Starting phenix.real_space_refine on Fri Jul 25 22:45:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f3q_31434/07_2025/7f3q_31434.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f3q_31434/07_2025/7f3q_31434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f3q_31434/07_2025/7f3q_31434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f3q_31434/07_2025/7f3q_31434.map" model { file = "/net/cci-nas-00/data/ceres_data/7f3q_31434/07_2025/7f3q_31434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f3q_31434/07_2025/7f3q_31434.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 5055 2.51 5 N 1339 2.21 5 O 1578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8003 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "H" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1594 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain breaks: 1 Chain: "L" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1596 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 195} Chain: "C" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1691 Classifications: {'peptide': 227} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 215} Chain: "B" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1560 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 13, 'TRANS': 191} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MES': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.47, per 1000 atoms: 0.68 Number of scatterers: 8003 At special positions: 0 Unit cell: (97.11, 87.98, 146.08, 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 1578 8.00 N 1339 7.00 C 5055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 110 " distance=2.05 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.02 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 193 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.1 seconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 25 sheets defined 9.5% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.516A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.970A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.798A pdb=" N SER H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.792A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'H' and resid 191 through 195 removed outlier: 3.848A pdb=" N SER H 194 " --> pdb=" O PRO H 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'C' and resid 42 through 46 Processing helix chain 'C' and resid 76 through 79 Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.733A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 183 through 187 removed outlier: 3.880A pdb=" N GLU B 186 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS B 187 " --> pdb=" O ASP B 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 183 through 187' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.614A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' 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: 6.800A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 126 through 130 removed outlier: 4.051A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 126 through 130 removed outlier: 4.051A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 157 through 160 removed outlier: 3.698A pdb=" N VAL H 213 " --> pdb=" O VAL H 204 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AB1, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.750A pdb=" N THR L 69 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER L 66 " --> pdb=" O THR L 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 44 through 47 removed outlier: 7.046A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 117 through 118 Processing sheet with id=AB4, first strand: chain 'L' and resid 132 through 134 Processing sheet with id=AB5, first strand: chain 'L' and resid 155 through 156 removed outlier: 3.720A pdb=" N THR L 147 " --> pdb=" O THR L 198 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 167 through 169 removed outlier: 6.494A pdb=" N SER L 167 " --> pdb=" O TYR L 174 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N TYR L 174 " --> pdb=" O SER L 167 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN L 169 " --> pdb=" O ASN L 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 17 through 21 Processing sheet with id=AB8, first strand: chain 'C' and resid 25 through 26 removed outlier: 6.319A pdb=" N ARG C 52 " --> pdb=" O TRP C 61 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N