Starting phenix.real_space_refine on Wed Feb 12 16:43:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f3q_31434/02_2025/7f3q_31434.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f3q_31434/02_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_31434/02_2025/7f3q_31434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f3q_31434/02_2025/7f3q_31434.map" model { file = "/net/cci-nas-00/data/ceres_data/7f3q_31434/02_2025/7f3q_31434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f3q_31434/02_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-5592/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: 4.93, per 1000 atoms: 0.62 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: 2.03 Conformation dependent library (CDL) restraints added in 988.7 milliseconds 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: 1.19 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: 2.44 Time building geometry restraints manager: 2.18 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: 0.080 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: 21.190 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.900 ------------------------------------------------------------------------------- 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 : 0.917 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: 0.2484 time to fit residues: 71.6668 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 : 0.880 ------------------------------------------------------------------------------- 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 = 0.127128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.088958 restraints weight = 12214.774| |-----------------------------------------------------------------------------| 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: 4.66 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 : 0.848 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: 0.9115 (m-80) cc_final: 0.8847 (m-10) REVERT: L 78 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7771 (mt-10) REVERT: L 110 GLN cc_start: 0.8633 (mm110) cc_final: 0.8339 (mt0) REVERT: C 20 GLU cc_start: 0.8393 (mp0) cc_final: 0.8169 (mp0) REVERT: C 60 GLU cc_start: 0.8595 (pt0) cc_final: 0.8379 (pt0) REVERT: C 173 TYR cc_start: 0.8601 (p90) cc_final: 0.8050 (p90) REVERT: C 238 LYS cc_start: 0.8092 (tttp) cc_final: 0.7877 (tttp) REVERT: B 17 ASP cc_start: 0.8103 (m-30) cc_final: 0.7408 (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: 0.8420 (tt) outliers start: 22 outliers final: 12 residues processed: 195 average time/residue: 0.2631 time to fit residues: 64.7761 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 : 0.915 ------------------------------------------------------------------------------- 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: 7.9990 chunk 71 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 44 optimal weight: 0.0370 chunk 95 optimal weight: 20.0000 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 overall best weight: 1.9262 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.127557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.086811 restraints weight = 12338.119| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.65 r_work: 0.2841 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8205 Z= 0.173 Angle : 0.576 8.769 11184 Z= 0.296 Chirality : 0.043 0.152 1245 Planarity : 0.004 0.066 1438 Dihedral : 4.723 30.924 1167 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.60 % Allowed : 12.75 % Favored : 84.65 % 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: -0.30 (0.25), residues: 1038 helix: -2.66 (0.56), residues: 50 sheet: 0.98 (0.25), residues: 419 loop : -0.91 (0.25), residues: 569 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 0.011 0.001 PHE C 150 TYR 0.019 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 169 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: H 80 TYR cc_start: 0.9084 (m-80) cc_final: 0.8828 (m-10) REVERT: H 123 LYS cc_start: 0.9009 (ttmt) cc_final: 0.8739 (ttmm) REVERT: H 207 LYS cc_start: 0.8802 (mtpt) cc_final: 0.8418 (ttmt) REVERT: L 78 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7664 (mt-10) REVERT: L 110 GLN cc_start: 0.8573 (mm110) cc_final: 0.8026 (mt0) REVERT: C 20 GLU cc_start: 0.8384 (mp0) cc_final: 0.8170 (mp0) REVERT: C 60 GLU cc_start: 0.8603 (pt0) cc_final: 0.8393 (pt0) REVERT: C 238 LYS cc_start: 0.8110 (tttp) cc_final: 0.7895 (tttp) REVERT: B 17 ASP cc_start: 0.8035 (m-30) cc_final: 0.7304 (m-30) outliers start: 23 outliers final: 15 residues processed: 159 average time/residue: 0.2476 time to fit residues: 51.0995 Evaluate side-chains 153 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 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: 