) cc_final: 0.8966 (mt) REVERT: C 39 GLN cc_start: 0.8916 (tt0) cc_final: 0.8563 (tp40) REVERT: C 43 LYS cc_start: 0.9090 (mtmm) cc_final: 0.8569 (mppt) REVERT: C 65 LYS cc_start: 0.9181 (tttt) cc_final: 0.8899 (tppp) REVERT: C 76 ASN cc_start: 0.9444 (p0) cc_final: 0.9236 (p0) REVERT: C 77 ASN cc_start: 0.9218 (t0) cc_final: 0.8950 (t0) REVERT: C 80 TYR cc_start: 0.8943 (m-80) cc_final: 0.8638 (m-80) REVERT: C 85 MET cc_start: 0.8703 (mpp) cc_final: 0.8438 (mpp) REVERT: C 87 LYS cc_start: 0.8443 (ttpp) cc_final: 0.8167 (tmtt) REVERT: C 93 ILE cc_start: 0.8816 (mt) cc_final: 0.8513 (mm) REVERT: C 105 ASP cc_start: 0.8985 (t0) cc_final: 0.8779 (t0) outliers start: 22 outliers final: 10 residues processed: 171 average time/residue: 0.6766 time to fit residues: 122.3925 Evaluate side-chains 158 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 51 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.094016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.053697 restraints weight = 21328.729| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 3.72 r_work: 0.2655 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 9263 Z= 0.235 Angle : 0.659 9.464 12623 Z= 0.335 Chirality : 0.046 0.183 1411 Planarity : 0.005 0.058 1605 Dihedral : 4.910 42.688 1344 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.47 % Allowed : 17.61 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % 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 aren not related in a simple way. whole: 0.62 (0.25), residues: 1152 helix: -2.75 (0.58), residues: 52 sheet: 1.03 (0.22), residues: 523 loop : 0.24 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 223 TYR 0.022 0.002 TYR B 140 PHE 0.030 0.002 PHE B 118 TRP 0.037 0.002 TRP A 167 HIS 0.009 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 9247) covalent geometry : angle 0.65699 (12587) SS BOND : bond 0.00278 ( 12) SS BOND : angle 0.83425 ( 24) hydrogen bonds : bond 0.03118 ( 365) hydrogen bonds : angle 5.60381 ( 996) link_BETA1-4 : bond 0.00252 ( 2) link_BETA1-4 : angle 1.79408 ( 6) link_BETA1-6 : bond 0.00105 ( 1) link_BETA1-6 : angle 1.52872 ( 3) link_NAG-ASN : bond 0.00282 ( 1) link_NAG-ASN : angle 1.79804 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.320 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: E 340 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8455 (tp30) REVERT: E 357 ARG cc_start: 0.9028 (ttp80) cc_final: 0.8266 (ttm-80) REVERT: E 386 LYS cc_start: 0.9216 (mmmm) cc_final: 0.8868 (mmmm) REVERT: E 389 ASP cc_start: 0.9317 (m-30) cc_final: 0.9042 (m-30) REVERT: E 420 ASP cc_start: 0.8821 (m-30) cc_final: 0.8617 (m-30) REVERT: E 462 LYS cc_start: 0.8252 (mttp) cc_final: 0.7984 (mtpm) REVERT: H 3 GLN cc_start: 0.8886 (mt0) cc_final: 0.8507 (mp10) REVERT: H 43 LYS cc_start: 0.8855 (mmmm) cc_final: 0.8642 (mmmm) REVERT: H 72 ASP cc_start: 0.7596 (t0) cc_final: 0.6382 (t0) REVERT: H 75 LYS cc_start: 0.9457 (mttp) cc_final: 0.9148 (mtmm) REVERT: H 114 GLN cc_start: 0.9390 (tp40) cc_final: 0.8778 (mp10) REVERT: H 116 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8269 (p) REVERT: H 219 ARG cc_start: 0.9103 (ttt180) cc_final: 0.8806 (tpt170) REVERT: L 17 ASP cc_start: 0.8963 (t0) cc_final: 0.7971 (m-30) REVERT: L 70 