TRP C 61 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 25 through 26 removed outlier: 4.094A pdb=" N TYR C 130 " --> pdb=" O LYS C 112 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AC2, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AC3, first strand: chain 'C' and resid 179 through 182 Processing sheet with id=AC4, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.523A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.596A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 113 through 117 removed outlier: 3.569A pdb=" N ASN B 136 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 176 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N TYR B 172 " --> pdb=" O ASN B 137 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.574A pdb=" N CYS B 193 " --> pdb=" O LYS B 206 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 744 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.85 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2497 1.34 - 1.47: 2164 1.47 - 1.59: 3508 1.59 - 1.72: 1 1.72 - 1.85: 35 Bond restraints: 8205 Sorted by residual: bond pdb=" C8 MES H 301 " pdb=" S MES H 301 " ideal model delta sigma weight residual 1.814 1.662 0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" CB ASN B 31 " pdb=" CG ASN B 31 " ideal model delta sigma weight residual 1.516 1.415 0.101 2.50e-02 1.60e+03 1.63e+01 bond pdb=" N TYR L 174 " pdb=" CA TYR L 174 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.22e-02 6.72e+03 7.68e+00 bond pdb=" N LYS C 237 " pdb=" CA LYS C 237 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.26e+00 bond pdb=" N LYS B 45 " pdb=" CA LYS B 45 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 5.76e+00 ... (remaining 8200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 10725 1.86 - 3.72: 391 3.72 - 5.58: 54 5.58 - 7.45: 11 7.45 - 9.31: 3 Bond angle restraints: 11184 Sorted by residual: angle pdb=" N CYS A 379 " pdb=" CA CYS A 379 " pdb=" C CYS A 379 " ideal model delta sigma weight residual 108.60 114.22 -5.62 1.46e+00 4.69e-01 1.48e+01 angle pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 114.40 122.28 -7.88 2.30e+00 1.89e-01 1.17e+01 angle pdb=" C ALA B 50 " pdb=" N ALA B 51 " pdb=" CA ALA B 51 " ideal model delta sigma weight residual 121.54 127.09 -5.55 1.91e+00 2.74e-01 8.43e+00 angle pdb=" CA GLN C 53 " pdb=" CB GLN C 53 " pdb=" CG GLN C 53 " ideal model delta sigma weight residual 114.10 108.41 5.69 2.00e+00 2.50e-01 8.08e+00 angle pdb=" C3 MES H 301 " pdb=" N4 MES H 301 " pdb=" C5 MES H 301 " ideal model delta sigma weight residual 109.71 117.80 -8.09 3.00e+00 1.11e-01 7.27e+00 ... (remaining 11179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4472 17.95 - 35.90: 314 35.90 - 53.85: 63 53.85 - 71.80: 27 71.80 - 89.74: 7 Dihedral angle restraints: 4883 sinusoidal: 1859 harmonic: 3024 Sorted by residual: dihedral pdb=" CA TYR L 142 " pdb=" C TYR L 142 " pdb=" N PRO L 143 " pdb=" CA PRO L 143 " ideal model delta harmonic sigma weight residual 180.00 142.62 37.38 0 5.00e+00 4.00e-02 5.59e+01 dihedral pdb=" CB CYS H 146 " pdb=" SG CYS H 146 " pdb=" SG CYS H 202 " pdb=" CB CYS H 202 " ideal model delta sinusoidal sigma weight residual 93.00 147.11 -54.11 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CA CYS A 361 " pdb=" C CYS A 361 " pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta harmonic sigma weight residual 180.00 150.49 29.51 0 5.00e+00 4.00e-02 3.48e+01 ... (remaining 4880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.228: 1244 0.228 - 0.455: 0 0.455 - 0.683: 0 0.683 - 0.910: 0 0.910 - 1.137: 1 Chirality restraints: 1245 Sorted by residual: chirality pdb=" N4 MES H 301 " pdb=" C3 MES H 301 " pdb=" C5 MES H 301 " pdb=" C7 MES H 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.26 -1.14 2.00e-01 2.50e+01 3.23e+01 chirality pdb=" CG LEU B 33 " pdb=" CB LEU B 33 " pdb=" CD1 LEU B 33 " pdb=" CD2 LEU B 33 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE C 65 " pdb=" N ILE C 65 " pdb=" C ILE C 65 " pdb=" CB ILE C 65 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1242 not shown) Planarity restraints: 1439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 128 " 0.030 2.00e-02 2.50e+03 1.97e-02 6.81e+00 pdb=" CG PHE C 128 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE C 128 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 128 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 128 