0.0050 chunk 29 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 55 optimal weight: 50.0000 chunk 39 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 overall best weight: 3.3800 ------------------------------------------------------------------------------- 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 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.124085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.083093 restraints weight = 12216.380| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.63 r_work: 0.2788 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8205 Z= 0.213 Angle : 0.578 7.401 11184 Z= 0.301 Chirality : 0.044 0.148 1245 Planarity : 0.005 0.074 1438 Dihedral : 4.696 34.744 1167 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.82 % Allowed : 14.33 % Favored : 82.84 % 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: -0.15 (0.26), residues: 1038 helix: -2.50 (0.59), residues: 50 sheet: 1.08 (0.25), residues: 422 loop : -0.82 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 103 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.001 PHE B 71 TYR 0.019 0.001 TYR H 151 ARG 0.004 0.000 ARG H 16 *********************** 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 177 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: H 57 ARG cc_start: 0.9147 (mmm-85) cc_final: 0.8943 (mmm-85) REVERT: H 80 TYR cc_start: 0.9114 (m-80) cc_final: 0.8739 (m-10) REVERT: H 123 LYS cc_start: 0.9044 (ttmt) cc_final: 0.8757 (ttmm) REVERT: H 207 LYS cc_start: 0.8823 (mtpt) cc_final: 0.8454 (ttmt) REVERT: H 214 ASP cc_start: 0.8709 (t0) cc_final: 0.8378 (t0) REVERT: L 78 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7670 (mt-10) REVERT: L 108 LEU cc_start: 0.7286 (mm) cc_final: 0.7050 (mm) REVERT: L 110 GLN cc_start: 0.8631 (mm110) cc_final: 0.8112 (mt0) REVERT: C 20 GLU cc_start: 0.8486 (mp0) cc_final: 0.8192 (mp0) REVERT: C 60 GLU cc_start: 0.8712 (pt0) cc_final: 0.8456 (pt0) REVERT: B 17 ASP cc_start: 0.8169 (m-30) cc_final: 0.7354 (m-30) REVERT: B 144 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7725 (tttm) REVERT: B 153 LEU cc_start: 0.8580 (tp) cc_final: 0.8371 (tp) REVERT: B 169 ASP cc_start: 0.8316 (t0) cc_final: 0.8107 (t0) outliers start: 25 outliers final: 18 residues processed: 169 average time/residue: 0.2380 time to fit residues: 52.3067 Evaluate side-chains 159 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR 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 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 29 ILE 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 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: 8.9990 chunk 85 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 37 optimal weight: 30.0000 chunk 26 optimal weight: 9.9990 chunk 20 optimal weight: 30.0000 chunk 81 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.119885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.083406 restraints weight = 12108.606| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.73 r_work: 0.2711 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8205 Z= 0.375 Angle : 0.646 8.742 11184 Z= 0.338 Chirality : 0.045 0.189 1245 Planarity : 0.005 0.072 1438 Dihedral : 5.103 38.046 1167 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.50 % Allowed : 14.90 % Favored : 81.60 % 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: -2.48 (0.61), residues: 50 sheet: 1.15 (0.25), residues: 420 loop : -0.98 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 103 HIS 0.004 0.001 HIS H 35 PHE 0.015 0.001 PHE B 71 TYR 0.024 0.002 TYR A 495 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 175 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8682 (mmtp) cc_final: 0.8266 (mtpt) REVERT: A 495 TYR cc_start: 0.7096 (t80) cc_final: 0.6811 (t80) REVERT: H 123 LYS cc_start: 0.9089 (ttmt) cc_final: 0.8796 (ttmm) REVERT: L 78 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7711 (mt-10) REVERT: L 108 LEU cc_start: 0.7230 (mm) cc_final: 0.6905 (mm) REVERT: L 110 GLN cc_start: 0.8645 (mm110) cc_final: 0.8099 (mt0) REVERT: L 186 GLN cc_start: 0.8560 (mm110) cc_final: 0.8290 (mm-40) REVERT: C 20 GLU cc_start: 0.8555 (mp0) cc_final: 0.8210 (mp0) REVERT: C 60 GLU cc_start: 0.8726 (pt0) cc_final: 0.8464 (pt0) REVERT: C 87 ASP cc_start: 0.8406 (t0) cc_final: 0.8162 (t0) REVERT: B 77 SER cc_start: 0.8268 (t) cc_final: 0.7871 (p) REVERT: B 144 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7983 (tttm) REVERT: B 169 ASP cc_start: 0.8473 (t0) cc_final: 0.8251 (t0) outliers start: 31 outliers final: 21 residues processed: 166 average time/residue: 0.2386 time to fit residues: 51.3641 Evaluate side-chains 161 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 478 THR 