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7551 (mp0) REVERT: L 81 ASP cc_start: 0.9295 (m-30) cc_final: 0.8684 (t0) REVERT: L 90 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8571 (pp30) REVERT: L 105 GLU cc_start: 0.8242 (pp20) cc_final: 0.7987 (pp20) REVERT: L 140 TYR cc_start: 0.7166 (t80) cc_final: 0.6960 (t80) REVERT: A 82 GLU cc_start: 0.9081 (tt0) cc_final: 0.8413 (tm-30) REVERT: A 87 ARG cc_start: 0.7487 (mpp80) cc_final: 0.7135 (mpp80) REVERT: A 89 ASP cc_start: 0.9193 (m-30) cc_final: 0.8639 (p0) REVERT: A 205 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8153 (tm-30) REVERT: A 219 LYS cc_start: 0.9315 (mtpt) cc_final: 0.8925 (mmtt) REVERT: A 225 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7580 (mm-30) REVERT: B 77 ARG cc_start: 0.8864 (ttp80) cc_final: 0.8518 (ttp80) REVERT: B 82 ASP cc_start: 0.8634 (m-30) cc_final: 0.7935 (m-30) REVERT: B 105 GLU cc_start: 0.7874 (pp20) cc_final: 0.7651 (pp20) REVERT: B 140 TYR cc_start: 0.7468 (t80) cc_final: 0.7256 (t80) REVERT: B 201 LEU cc_start: 0.9265 (mt) cc_final: 0.8982 (mt) REVERT: B 210 ASN cc_start: 0.8719 (m-40) cc_final: 0.8405 (p0) REVERT: C 39 GLN cc_start: 0.8911 (tt0) cc_final: 0.8529 (tp40) REVERT: C 43 LYS cc_start: 0.9067 (mtmm) cc_final: 0.8511 (mppt) REVERT: C 65 LYS cc_start: 0.9190 (tttt) cc_final: 0.8917 (tppp) REVERT: C 76 ASN cc_start: 0.9446 (p0) cc_final: 0.9221 (p0) REVERT: C 77 ASN cc_start: 0.9212 (t0) cc_final: 0.8955 (t0) REVERT: C 80 TYR cc_start: 0.8960 (m-80) cc_final: 0.8694 (m-80) REVERT: C 85 MET cc_start: 0.8792 (mpp) cc_final: 0.8511 (mpp) REVERT: C 87 LYS cc_start: 0.8446 (ttpp) cc_final: 0.8218 (tmtm) REVERT: C 93 ILE cc_start: 0.8789 (mt) cc_final: 0.8436 (mm) outliers start: 25 outliers final: 12 residues processed: 168 average time/residue: 0.7050 time to fit residues: 125.0615 Evaluate side-chains 160 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 113 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.094699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.054330 restraints weight = 21262.311| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.73 r_work: 0.2688 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9263 Z= 0.181 Angle : 0.656 9.136 12623 Z= 0.333 Chirality : 0.046 0.163 1411 Planarity : 0.005 0.057 1605 Dihedral : 4.831 42.624 1344 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.98 % Allowed : 18.30 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % 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 aren not related in a simple way. whole: 0.63 (0.25), residues: 1152 helix: -2.74 (0.59), residues: 52 sheet: 1.03 (0.23), residues: 524 loop : 0.25 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 142 TYR 0.024 0.001 TYR B 140 PHE 0.013 0.001 PHE L 83 TRP 0.035 0.001 TRP A 167 HIS 0.003 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 9247) covalent geometry : angle 0.65406 (12587) SS BOND : bond 0.00257 ( 12) SS BOND : angle 0.79456 ( 24) hydrogen bonds : bond 0.02970 ( 365) hydrogen bonds : angle 5.49767 ( 996) link_BETA1-4 : bond 0.00243 ( 2) link_BETA1-4 : angle 1.65854 ( 6) link_BETA1-6 : bond 0.00001 ( 1) link_BETA1-6 : angle 1.45924 ( 3) link_NAG-ASN : bond 0.00103 ( 1) link_NAG-ASN : angle 1.60827 