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 128 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 128 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR L 142 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.77e+00 pdb=" N PRO L 143 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO L 143 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 143 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 187 " 0.014 2.00e-02 2.50e+03 1.51e-02 5.68e+00 pdb=" CG TRP L 187 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP L 187 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP L 187 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 187 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP L 187 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 187 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 187 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 187 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP L 187 " 0.001 2.00e-02 2.50e+03 ... (remaining 1436 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 21 2.46 - 3.07: 5098 3.07 - 3.68: 11450 3.68 - 4.29: 17115 4.29 - 4.90: 29261 Nonbonded interactions: 62945 Sorted by model distance: nonbonded pdb=" O ASP L 153 " pdb=" OG SER L 154 " model vdw 1.848 3.040 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.212 3.040 nonbonded pdb=" OD1 ASP B 169 " pdb=" OG1 THR B 171 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR A 393 " pdb=" O GLU A 516 " model vdw 2.256 3.040 nonbonded pdb=" NH1 ARG B 107 " pdb=" O THR B 108 " model vdw 2.264 3.120 ... (remaining 62940 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.220 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: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.450 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.006 0.152 8218 Z= 0.283 Angle : 0.811 9.306 11211 Z= 0.443 Chirality : 0.058 1.137 1245 Planarity : 0.005 0.065 1438 Dihedral : 13.817 89.744 2921 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.59 % Favored : 94.32 % Rotamer: Outliers : 2.14 % Allowed : 3.61 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.26), residues: 1038 helix: -3.16 (0.55), residues: 57 sheet: 0.48 (0.26), residues: 425 loop : -1.26 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP L 187 HIS 0.006 0.001 HIS C 118 PHE 0.038 0.002 PHE C 128 TYR 0.019 0.003 TYR C 108 ARG 0.006 0.001 ARG C 33 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 1) link_NAG-ASN : angle 1.05542 ( 3) hydrogen bonds : bond 0.19233 ( 289) hydrogen bonds : angle 8.81459 ( 744) SS BOND : bond 0.00875 ( 12) SS BOND : angle 1.37889 ( 24) covalent geometry : bond 0.00580 ( 8205) covalent geometry : angle 0.80942 (11184) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: H 31 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7512 (mt-10) REVERT: H 207 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8454 (ttmt) REVERT: L 78 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7472 (mt-10) REVERT: L 187 TRP cc_start: 0.7702 (t60) cc_final: 0.7244 (t-100) REVERT: B 17 ASP cc_start: 0.7164 (m-30) cc_final: 0.6837 (m-30) REVERT: B 153 LEU cc_start: 0.8540 (mp) cc_final: 0.8010 (mp) REVERT: B 166 ASP cc_start: 0.8446 (t0) cc_final: 0.8176 (t70) outliers start: 19 outliers final: 5 residues processed: 225 average time/residue: 0.2507 time to fit residues: 72.4849 Evaluate side-chains 161 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 156 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 29 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.7980 chunk 78 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 52 optimal weight: 50.0000 chunk 41 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 49 optimal weight: 0.3980 chunk 60 optimal weight: 30.0000 chunk 93 optimal weight: 3.9990 overall best weight: 4.