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 47 ILE Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 144 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 124 LEU 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: 20.0000 chunk 31 optimal weight: 7.9990 chunk 37 optimal weight: 50.0000 chunk 81 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.119201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.078407 restraints weight = 12197.102| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.61 r_work: 0.2713 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8205 Z= 0.354 Angle : 0.637 9.270 11184 Z= 0.332 Chirality : 0.045 0.221 1245 Planarity : 0.005 0.072 1438 Dihedral : 5.104 39.298 1167 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.82 % Allowed : 15.69 % 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: -0.25 (0.26), residues: 1038 helix: -2.48 (0.61), residues: 50 sheet: 1.16 (0.25), residues: 414 loop : -1.00 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS C 192 PHE 0.012 0.001 PHE B 71 TYR 0.024 0.002 TYR A 495 ARG 0.005 0.001 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 171 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8678 (mmtp) cc_final: 0.8280 (mtpt) REVERT: A 495 TYR cc_start: 0.7053 (t80) cc_final: 0.6774 (t80) REVERT: H 123 LYS cc_start: 0.9077 (ttmt) cc_final: 0.8776 (ttmm) REVERT: H 203 ASN cc_start: 0.8426 (m110) cc_final: 0.7822 (m-40) REVERT: L 78 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7781 (mt-10) REVERT: L 108 LEU cc_start: 0.7255 (mm) cc_final: 0.6929 (mm) REVERT: L 110 GLN cc_start: 0.8697 (mm110) cc_final: 0.7932 (mt0) REVERT: C 20 GLU cc_start: 0.8553 (mp0) cc_final: 0.8224 (mp0) REVERT: C 60 GLU cc_start: 0.8666 (pt0) cc_final: 0.8419 (pt0) REVERT: C 87 ASP cc_start: 0.8424 (t0) cc_final: 0.8141 (t0) REVERT: C 238 LYS cc_start: 0.8511 (tttp) cc_final: 0.8173 (tptp) REVERT: B 17 ASP cc_start: 0.8321 (m-30) cc_final: 0.7651 (m-30) REVERT: B 77 SER cc_start: 0.8292 (t) cc_final: 0.7920 (p) REVERT: B 144 LYS cc_start: 0.8430 (mmtt) cc_final: 0.8180 (ttpt) REVERT: B 186 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7612 (mm-30) outliers start: 25 outliers final: 24 residues processed: 162 average time/residue: 0.2312 time to fit residues: 49.2492 Evaluate side-chains 165 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 478 THR 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 144 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 124 LEU Chi-restraints excluded: chain B residue 176 SER 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: 5.9990 chunk 98 optimal weight: 20.0000 chunk 5 optimal weight: 0.0040 chunk 16 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 31 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 overall best weight: 2.3798 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.123255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.082207 restraints weight = 12203.683| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.62 r_work: 0.2768 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8205 Z= 0.183 Angle : 0.584 8.897 11184 Z= 0.301 Chirality : 0.043 0.156 1245 Planarity : 0.004 0.070 1438 Dihedral : 4.681 33.641 1167 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.48 % Allowed : 16.25 % Favored : 81.26 % 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: -0.04 (0.26), residues: 1038 helix: -2.38 (0.61), residues: 50 sheet: 1.25 (0.25), residues: 422 loop : -0.83 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS L 33 PHE 0.007 0.001 PHE C 43 TYR 0.020 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 170 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8625 (mmtp) cc_final: 0.8202 (mtpt) REVERT: H 123 LYS cc_start: 0.9033 (ttmt) cc_final: 0.8737 (ttmm) REVERT: H 207 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8394 (ttmt) REVERT: L 78 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7778 (mt-10) REVERT: L 108 LEU cc_start: 0.7346 (mm) cc_final: 0.7090 (mm) REVERT: L 110 GLN cc_start: 0.8632 (mm110) cc_final: 0.8125 (mt0) REVERT: C 20 GLU cc_start: 0.8508 (mp0) cc_final: 0.8301 (mp0) REVERT: C 60 GLU cc_start: 0.8673 (pt0) cc_final: 0.8467 (pt0) REVERT: C 87 ASP cc_start: 0.8286 (t0) cc_final: 0.8034 (t0) REVERT: C 238 LYS cc_start: 0.8468 (tttp) cc_final: 0.8243 (tptm) REVERT: B 17 ASP cc_start: 0.8313 (m-30) cc_final: 0.7680 (m-30) REVERT: B 77 SER cc_start: 0.8216 (t) cc_final: 0.7835 (p) REVERT: B 144 LYS cc_start: 0.8491 (mmtt) cc_final: 0.8137 (ttpt) REVERT: B 146 GLN cc_start: 0.8776 (tp40) cc_final: 0.8324 (tt0) outliers start: 22 outliers final: 20 residues processed: 163 average time/residue: 0.2529 time to fit residues: 53.3874 Evaluate side-chains 159 