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 340 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8405 (tp30) REVERT: E 386 LYS cc_start: 0.9185 (mmmm) cc_final: 0.8852 (mmmm) REVERT: E 389 ASP cc_start: 0.9340 (m-30) cc_final: 0.9052 (m-30) REVERT: E 420 ASP cc_start: 0.8794 (m-30) cc_final: 0.8587 (m-30) REVERT: E 462 LYS cc_start: 0.8219 (mttp) cc_final: 0.7953 (mtpm) REVERT: H 43 LYS cc_start: 0.8855 (mmmm) cc_final: 0.8640 (mmmm) REVERT: H 53 TYR cc_start: 0.9115 (OUTLIER) cc_final: 0.8546 (p90) REVERT: H 72 ASP cc_start: 0.7593 (t0) cc_final: 0.6375 (t0) REVERT: H 75 LYS cc_start: 0.9431 (mttp) cc_final: 0.9104 (mtmm) REVERT: H 116 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8245 (p) REVERT: H 219 ARG cc_start: 0.9108 (ttt180) cc_final: 0.8749 (tpt-90) REVERT: L 17 ASP cc_start: 0.8952 (t0) cc_final: 0.7956 (m-30) REVERT: L 70 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7527 (mp0) REVERT: L 81 ASP cc_start: 0.9283 (m-30) cc_final: 0.8670 (t0) REVERT: L 90 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8567 (pp30) REVERT: L 105 GLU cc_start: 0.8340 (pp20) cc_final: 0.8048 (pp20) REVERT: L 140 TYR cc_start: 0.7237 (OUTLIER) cc_final: 0.6968 (t80) REVERT: L 142 ARG cc_start: 0.8590 (mmm-85) cc_final: 0.8338 (mmm-85) REVERT: A 73 ASP cc_start: 0.8448 (t0) cc_final: 0.7982 (t0) REVERT: A 82 GLU cc_start: 0.9055 (tt0) cc_final: 0.8427 (tm-30) REVERT: A 87 ARG cc_start: 0.7448 (mpp80) cc_final: 0.7087 (mpp80) REVERT: A 89 ASP cc_start: 0.9199 (m-30) cc_final: 0.8667 (p0) REVERT: A 90 ASP cc_start: 0.9180 (m-30) cc_final: 0.8918 (m-30) REVERT: A 205 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8202 (tm-30) REVERT: A 219 LYS cc_start: 0.9318 (mtpt) cc_final: 0.8928 (mmtt) REVERT: B 70 ASP cc_start: 0.8217 (m-30) cc_final: 0.7884 (t0) REVERT: B 77 ARG cc_start: 0.8842 (ttp80) cc_final: 0.8481 (ttp80) REVERT: B 81 GLU cc_start: 0.8762 (pm20) cc_final: 0.8556 (pm20) REVERT: B 82 ASP cc_start: 0.8639 (m-30) cc_final: 0.7841 (m-30) REVERT: B 201 LEU cc_start: 0.9281 (mt) cc_final: 0.9014 (mt) REVERT: B 210 ASN cc_start: 0.8639 (m-40) cc_final: 0.8289 (p0) REVERT: C 39 GLN cc_start: 0.8888 (tt0) cc_final: 0.8545 (tp40) REVERT: C 65 LYS cc_start: 0.9169 (tttt) cc_final: 0.8895 (tppp) REVERT: C 76 ASN cc_start: 0.9465 (p0) cc_final: 0.9241 (p0) REVERT: C 77 ASN cc_start: 0.9212 (t0) cc_final: 0.8896 (t0) REVERT: C 80 TYR cc_start: 0.8928 (m-80) cc_final: 0.8705 (m-80) REVERT: C 87 LYS cc_start: 0.8438 (ttpp) cc_final: 0.8197 (tmtt) REVERT: C 93 ILE cc_start: 0.8727 (mt) cc_final: 0.8488 (mm) outliers start: 20 outliers final: 10 residues processed: 168 average time/residue: 0.7091 time to fit residues: 125.7650 Evaluate side-chains 161 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 140 TYR Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.095688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.056157 restraints weight = 21065.138| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.61 r_work: 0.2707 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9263 Z= 0.158 Angle : 0.693 10.687 12623 Z= 0.348 Chirality : 0.046 0.174 1411 Planarity : 0.005 0.058 1605 Dihedral : 4.824 42.416 1344 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.18 % Allowed : 18.79 