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN L 25 ASN L 169 GLN L 171 ASN L 186 GLN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.127129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.088957 restraints weight = 12214.764| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.85 r_work: 0.2851 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8218 Z= 0.181 Angle : 0.671 11.062 11211 Z= 0.345 Chirality : 0.045 0.164 1245 Planarity : 0.005 0.076 1438 Dihedral : 5.206 33.341 1173 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.48 % Allowed : 11.17 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.25), residues: 1038 helix: -3.08 (0.49), residues: 58 sheet: 0.73 (0.26), residues: 415 loop : -1.01 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP H 103 HIS 0.004 0.001 HIS C 228 PHE 0.020 0.001 PHE C 150 TYR 0.024 0.002 TYR H 151 ARG 0.004 0.001 ARG H 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00006 ( 1) link_NAG-ASN : angle 1.53926 ( 3) hydrogen bonds : bond 0.04012 ( 289) hydrogen bonds : angle 5.80889 ( 744) SS BOND : bond 0.00506 ( 12) SS BOND : angle 1.47406 ( 24) covalent geometry : bond 0.00427 ( 8205) covalent geometry : angle 0.66743 (11184) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: H 31 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8673 (mt-10) REVERT: H 80 TYR cc_start: 0.9116 (m-80) cc_final: 0.8848 (m-10) REVERT: L 78 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7772 (mt-10) REVERT: L 110 GLN cc_start: 0.8632 (mm110) cc_final: 0.8339 (mt0) REVERT: C 20 GLU cc_start: 0.8394 (mp0) cc_final: 0.8169 (mp0) REVERT: C 60 GLU cc_start: 0.8595 (pt0) cc_final: 0.8380 (pt0) REVERT: C 173 TYR cc_start: 0.8600 (p90) cc_final: 0.8049 (p90) REVERT: C 238 LYS cc_start: 0.8092 (tttp) cc_final: 0.7878 (tttp) REVERT: B 17 ASP cc_start: 0.8104 (m-30) cc_final: 0.7409 (m-30) REVERT: B 121 ASP cc_start: 0.7571 (p0) cc_final: 0.6981 (p0) REVERT: B 153 LEU cc_start: 0.8630 (mp) cc_final: 0.8421 (tt) outliers start: 22 outliers final: 12 residues processed: 195 average time/residue: 0.2668 time to fit residues: 65.5716 Evaluate side-chains 152 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 215 LYS Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 77 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 44 optimal weight: 0.0070 chunk 95 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 68 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 overall best weight: 1.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN C 228 HIS B 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.127869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.087213 restraints weight = 12323.865| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.64 r_work: 0.2846 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8218 Z= 0.109 Angle : 0.575 8.633 11211 Z= 0.295 Chirality : 0.043 0.152 1245 Planarity : 0.004 0.065 1438 Dihedral : 4.696 30.827 1167 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.48 % Allowed : 12.64 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.26), residues: 1038 helix: -2.63 (0.56), residues: 50 sheet: 0.96 (0.25), residues: 421 loop : -0.89 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 187 HIS 0.004 0.001 HIS C 228 PHE 0.012 0.001 PHE C 150 TYR 0.019 0.001 TYR H 151 ARG 0.004 0.000 ARG H 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00148 ( 1) link_NAG-ASN : angle 1.30754 ( 3) hydrogen bonds : bond 0.03321 ( 289) hydrogen bonds : angle 5.39447 ( 744) SS BOND : bond 0.00366 ( 12) SS BOND : angle 1.09693 ( 24) covalent geometry : bond 0.00255 ( 8205) covalent geometry : angle 0.57347 (11184) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: H 80 TYR cc_start: 0.9075 (m-80) cc_final: 0.8829 (m-10) REVERT: H 123 LYS cc_start: 0.9004 (ttmt) cc_final: 0.8737 (ttmm) REVERT: H 207 LYS cc_start: 0.8806 (mtpt) cc_final: 0.8422 (ttmt) REVERT: L 78 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7660 (mt-10) REVERT: L 110 GLN cc_start: 0.8561 (mm110) cc_final: 0.8019 (mt0) REVERT: C 20 GLU cc_start: 0.8382 (mp0) cc_final: 0.8163 (mp0) REVERT: C 60 GLU cc_start: 0.8611 (pt0) cc_final: 0.8399 (pt0) REVERT: C 238 LYS cc_start: 0.8111 (tttp) cc_final: 0.7899 (tttp) REVERT: B 17 ASP cc_start: 0.8055 (m-30) cc_final: 0.7343 (m-30) outliers start: 22 outliers final: 14 residues processed: 159 average time/residue: 0.2380 time to fit residues: 48.9684 Evaluate side-chains 152 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 88 optimal weight: 30.0000 chunk 51 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 55 optimal weight: 50.0000 chunk 39 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 501 ASN L 186 GLN C 225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.120860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.086763 restraints weight = 12297.428| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.33 r_work: 0.2677 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8218 Z= 0.217 Angle : 0.657 