Starting phenix.real_space_refine on Wed Mar 12 17:12:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f3q_31434/03_2025/7f3q_31434.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f3q_31434/03_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_31434/03_2025/7f3q_31434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f3q_31434/03_2025/7f3q_31434.map" model { file = "/net/cci-nas-00/data/ceres_data/7f3q_31434/03_2025/7f3q_31434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f3q_31434/03_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.88, per 1000 atoms: 0.61 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: 2.15 Conformation dependent library (CDL) restraints added in 1.0 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: 1.29 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: 2.57 Time building geometry restraints manager: 2.53 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: 0.130 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.560 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.250 ------------------------------------------------------------------------------- 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 8205 Z= 0.363 Angle : 0.809 9.306 11184 Z= 0.442 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 *********************** 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 : 1.006 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: 0.2469 time to fit residues: 71.0790 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 : 0.861 ------------------------------------------------------------------------------- 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 8205 Z= 0.279 Angle : 0.667 11.062 11184 Z= 0.343 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 *********************** 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 : 1.429 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: 0.2706 time to fit residues: 66.5864 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 : 0.987 ------------------------------------------------------------------------------- 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: 2.9990 chunk 68 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 overall best weight: 2.4004 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.127103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.092997 restraints weight = 12339.982| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.38 r_work: 0.2790 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8205 Z= 0.178 Angle : 0.577 8.541 11184 Z= 0.297 Chirality : 0.043 0.153 1245 Planarity : 0.004 0.065 1438 Dihedral : 4.726 31.683 1167 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.60 % Allowed : 12.64 % Favored : 84.76 % 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: -2.61 (0.57), residues: 50 sheet: 0.99 (0.25), residues: 420 loop : -0.90 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 187 HIS 0.004 0.001 HIS C 228 PHE 0.010 0.001 PHE C 150 TYR 0.020 0.001 TYR H 151 ARG 0.004 0.000 ARG H 16 *********************** 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 173 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: H 80 TYR cc_start: 0.9033 (m-80) cc_final: 0.8767 (m-10) REVERT: H 123 LYS cc_start: 0.9010 (ttmt) cc_final: 0.8748 (ttmm) REVERT: H 207 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8398 (ttmt) REVERT: L 78 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7572 (mt-10) REVERT: L 110 GLN cc_start: 0.8569 (mm110) cc_final: 0.8051 (mt0) REVERT: C 60 GLU cc_start: 0.8459 (pt0) cc_final: 0.8252 (pt0) REVERT: C 238 LYS cc_start: 0.8143 (tttp) cc_final: 0.7934 (tttp) REVERT: B 17 ASP cc_start: 0.8037 (m-30) cc_final: 0.7390 (m-30) outliers start: 23 outliers final: 14 residues processed: 163 average time/residue: 0.2358 time to fit residues: 49.8859 Evaluate side-chains 154 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 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 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: 6.9990 chunk 29 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 chunk 39 optimal weight: 30.0000 chunk 40 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.121930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.087717 restraints weight = 12303.046| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.40 r_work: 0.2695 