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % 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 aren not related in a simple way. whole: 0.66 (0.25), residues: 1152 helix: -2.78 (0.57), residues: 52 sheet: 1.08 (0.23), residues: 522 loop : 0.26 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 211 TYR 0.046 0.002 TYR B 32 PHE 0.028 0.001 PHE C 68 TRP 0.032 0.001 TRP A 167 HIS 0.008 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 9247) covalent geometry : angle 0.69184 (12587) SS BOND : bond 0.00244 ( 12) SS BOND : angle 0.82660 ( 24) hydrogen bonds : bond 0.02961 ( 365) hydrogen bonds : angle 5.50073 ( 996) link_BETA1-4 : bond 0.00278 ( 2) link_BETA1-4 : angle 1.61511 ( 6) link_BETA1-6 : bond 0.00049 ( 1) link_BETA1-6 : angle 1.43220 ( 3) link_NAG-ASN : bond 0.00036 ( 1) link_NAG-ASN : angle 1.54592 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 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: E 340 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8432 (tp30) REVERT: E 357 ARG cc_start: 0.9043 (ttp80) cc_final: 0.8762 (ttm-80) REVERT: E 386 LYS cc_start: 0.9212 (mmmm) cc_final: 0.8857 (mmmm) REVERT: E 389 ASP cc_start: 0.9344 (m-30) cc_final: 0.9063 (m-30) REVERT: E 420 ASP cc_start: 0.8859 (m-30) cc_final: 0.8651 (m-30) REVERT: E 462 LYS cc_start: 0.8348 (mttp) cc_final: 0.8071 (mtpp) REVERT: H 72 ASP cc_start: 0.7755 (t0) cc_final: 0.6524 (t0) REVERT: H 75 LYS cc_start: 0.9454 (mttp) cc_final: 0.9132 (mtmm) REVERT: H 219 ARG cc_start: 0.9076 (ttt180) cc_final: 0.8718 (tpt170) REVERT: H 221 GLU cc_start: 0.9152 (pt0) cc_final: 0.8433 (pp20) REVERT: L 17 ASP cc_start: 0.9028 (t0) cc_final: 0.8030 (m-30) REVERT: L 70 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7598 (mp0) REVERT: L 81 ASP cc_start: 0.9273 (m-30) cc_final: 0.8683 (t0) REVERT: L 90 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8665 (pp30) REVERT: L 105 GLU cc_start: 0.8443 (pp20) cc_final: 0.8072 (pp20) REVERT: L 140 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.6998 (t80) REVERT: A 82 GLU cc_start: 0.9054 (tt0) cc_final: 0.8454 (tm-30) REVERT: A 87 ARG cc_start: 0.7556 (mpp80) cc_final: 0.7199 (mpp80) REVERT: A 89 ASP cc_start: 0.9196 (m-30) cc_final: 0.8682 (p0) REVERT: A 90 ASP cc_start: 0.9195 (m-30) cc_final: 0.8958 (m-30) REVERT: A 205 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: A 219 LYS cc_start: 0.9320 (mtpt) cc_final: 0.8951 (mmtt) REVERT: B 70 ASP cc_start: 0.8246 (m-30) cc_final: 0.7916 (t0) REVERT: B 77 ARG cc_start: 0.8822 (ttp80) cc_final: 0.8470 (ttp80) REVERT: B 81 GLU cc_start: 0.8744 (pm20) cc_final: 0.8538 (pm20) REVERT: B 82 ASP cc_start: 0.8671 (m-30) cc_final: 0.7867 (m-30) REVERT: B 105 GLU cc_start: 0.7880 (pp20) cc_final: 0.7632 (pp20) REVERT: B 140 TYR cc_start: 0.7306 (t80) cc_final: 0.7051 (t80) REVERT: B 201 LEU cc_start: 0.9286 (mt) cc_final: 0.9024 (mt) REVERT: B 210 ASN cc_start: 0.8709 (m-40) cc_final: 0.8350 (p0) REVERT: C 39 GLN cc_start: 0.8915 (tt0) cc_final: 0.8561 (tp40) REVERT: C 43 LYS cc_start: 0.9144 (mtmm) cc_final: 0.8545 (mppt) REVERT: C 65 LYS cc_start: 0.9192 (tttt) cc_final: 0.8881 (tppp) REVERT: C 68 PHE cc_start: 0.9074 (m-10) cc_final: 0.8709 (m-80) REVERT: C 76 ASN cc_start: 0.9493 (p0) cc_final: 0.9209 (p0) REVERT: C 77 ASN cc_start: 0.9190 (t0) cc_final: 0.8877 (t0) REVERT: C 80 TYR cc_start: 0.8960 (m-80) cc_final: 0.8742 (m-80) REVERT: C 87 LYS cc_start: 0.8377 (ttpp) cc_final: 0.8145 (tmtt) REVERT: C 93 ILE cc_start: 0.8784 (mt) cc_final: 0.8496 (mm) outliers start: 22 outliers final: 14 residues processed: 163 average time/residue: 0.7021 time to fit residues: 120.5662 Evaluate side-chains 161 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 140 TYR Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 72 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 90 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.095131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.055347 restraints weight = 21184.390| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.64 r_work: 0.2697 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9263 Z= 0.205 Angle : 0.737 14.753 12623 Z= 0.371 Chirality : 0.047 0.248 1411 Planarity : 0.005 0.059 1605 Dihedral : 4.739 42.451 1342 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.78 % Allowed : 19.78 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % 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 aren not related in a simple way. whole: 0.62 (0.25), residues: 1152 helix: -2.73 (0.59), residues: 52 sheet: 1.04 (0.23), residues: 524 loop : 0.22 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 211 TYR 0.036 0.002 TYR B 32 PHE 0.027 0.001 PHE C 68 TRP 0.030 0.001 TRP A 167 HIS 0.003 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 9247) covalent geometry : angle 0.73569 (12587) SS BOND : bond 0.00252 ( 12) SS BOND : angle 0.89928 ( 24) hydrogen bonds : bond 0.03097 ( 365) hydrogen bonds : angle 5.51113 ( 996) link_BETA1-4 : bond 0.00253 ( 2) link_BETA1-4 : angle 1.69867 ( 6) link_BETA1-6 : bond 0.00064 ( 1) link_BETA1-6 : angle 1.49598 ( 3) link_NAG-ASN : bond 0.00178 ( 1) link_NAG-ASN : angle 1.68225 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 340 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8462 (tp30) REVERT: E 357 ARG cc_start: 0.9049 (ttp80) cc_final: 0.8729 (ttm-80) REVERT: E 389 ASP cc_start: 0.9352 (m-30) cc_final: 0.9137 (m-30) REVERT: E 420 ASP cc_start: 0.8892 (m-30) cc_final: 0.8649 (m-30) REVERT: E 462 LYS cc_start: 0.8370 (mttp) cc_final: 0.8090 (mtpp) REVERT: E 516 GLU cc_start: 0.7721 (tp30) cc_final: 0.7386 (pt0) REVERT: H 16 GLU cc_start: 0.7812 (tt0) cc_final: 0.7570 (tm-30) REVERT: H 72 ASP cc_start: 0.7782 (t0) cc_final: 0.6554 (t0) REVERT: H 75 LYS cc_start: 0.9458 (mttp) cc_final: 0.9142 (mtmm) REVERT: H 116 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8353 (p) REVERT: H 219 ARG cc_start: 0.9083 (ttt180) cc_final: 0.8705 (tpt170) REVERT: H 221 GLU cc_start: 0.9154 (pt0) cc_final: 0.8431 (pp20) REVERT: L 17 ASP cc_start: 0.9042 (t0) cc_final: 0.8042 (m-30) REVERT: L 70 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7608 (mp0) REVERT: L 81 ASP cc_start: 0.9281 (m-30) cc_final: 0.8691 (t0) REVERT: L 90 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8661 (pp30) REVERT: L 105 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8205 (pp20) REVERT: L 140 TYR cc_start: 0.7324 (OUTLIER) cc_final: 0.7051 (t80) REVERT: A 73 ASP cc_start: 0.8644 (t0) cc_final: 0.8237 (OUTLIER) REVERT: A 82 GLU cc_start: 0.9061 (tt0) cc_final: 0.8467 (tm-30) REVERT: A 87 ARG cc_start: 0.7603 (mpp80) cc_final: 0.7226 (mpp80) REVERT: A 89 ASP cc_start: 0.9198 (m-30) cc_final: 0.8696 (p0) REVERT: A 205 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8203 (tm-30) REVERT: A 219 LYS cc_start: 0.9305 (mtpt) cc_final: 0.8922 (mmtt) REVERT: B 70 ASP cc_start: 0.8255 (m-30) cc_final: 0.7939 (t0) REVERT: B 77 ARG cc_start: 0.8817 (ttp80) cc_final: 0.8477 (ttp80) REVERT: B 81 GLU cc_start: 0.8735 (pm20) cc_final: 0.8528 (pm20) REVERT: B 82 ASP cc_start: 0.8668 (m-30) cc_final: 0.7840 (m-30) REVERT: B 105 GLU cc_start: 0.7876 (pp20) cc_final: 0.7645 (pp20) REVERT: B 140 TYR cc_start: 0.7349 (t80) cc_final: 0.7121 (t80) REVERT: B 201 LEU cc_start: 0.9292 (mt) cc_final: 0.9031 (mt) REVERT: B 210 ASN cc_start: 0.8685 (m-40) cc_final: 0.8290 (p0) REVERT: C 39 GLN cc_start: 0.8931 (tt0) cc_final: 0.8579 (tp40) REVERT: C 65 LYS cc_start: 0.9154 (tttt) cc_final: 0.8903 (tppp) REVERT: C 76 ASN cc_start: 0.9492 (p0) cc_final: 0.9216 (p0) REVERT: C 77 ASN cc_start: 0.9227 (t0) cc_final: 0.8940 (t0) REVERT: C 87 LYS cc_start: 0.8406 (ttpp) cc_final: 0.8133 (tmtm) REVERT: C 93 ILE cc_start: 0.8806 (mt) cc_final: 0.8498 (mm) outliers start: 18 outliers final: 12 residues processed: 160 average time/residue: 0.6966 time to fit residues: 117.9411 Evaluate side-chains 156 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 140 TYR Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 72 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 67 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 55 optimal weight: 0.4980 chunk 53 optimal weight: 7.9990 chunk 59 optimal weight: 20.0000 chunk 86 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 50 optimal weight: 50.0000 chunk 40 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.096300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.056721 restraints weight = 21092.009| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.65 r_work: 0.2727 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9263 Z= 0.148 Angle : 0.721 13.759 12623 Z= 0.363 Chirality : 0.046 0.272 1411 Planarity : 0.005 0.055 1605 Dihedral : 4.654 42.154 1342 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.38 % Allowed : 20.18 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % 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 aren not related in a simple way. whole: 0.68 (0.25), residues: 1152 helix: -2.63 (0.60), residues: 52 sheet: 1.09 (0.23), residues: 523 loop : 0.24 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 211 TYR 0.028 0.001 TYR B 32 PHE 0.031 0.001 PHE B 116 TRP 0.030 0.001 TRP A 167 HIS 0.008 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9247) covalent geometry : angle 0.72038 (12587) SS BOND : bond 0.00231 ( 12) SS BOND : angle 0.72626 ( 24) hydrogen bonds : bond 0.03006 ( 365) hydrogen bonds : angle 5.44665 ( 996) link_BETA1-4 : bond 0.00299 ( 2) link_BETA1-4 : angle 1.52459 ( 6) link_BETA1-6 : bond 0.00144 ( 1) link_BETA1-6 : angle 1.42236 ( 3) link_NAG-ASN : bond 0.00052 ( 1) link_NAG-ASN : angle 1.43834 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4519.84 seconds wall clock time: 77 minutes 44.80 seconds (4664.80 seconds total)