9.168 11211 Z= 0.343 Chirality : 0.046 0.206 1245 Planarity : 0.005 0.087 1438 Dihedral : 5.099 37.315 1167 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.50 % Allowed : 13.88 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.26), residues: 1038 helix: -2.59 (0.58), residues: 50 sheet: 1.11 (0.25), residues: 420 loop : -1.03 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 103 HIS 0.003 0.001 HIS H 35 PHE 0.016 0.002 PHE B 71 TYR 0.023 0.002 TYR A 495 ARG 0.004 0.001 ARG H 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00104 ( 1) link_NAG-ASN : angle 1.79099 ( 3) hydrogen bonds : bond 0.04176 ( 289) hydrogen bonds : angle 5.39754 ( 744) SS BOND : bond 0.00439 ( 12) SS BOND : angle 1.82175 ( 24) covalent geometry : bond 0.00523 ( 8205) covalent geometry : angle 0.65128 (11184) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8680 (mmtp) cc_final: 0.8325 (mtpt) REVERT: A 495 TYR cc_start: 0.6795 (t80) cc_final: 0.6581 (t80) REVERT: H 123 LYS cc_start: 0.9111 (ttmt) cc_final: 0.8835 (ttmm) REVERT: L 78 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7663 (mt-10) REVERT: L 108 LEU cc_start: 0.7455 (mm) cc_final: 0.7165 (mm) REVERT: L 110 GLN cc_start: 0.8658 (mm110) cc_final: 0.8192 (mt0) REVERT: L 186 GLN cc_start: 0.8662 (mm110) cc_final: 0.8316 (mm-40) REVERT: C 20 GLU cc_start: 0.8437 (mp0) cc_final: 0.8139 (mp0) REVERT: C 87 ASP cc_start: 0.8359 (t0) cc_final: 0.8143 (t0) REVERT: B 17 ASP cc_start: 0.8233 (m-30) cc_final: 0.7596 (m-30) REVERT: B 144 LYS cc_start: 0.8297 (mmtt) cc_final: 0.7939 (tttm) REVERT: B 191 TYR cc_start: 0.4058 (p90) cc_final: 0.3853 (p90) outliers start: 31 outliers final: 20 residues processed: 174 average time/residue: 0.2386 time to fit residues: 53.9232 Evaluate side-chains 163 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 176 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 43 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 37 optimal weight: 30.0000 chunk 26 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 0.0670 chunk 28 optimal weight: 5.9990 overall best weight: 4.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN C 225 ASN B 154 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.121851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.085117 restraints weight = 12175.912| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.72 r_work: 0.2723 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8218 Z= 0.169 Angle : 0.610 9.081 11211 Z= 0.314 Chirality : 0.044 0.174 1245 Planarity : 0.005 0.068 1438 Dihedral : 4.919 32.822 1167 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.05 % Allowed : 15.46 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.26), residues: 1038 helix: -2.66 (0.57), residues: 50 sheet: 1.15 (0.25), residues: 415 loop : -0.94 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 103 HIS 0.003 0.001 HIS C 192 PHE 0.009 0.001 PHE B 71 TYR 0.020 0.002 TYR H 151 ARG 0.004 0.000 ARG H 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00089 ( 1) link_NAG-ASN : angle 1.58220 ( 3) hydrogen bonds : bond 0.03607 ( 289) hydrogen bonds : angle 5.25757 ( 744) SS BOND : bond 0.00551 ( 12) SS BOND : angle 1.46033 ( 24) covalent geometry : bond 0.00409 ( 8205) covalent geometry : angle 0.60656 (11184) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8644 (mmtp) cc_final: 0.8218 (mtpt) REVERT: H 80 TYR cc_start: 0.9144 (m-10) cc_final: 0.8753 (m-10) REVERT: H 99 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.9083 (p) REVERT: H 123 LYS cc_start: 0.9064 (ttmt) cc_final: 0.8767 (ttmm) REVERT: L 78 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7777 (mt-10) REVERT: L 108 LEU cc_start: 0.7318 (mm) cc_final: 0.7023 (mm) REVERT: L 110 GLN cc_start: 0.8721 (mm110) cc_final: 0.7932 (mt0) REVERT: C 20 GLU cc_start: 0.8556 (mp0) cc_final: 0.8207 (mp0) REVERT: C 87 ASP cc_start: 0.8316 (t0) cc_final: 0.8050 (t0) REVERT: C 238 LYS cc_start: 0.8372 (tttp) cc_final: 0.8051 (tptp) REVERT: B 17 ASP cc_start: 0.8347 (m-30) cc_final: 0.7642 (m-30) REVERT: B 77 SER cc_start: 0.8267 (t) cc_final: 0.7876 (p) REVERT: B 144 LYS cc_start: 0.8291 (mmtt) cc_final: 0.7982 (tttm) REVERT: B 169 ASP cc_start: 0.8405 (t0) cc_final: 0.8057 (t0) outliers start: 27 outliers final: 19 residues processed: 169 average time/residue: 0.2351 time to fit residues: 51.5855 Evaluate side-chains 161 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 176 