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8205 Z= 0.299 Angle : 0.628 8.204 11184 Z= 0.327 Chirality : 0.045 0.174 1245 Planarity : 0.005 0.082 1438 Dihedral : 4.947 35.759 1167 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.50 % Allowed : 14.00 % Favored : 82.51 % 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: -0.25 (0.26), residues: 1038 helix: -2.60 (0.58), residues: 50 sheet: 1.11 (0.25), residues: 418 loop : -0.96 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 103 HIS 0.003 0.001 HIS H 35 PHE 0.014 0.001 PHE B 71 TYR 0.021 0.002 TYR L 48 ARG 0.004 0.000 ARG H 87 *********************** 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 : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8645 (mmtp) cc_final: 0.8259 (mtpt) REVERT: H 99 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8984 (p) REVERT: H 123 LYS cc_start: 0.9091 (ttmt) cc_final: 0.8808 (ttmm) REVERT: H 207 LYS cc_start: 0.8769 (mtpt) cc_final: 0.8408 (ttmt) REVERT: L 78 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7626 (mt-10) REVERT: L 108 LEU cc_start: 0.7372 (mm) cc_final: 0.7096 (mm) REVERT: L 110 GLN cc_start: 0.8665 (mm110) cc_final: 0.8165 (mt0) REVERT: C 87 ASP cc_start: 0.8279 (t0) cc_final: 0.8060 (t0) REVERT: B 146 GLN cc_start: 0.8939 (tt0) cc_final: 0.8652 (tt0) REVERT: B 191 TYR cc_start: 0.4015 (p90) cc_final: 0.3797 (p90) outliers start: 31 outliers final: 20 residues processed: 174 average time/residue: 0.2354 time to fit residues: 53.1740 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 : 0.947 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 200 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 43 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 37 optimal weight: 40.0000 chunk 26 optimal weight: 8.9990 chunk 20 optimal weight: 0.0970 chunk 81 optimal weight: 0.0050 chunk 28 optimal weight: 5.9990 overall best weight: 3.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN L 186 GLN C 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.123013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.085998 restraints weight = 12138.278| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.71 r_work: 0.2762 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8205 Z= 0.213 Angle : 0.582 7.399 11184 Z= 0.302 Chirality : 0.044 0.166 1245 Planarity : 0.004 0.066 1438 Dihedral : 4.749 33.357 1167 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.05 % Allowed : 16.03 % 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: -0.17 (0.26), residues: 1038 helix: -2.69 (0.57), residues: 50 sheet: 1.12 (0.25), residues: 420 loop : -0.85 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 103 HIS 0.002 0.001 HIS H 35 PHE 0.007 0.001 PHE B 71 TYR 0.019 0.001 TYR H 151 ARG 0.004 0.000 ARG H 16 *********************** 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 177 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8618 (mmtp) cc_final: 0.8185 (mtpt) REVERT: H 80 TYR cc_start: 0.9112 (m-10) cc_final: 0.8753 (m-10) REVERT: H 99 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.9054 (p) REVERT: H 123 LYS cc_start: 0.9064 (ttmt) cc_final: 0.8775 (ttmm) REVERT: H 207 LYS cc_start: 0.8778 (mtpt) cc_final: 0.8402 (ttmt) REVERT: L 78 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7769 (mt-10) REVERT: L 108 LEU cc_start: 0.7286 (mm) cc_final: 0.7004 (mm) REVERT: L 110 GLN cc_start: 0.8645 (mm110) cc_final: 0.7902 (mt0) REVERT: L 186 GLN cc_start: 0.8503 (mm110) cc_final: 0.8278 (mm-40) REVERT: C 60 GLU cc_start: 0.8697 (pt0) cc_final: 0.8490 (pt0) REVERT: C 87 ASP cc_start: 0.8249 (t0) cc_final: 0.7992 (t0) REVERT: B 17 ASP cc_start: 0.8318 (m-30) cc_final: 0.7640 (m-30) REVERT: B 77 SER cc_start: 0.8228 (t) cc_final: 0.7833 (p) outliers start: 27 outliers final: 19 residues processed: 168 average time/residue: 0.2277 time to fit residues: 50.0032 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 : 0.866 ------------------------------------------------------------------------------- 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 99 THR 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 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 108 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: 8.9990 chunk 31 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 19 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 99 