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 37 optimal weight: 50.0000 chunk 81 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN C 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.120960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.086958 restraints weight = 12089.600| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.20 r_work: 0.2707 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8218 Z= 0.151 Angle : 0.596 10.082 11211 Z= 0.306 Chirality : 0.044 0.178 1245 Planarity : 0.005 0.081 1438 Dihedral : 4.759 36.176 1167 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.71 % Allowed : 16.37 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 1038 helix: -2.46 (0.61), residues: 50 sheet: 1.23 (0.25), residues: 414 loop : -0.90 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS C 192 PHE 0.008 0.001 PHE B 71 TYR 0.020 0.001 TYR H 151 ARG 0.005 0.000 ARG H 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 1) link_NAG-ASN : angle 1.46561 ( 3) hydrogen bonds : bond 0.03404 ( 289) hydrogen bonds : angle 5.14073 ( 744) SS BOND : bond 0.00472 ( 12) SS BOND : angle 1.36243 ( 24) covalent geometry : bond 0.00363 ( 8205) covalent geometry : angle 0.59254 (11184) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8669 (mmtp) cc_final: 0.8349 (mtpt) REVERT: H 80 TYR cc_start: 0.9084 (m-10) cc_final: 0.8721 (m-10) REVERT: H 123 LYS cc_start: 0.9059 (ttmt) cc_final: 0.8767 (ttmm) REVERT: H 207 LYS cc_start: 0.8759 (mtpt) cc_final: 0.8391 (ttmt) REVERT: L 78 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7660 (mt-10) REVERT: L 108 LEU cc_start: 0.7339 (mm) cc_final: 0.7072 (mm) REVERT: L 110 GLN cc_start: 0.8671 (mm110) cc_final: 0.8112 (mt0) REVERT: C 20 GLU cc_start: 0.8398 (mp0) cc_final: 0.8110 (mp0) REVERT: C 87 ASP cc_start: 0.8314 (t0) cc_final: 0.8077 (t0) REVERT: C 238 LYS cc_start: 0.8460 (tttp) cc_final: 0.8091 (tptp) REVERT: B 17 ASP cc_start: 0.8234 (m-30) cc_final: 0.7635 (m-30) REVERT: B 77 SER cc_start: 0.8162 (t) cc_final: 0.7781 (p) REVERT: B 144 LYS cc_start: 0.8446 (mmtt) cc_final: 0.8099 (tttm) outliers start: 24 outliers final: 20 residues processed: 163 average time/residue: 0.2268 time to fit residues: 48.2539 Evaluate side-chains 158 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 67 optimal weight: 0.0270 chunk 31 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS C 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.122418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.082017 restraints weight = 12115.198| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.59 r_work: 0.2774 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8218 Z= 0.121 Angle : 0.589 10.024 11211 Z= 0.302 Chirality : 0.043 0.156 1245 Planarity : 0.004 0.067 1438 Dihedral : 4.604 33.524 1167 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.82 % Allowed : 17.27 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.26), residues: 1038 helix: -2.44 (0.60), residues: 50 sheet: 1.19 (0.25), residues: 423 loop : -0.79 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS C 192 PHE 0.007 0.001 PHE C 43 TYR 0.020 0.001 TYR H 151 ARG 0.005 0.000 ARG H 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 1) link_NAG-ASN : angle 1.44302 ( 3) hydrogen bonds : bond 0.03136 ( 289) hydrogen bonds : angle 5.02141 ( 744) SS BOND : bond 0.00421 ( 12) SS BOND : angle 1.24253 ( 24) covalent geometry : bond 0.00290 ( 8205) covalent geometry : angle 0.58604 (11184) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8632 (mmtp) cc_final: 0.8260 (mtpt) REVERT: H 123 LYS cc_start: 0.9052 (ttmt) cc_final: 0.8760 (ttmm) REVERT: H 207 LYS cc_start: 0.8814 (mtpt) cc_final: 0.8442 (ttmt) REVERT: L 78 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7732 (mt-10) REVERT: L 108 LEU cc_start: 0.7327 (mm) cc_final: 0.7052 (mm) REVERT: L 110 GLN cc_start: 0.8630 (mm110) cc_final: 0.8107 (mt0) REVERT: C 20 GLU cc_start: 0.8510 (mp0) cc_final: 0.8287 (mp0) REVERT: C 87 ASP cc_start: 0.8274 (t0) cc_final: 0.8011 (t0) REVERT: C 238 LYS cc_start: 0.8488 (tttp) cc_final: 0.8237 (tptm) REVERT: B 17 ASP cc_start: 0.8285 (m-30) cc_final: 0.7671 (m-30) REVERT: B 77 SER cc_start: 0.8202 (t) cc_final: 0.7817 (p) REVERT: B 121 ASP cc_start: 0.8026 (p0) cc_final: 0.7603 (p0) REVERT: B 144 LYS cc_start: 0.8492 (mmtt) cc_final: 0.8147 (ttpt) outliers start: 25 outliers final: 21 residues processed: 166 average time/residue: 0.2677 time to fit residues: 57.1708 Evaluate side-chains 163 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 83 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 97 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.121247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.080902 restraints weight = 12332.144| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.60 r_work: 0.2758 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8218 Z= 0.141 Angle : 0.597 7.923 11211 Z= 0.307 Chirality : 0.044 0.160 1245 Planarity : 0.005 0.075 1438 Dihedral : 4.592 34.549 1167 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.93 % Allowed : 17.16 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.26), residues: 1038 helix: -2.81 (0.56), residues: 50 sheet: 1.20 (0.25), residues: 423 loop : -0.77 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.008 0.001 PHE C 43 TYR 0.022 0.001 TYR H 151 ARG 0.005 0.000 ARG H 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00110 ( 1) link_NAG-ASN : angle 1.50152 ( 3) hydrogen bonds : bond 0.03267 ( 289) hydrogen bonds : angle 5.02534 ( 744) SS BOND : bond 0.00440 ( 12) SS BOND : angle 1.30369 ( 24) covalent geometry : bond 0.00342 ( 8205) covalent geometry : angle 0.59446 (11184) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8649 (mmtp) cc_final: 0.8282 (mtpt) REVERT: H 80 TYR cc_start: 0.9102 (m-10) cc_final: 0.8792 (m-10) REVERT: H 123 LYS cc_start: 0.9056 (ttmt) cc_final: 0.8755 (ttmm) REVERT: H 207 LYS cc_start: 0.8781 (mtpt) cc_final: 0.8410 (ttmt) REVERT: L 78 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7715 (mt-10) REVERT: L 108 LEU cc_start: 0.7355 (mm) cc_final: 0.7077 (mm) REVERT: L 110 GLN cc_start: 0.8655 (mm110) cc_final: 0.8239 (mt0) REVERT: C 20 GLU cc_start: 0.8529 (mp0) cc_final: 0.8270 (mp0) REVERT: C 87 ASP cc_start: 0.8331 (t0) cc_final: 0.8050 (t0) REVERT: C 238 LYS cc_start: 0.8545 (tttp) cc_final: 0.8333 (tptm) REVERT: B 17 ASP cc_start: 0.8310 (m-30) cc_final: 0.7682 (m-30) REVERT: B 77 SER cc_start: 0.8210 (t) cc_final: 0.7831 (p) REVERT: B 144 LYS cc_start: 0.8528 (mmtt) cc_final: 0.8145 (tttm) outliers start: 26 outliers final: 24 residues processed: 165 average time/residue: 0.2436 time to fit residues: 51.5454 Evaluate side-chains 170 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 99 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 74 optimal weight: 0.0060 chunk 9 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 overall best weight: 6.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.120006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.078935 restraints weight = 12617.793| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.65 r_work: 0.2716 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8218 Z= 0.206 Angle : 0.650 9.608 11211 Z= 0.337 Chirality : 0.045 0.219 1245 Planarity : 0.005 0.071 1438 Dihedral : 4.904 38.181 1167 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.05 % Allowed : 16.93 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 1038 helix: -2.72 (0.58), residues: 49 sheet: 1.20 (0.25), residues: 421 loop : -0.91 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS L 33 PHE 0.012 0.001 PHE B 71 TYR 0.023 0.002 TYR H 151 ARG 0.002 0.000 ARG C 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00070 ( 1) link_NAG-ASN : angle 1.75059 ( 3) hydrogen bonds : bond 0.03733 ( 289) hydrogen bonds : angle 5.25481 ( 744) SS BOND : bond 0.00512 ( 12) SS BOND : angle 1.59037 ( 24) covalent geometry : bond 0.00500 ( 8205) covalent geometry : angle 0.64626 (11184) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.922 Fit side-chains REVERT: A 462 LYS cc_start: 0.8716 (mmtp) cc_final: 0.8356 (mtpt) REVERT: A 487 ASN cc_start: 0.7595 (m-40) cc_final: 0.7326 (m110) REVERT: A 495 TYR cc_start: 0.7149 (t80) cc_final: 0.6811 (t80) REVERT: H 123 LYS cc_start: 0.9085 (ttmt) cc_final: 0.8770 (ttmm) REVERT: H 203 ASN cc_start: 0.8436 (m110) cc_final: 0.7877 (m-40) REVERT: H 207 LYS cc_start: 0.8760 (mtpt) cc_final: 0.8384 (ttmt) REVERT: L 78 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7748 (mt-10) REVERT: L 108 LEU cc_start: 0.7251 (mm) cc_final: 0.6935 (mm) REVERT: L 110 GLN cc_start: 0.8578 (mm110) cc_final: 0.8074 (mt0) REVERT: L 127 LEU cc_start: 0.9245 (mt) cc_final: 0.8982 (mm) REVERT: L 142 TYR cc_start: 0.7179 (t80) cc_final: 0.6970 (t80) REVERT: C 20 GLU cc_start: 0.8559 (mp0) cc_final: 0.8283 (mp0) REVERT: C 87 ASP cc_start: 0.8465 (t0) cc_final: 0.8133 (t0) REVERT: C 238 LYS cc_start: 0.8638 (tttp) cc_final: 0.8435 (tptm) REVERT: B 17 ASP cc_start: 0.8302 (m-30) cc_final: 0.7645 (m-30) REVERT: B 77 SER cc_start: 0.8300 (t) cc_final: 0.7912 (p) REVERT: B 144 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8322 (tttm) outliers start: 27 outliers final: 22 residues processed: 158 average time/residue: 0.2561 time to fit residues: 53.2672 Evaluate side-chains 160 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 155 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 100 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN C 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.120937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.080378 restraints weight = 12309.776| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.63 r_work: 0.2744 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8218 Z= 0.135 Angle : 0.616 8.941 11211 Z= 0.315 Chirality : 0.044 0.176 1245 Planarity : 0.005 0.073 1438 Dihedral : 4.717 35.314 1167 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.37 % Allowed : 18.17 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.26), residues: 1038 helix: -2.65 (0.59), residues: 49 sheet: 1.25 (0.25), residues: 420 loop : -0.84 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.008 0.001 PHE C 43 TYR 0.022 0.001 TYR H 151 ARG 0.003 0.000 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00124 ( 1) link_NAG-ASN : angle 1.53761 ( 3) hydrogen bonds : bond 0.03238 ( 289) hydrogen bonds : angle 5.10483 ( 744) SS BOND : bond 0.00496 ( 12) SS BOND : angle 1.35433 ( 24) covalent geometry : bond 0.00327 ( 8205) covalent geometry : angle 0.61302 (11184) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8692 (mmtp) cc_final: 0.8331 (mtpt) REVERT: A 487 ASN cc_start: 0.7594 (m-40) cc_final: 0.7306 (m110) REVERT: H 80 TYR cc_start: 0.9118 (m-10) cc_final: 0.8730 (m-10) REVERT: H 123 LYS cc_start: 0.9065 (ttmt) cc_final: 0.8765 (ttmm) REVERT: H 203 ASN cc_start: 0.8460 (m110) cc_final: 0.7942 (m-40) REVERT: H 207 LYS cc_start: 0.8782 (mtpt) cc_final: 0.8415 (ttmt) REVERT: L 78 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7782 (mt-10) REVERT: L 108 LEU cc_start: 0.7363 (mm) cc_final: 0.7087 (mm) REVERT: L 110 GLN cc_start: 0.8564 (mm110) cc_final: 0.8268 (mt0) REVERT: L 127 LEU cc_start: 0.9221 (mt) cc_final: 0.8951 (mm) REVERT: C 20 GLU cc_start: 0.8537 (mp0) cc_final: 0.8296 (mp0) REVERT: C 87 ASP cc_start: 0.8373 (t0) cc_final: 0.8045 (t0) REVERT: C 133 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8600 (mm110) REVERT: B 17 ASP cc_start: 0.8310 (m-30) cc_final: 0.7630 (m-30) REVERT: B 77 SER cc_start: 0.8280 (t) cc_final: 0.7900 (p) REVERT: B 144 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8358 (ttpt) outliers start: 21 outliers final: 21 residues processed: 162 average time/residue: 0.2720 time to fit residues: 57.2015 Evaluate side-chains 164 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 155 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 12 optimal weight: 5.9990 chunk 34 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN C 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.121036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.080058 restraints weight = 12436.937| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.64 r_work: 0.2730 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8218 Z= 0.164 Angle : 0.630 8.799 11211 Z= 0.324 Chirality : 0.044 0.187 1245 Planarity : 0.005 0.073 1438 Dihedral : 4.757 36.098 1167 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.93 % Allowed : 17.27 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.26), residues: 1038 helix: -2.54 (0.60), residues: 49 sheet: 1.22 (0.24), residues: 426 loop : -0.84 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.009 0.001 PHE H 95 TYR 0.022 0.002 TYR H 151 ARG 0.006 0.000 ARG H 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 1) link_NAG-ASN : angle 1.58552 ( 3) hydrogen bonds : bond 0.03431 ( 289) hydrogen bonds : angle 5.12537 ( 744) SS BOND : bond 0.00521 ( 12) SS BOND : angle 1.44761 ( 24) covalent geometry : bond 0.00399 ( 8205) covalent geometry : angle 0.62640 (11184) =============================================================================== Job complete usr+sys time: 4881.66 seconds wall clock time: 86 minutes 24.64 seconds (5184.64 seconds total)