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.122866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.082323 restraints weight = 12115.523| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.59 r_work: 0.2763 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8205 Z= 0.209 Angle : 0.576 8.434 11184 Z= 0.297 Chirality : 0.043 0.148 1245 Planarity : 0.004 0.073 1438 Dihedral : 4.753 35.626 1167 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.05 % Allowed : 16.03 % 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: -0.11 (0.26), residues: 1038 helix: -2.61 (0.58), residues: 50 sheet: 1.13 (0.25), residues: 430 loop : -0.82 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.008 0.001 PHE B 71 TYR 0.021 0.001 TYR H 151 ARG 0.005 0.000 ARG H 16 *********************** 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 167 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.876 Fit side-chains REVERT: A 462 LYS cc_start: 0.8626 (mmtp) cc_final: 0.8240 (mtpt) REVERT: H 80 TYR cc_start: 0.9111 (m-10) cc_final: 0.8744 (m-10) REVERT: H 99 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.9065 (p) REVERT: H 123 LYS cc_start: 0.9061 (ttmt) cc_final: 0.8770 (ttmm) REVERT: H 207 LYS cc_start: 0.8810 (mtpt) cc_final: 0.8443 (ttmt) REVERT: L 78 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7724 (mt-10) REVERT: L 108 LEU cc_start: 0.7323 (mm) cc_final: 0.7050 (mm) REVERT: L 110 GLN cc_start: 0.8575 (mm110) cc_final: 0.8235 (mt0) REVERT: C 87 ASP cc_start: 0.8286 (t0) cc_final: 0.8027 (t0) REVERT: C 238 LYS cc_start: 0.8378 (tttp) cc_final: 0.8137 (tptm) REVERT: B 17 ASP cc_start: 0.8311 (m-30) cc_final: 0.7655 (m-30) REVERT: B 42 LYS cc_start: 0.8717 (mmtt) cc_final: 0.8110 (mtpt) REVERT: B 169 ASP cc_start: 0.8425 (t0) cc_final: 0.8211 (t0) REVERT: B 186 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7748 (mm-30) outliers start: 27 outliers final: 20 residues processed: 158 average time/residue: 0.2240 time to fit residues: 46.4127 Evaluate side-chains 155 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 99 THR 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 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 108 THR Chi-restraints excluded: chain B residue 200 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 0.0470 chunk 31 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 overall best weight: 2.9884 ------------------------------------------------------------------------------- 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 B 154 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.123285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.089379 restraints weight = 12176.139| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.23 r_work: 0.2745 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 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 : 0.003 0.043 8205 Z= 0.197 Angle : 0.570 7.631 11184 Z= 0.295 Chirality : 0.043 0.162 1245 Planarity : 0.004 0.069 1438 Dihedral : 4.604 32.572 1167 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.60 % Allowed : 17.49 % 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: -0.01 (0.26), residues: 1038 helix: -2.58 (0.58), residues: 50 sheet: 1.24 (0.25), residues: 428 loop : -0.78 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 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 0.005 0.000 ARG H 16 *********************** 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 160 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.954 Fit side-chains REVERT: A 462 LYS cc_start: 0.8608 (mmtp) cc_final: 0.8266 (mtpt) REVERT: H 80 TYR cc_start: 0.9038 (m-10) cc_final: 0.8656 (m-10) REVERT: H 123 LYS cc_start: 0.9031 (ttmt) cc_final: 0.8740 (ttmm) REVERT: H 203 ASN cc_start: 0.8373 (m-40) cc_final: 0.7430 (m-40) REVERT: H 207 LYS cc_start: 0.8783 (mtpt) cc_final: 0.8416 (ttmt) REVERT: L 78 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7593 (mt-10) REVERT: L 108 LEU cc_start: 0.7375 (mm) cc_final: 0.7131 (mm) REVERT: L 110 GLN cc_start: 0.8555 (mm110) cc_final: 0.8324 (mt0) REVERT: C 87 ASP cc_start: 0.8257 (t0) cc_final: 0.8014 (t0) REVERT: C 238 LYS cc_start: 0.8417 (tttp) cc_final: 0.8173 (tptm) REVERT: B 17 ASP cc_start: 0.8251 (m-30) cc_final: 0.7667 (m-30) REVERT: B 31 ASN cc_start: 0.8084 (t0) cc_final: 0.7805 (t0) REVERT: B 169 ASP cc_start: 0.8394 (t0) cc_final: 0.8153 (t0) REVERT: B 186 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7625 (mm-30) outliers start: 23 outliers final: 18 residues processed: 151 average time/residue: 0.2390 time to fit residues: 47.5691 Evaluate side-chains 152 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 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 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 108 THR Chi-restraints excluded: chain B residue 200 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 83 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- 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 ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.079134 restraints weight = 12457.537| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.59 r_work: 0.2705 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8205 Z= 0.356 Angle : 0.643 9.013 11184 Z= 0.336 Chirality : 0.045 0.216 1245 Planarity : 0.005 0.076 1438 Dihedral : 5.013 39.071 1167 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.60 % Allowed : 16.82 % Favored : 80.59 % 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: -0.14 (0.26), residues: 1038 helix: -2.56 (0.60), residues: 49 sheet: 1.20 (0.24), 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 H 35 PHE 0.014 0.001 PHE B 71 TYR 0.025 0.002 TYR A 495 ARG 0.005 0.000 ARG H 16 *********************** 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 158 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8708 (mmtp) cc_final: 0.8311 (mtpt) REVERT: A 495 TYR cc_start: 0.7152 (t80) cc_final: 0.6834 (t80) REVERT: H 80 TYR cc_start: 0.9161 (m-10) cc_final: 0.8879 (m-10) REVERT: H 123 LYS cc_start: 0.9088 (ttmt) cc_final: 0.8779 (ttmm) REVERT: H 203 ASN cc_start: 0.8515 (m-40) cc_final: 0.7524 (m-40) REVERT: H 207 LYS cc_start: 0.8773 (mtpt) cc_final: 0.8398 (ttmt) REVERT: L 78 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7789 (mt-10) REVERT: L 108 LEU cc_start: 0.7205 (mm) cc_final: 0.6886 (mm) REVERT: L 110 GLN cc_start: 0.8542 (mm110) cc_final: 0.8155 (mt0) REVERT: L 127 LEU cc_start: 0.9248 (mt) cc_final: 0.8984 (mm) REVERT: C 87 ASP cc_start: 0.8494 (t0) cc_final: 0.8176 (t0) REVERT: C 238 LYS cc_start: 0.8555 (tttp) cc_final: 0.8343 (tptm) REVERT: B 17 ASP cc_start: 0.8299 (m-30) cc_final: 0.7642 (m-30) REVERT: B 77 SER cc_start: 0.8309 (t) cc_final: 0.7922 (p) REVERT: B 186 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7720 (mm-30) REVERT: B 194 GLU cc_start: 0.8265 (mt-10) cc_final: 0.8062 (mt-10) outliers start: 23 outliers final: 18 residues processed: 152 average time/residue: 0.2600 time to fit residues: 51.8348 Evaluate side-chains 151 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 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 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 108 THR Chi-restraints excluded: chain B residue 200 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 99 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 74 optimal weight: 0.0270 chunk 9 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 overall best weight: 3.8044 ------------------------------------------------------------------------------- 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 133 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.121644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.080795 restraints weight = 12542.225| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.63 r_work: 0.2740 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8205 Z= 0.230 Angle : 0.599 7.783 11184 Z= 0.311 Chirality : 0.044 0.178 1245 Planarity : 0.004 0.067 1438 Dihedral : 4.801 38.330 1167 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.48 % Allowed : 17.04 % Favored : 80.47 % 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: -2.41 (0.61), residues: 49 sheet: 1.25 (0.24), 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 0.003 0.001 HIS H 35 PHE 0.008 0.001 PHE C 43 TYR 0.023 0.001 TYR H 151 ARG 0.002 0.000 ARG H 87 *********************** 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 161 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 1.042 Fit side-chains REVERT: A 462 LYS cc_start: 0.8669 (mmtp) cc_final: 0.8303 (mtpt) REVERT: H 123 LYS cc_start: 0.9048 (ttmt) cc_final: 0.8742 (ttmm) REVERT: H 203 ASN cc_start: 0.8569 (m-40) cc_final: 0.7589 (m-40) REVERT: H 207 LYS cc_start: 0.8775 (mtpt) cc_final: 0.8413 (ttmt) REVERT: L 78 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7766 (mt-10) REVERT: L 108 LEU cc_start: 0.7257 (mm) cc_final: 0.6960 (mm) REVERT: L 110 GLN cc_start: 0.8555 (mm110) cc_final: 0.8047 (mt0) REVERT: L 127 LEU cc_start: 0.9231 (mt) cc_final: 0.8967 (mm) REVERT: C 87 ASP cc_start: 0.8355 (t0) cc_final: 0.8059 (t0) REVERT: C 238 LYS cc_start: 0.8532 (tttp) cc_final: 0.8332 (tptm) REVERT: B 17 ASP cc_start: 0.8335 (m-30) cc_final: 0.7654 (m-30) REVERT: B 77 SER cc_start: 0.8296 (t) cc_final: 0.7917 (p) REVERT: B 186 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7675 (mm-30) outliers start: 22 outliers final: 19 residues processed: 154 average time/residue: 0.2347 time to fit residues: 47.6433 Evaluate side-chains 154 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 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 68 SER Chi-restraints excluded: chain C residue 135 THR 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 108 THR Chi-restraints excluded: chain B residue 153 LEU 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: 9.9990 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 98 optimal weight: 0.2980 chunk 68 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.123891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.082952 restraints weight = 12288.756| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.63 r_work: 0.2777 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8205 Z= 0.164 Angle : 0.577 7.148 11184 Z= 0.298 Chirality : 0.043 0.146 1245 Planarity : 0.004 0.070 1438 Dihedral : 4.571 38.559 1167 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.81 % Allowed : 17.38 % Favored : 80.81 % 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: 0.09 (0.26), residues: 1038 helix: -2.31 (0.61), residues: 49 sheet: 1.28 (0.25), residues: 421 loop : -0.69 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS H 35 PHE 0.010 0.001 PHE B 138 TYR 0.023 0.001 TYR H 151 ARG 0.002 0.000 ARG H 87 ********************** 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 158 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.903 Fit side-chains REVERT: A 462 LYS cc_start: 0.8624 (mmtp) cc_final: 0.8257 (mtpt) REVERT: H 123 LYS cc_start: 0.9034 (ttmt) cc_final: 0.8749 (ttmm) REVERT: H 203 ASN cc_start: 0.8563 (m-40) cc_final: 0.7594 (m-40) REVERT: H 207 LYS cc_start: 0.8804 (mtpt) cc_final: 0.8440 (ttmt) REVERT: L 78 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7777 (mt-10) REVERT: L 108 LEU cc_start: 0.7254 (mm) cc_final: 0.6973 (mm) REVERT: L 110 GLN cc_start: 0.8555 (mm110) cc_final: 0.8195 (mt0) REVERT: C 87 ASP cc_start: 0.8291 (t0) cc_final: 0.7991 (t0) REVERT: B 17 ASP cc_start: 0.8301 (m-30) cc_final: 0.7791 (m-30) REVERT: B 31 ASN cc_start: 0.8171 (t0) cc_final: 0.7873 (t0) REVERT: B 77 SER cc_start: 0.8221 (t) cc_final: 0.7851 (p) REVERT: B 186 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7685 (mm-30) outliers start: 16 outliers final: 15 residues processed: 155 average time/residue: 0.2901 time to fit residues: 58.4227 Evaluate side-chains 152 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 62 ASP 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 205 SER 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 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 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 133 GLN C 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.122455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.081768 restraints weight = 12428.040| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.65 r_work: 0.2762 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8205 Z= 0.255 Angle : 0.612 8.000 11184 Z= 0.318 Chirality : 0.044 0.172 1245 Planarity : 0.005 0.069 1438 Dihedral : 4.724 41.667 1167 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.60 % Allowed : 17.16 % Favored : 80.25 % 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: 0.03 (0.26), residues: 1038 helix: -2.18 (0.63), residues: 49 sheet: 1.25 (0.24), residues: 426 loop : -0.77 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.009 0.001 PHE C 43 TYR 0.023 0.002 TYR H 151 ARG 0.006 0.000 ARG H 16 =============================================================================== Job complete usr+sys time: 4733.52 seconds wall clock time: 84 minutes 14.70 seconds (5054.70 seconds total)