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 144 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 29 ILE 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: 6.9990 chunk 62 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 98 optimal weight: 30.0000 chunk 57 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.121957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.081731 restraints weight = 12385.328| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.58 r_work: 0.2754 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8205 Z= 0.217 Angle : 0.591 8.244 11184 Z= 0.306 Chirality : 0.044 0.180 1245 Planarity : 0.005 0.072 1438 Dihedral : 4.647 34.469 1167 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.60 % Allowed : 16.93 % 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: -0.00 (0.26), residues: 1038 helix: -2.53 (0.60), residues: 49 sheet: 1.24 (0.25), residues: 424 loop : -0.76 (0.27), residues: 565 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 C 43 TYR 0.021 0.001 TYR H 151 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 166 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.974 Fit side-chains REVERT: A 462 LYS cc_start: 0.8645 (mmtp) cc_final: 0.8277 (mtpt) REVERT: H 80 TYR cc_start: 0.9095 (m-10) cc_final: 0.8828 (m-10) REVERT: H 123 LYS cc_start: 0.9053 (ttmt) cc_final: 0.8754 (ttmm) REVERT: H 207 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8402 (ttmt) REVERT: L 78 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7747 (mt-10) REVERT: L 108 LEU cc_start: 0.7251 (mm) cc_final: 0.6968 (mm) REVERT: L 110 GLN cc_start: 0.8615 (mm110) cc_final: 0.8313 (mt0) REVERT: L 127 LEU cc_start: 0.9227 (mt) cc_final: 0.8971 (mm) REVERT: C 20 GLU cc_start: 0.8525 (mp0) cc_final: 0.8297 (mp0) REVERT: C 60 GLU cc_start: 0.8703 (pt0) cc_final: 0.8480 (pt0) REVERT: C 87 ASP cc_start: 0.8363 (t0) cc_final: 0.8063 (t0) REVERT: C 238 LYS cc_start: 0.8531 (tttp) cc_final: 0.8317 (tptm) REVERT: B 17 ASP cc_start: 0.8317 (m-30) cc_final: 0.7779 (m-30) REVERT: B 77 SER cc_start: 0.8221 (t) cc_final: 0.7841 (p) REVERT: B 144 LYS cc_start: 0.8568 (mmtt) cc_final: 0.8201 (ttpt) REVERT: B 146 GLN cc_start: 0.8785 (tp40) cc_final: 0.8376 (tt0) outliers start: 23 outliers final: 20 residues processed: 156 average time/residue: 0.2454 time to fit residues: 50.1028 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 : 0.869 ------------------------------------------------------------------------------- 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 57 LYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 152 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 99 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 74 optimal weight: 0.0870 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 overall best weight: 4.4166 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.121319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.080206 restraints weight = 12564.737| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.65 r_work: 0.2735 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8205 Z= 0.256 Angle : 0.605 8.444 11184 Z= 0.313 Chirality : 0.044 0.188 1245 Planarity : 0.005 0.072 1438 Dihedral : 4.715 35.268 1167 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.48 % Allowed : 17.16 % Favored : 80.36 % 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: -0.02 (0.26), residues: 1038 helix: -2.37 (0.61), residues: 49 sheet: 1.28 (0.25), residues: 420 loop : -0.82 (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 0.009 0.001 PHE H 95 TYR 0.022 0.001 TYR H 151 ARG 0.002 0.000 ARG H 57 *********************** 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: 22 poor density : 145 time to evaluate : 0.825 Fit side-chains REVERT: A 462 LYS cc_start: 0.8679 (mmtp) cc_final: 0.8317 (mtpt) REVERT: H 80 TYR cc_start: 0.9126 (m-10) cc_final: 0.8774 (m-10) REVERT: H 123 LYS cc_start: 0.9062 (ttmt) cc_final: 0.8760 (ttmm) REVERT: H 203 ASN cc_start: 0.8461 (m110) cc_final: 0.8020 (m-40) REVERT: H 207 LYS cc_start: 0.8770 (mtpt) cc_final: 0.8401 (ttmt) REVERT: L 78 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7807 (mt-10) REVERT: L 108 LEU cc_start: 0.7261 (mm) cc_final: 0.6963 (mm) REVERT: L 110 GLN cc_start: 0.8573 (mm110) cc_final: 0.8217 (mt0) REVERT: L 127 LEU cc_start: 0.9236 (mt) cc_final: 0.8973 (mm) REVERT: C 20 GLU cc_start: 0.8552 (mp0) cc_final: 0.8187 (mp0) REVERT: C 60 GLU cc_start: 0.8712 (pt0) cc_final: 0.8503 (pt0) REVERT: C 87 ASP cc_start: 0.8410 (t0) cc_final: 0.8106 (t0) REVERT: C 238 LYS cc_start: 0.8585 (tttp) cc_final: 0.8374 (tptm) REVERT: B 17 ASP cc_start: 0.8353 (m-30) cc_final: 0.7772 (m-30) REVERT: B 77 SER cc_start: 0.8240 (t) cc_final: 0.7861 (p) REVERT: B 144 LYS cc_start: 0.8647 (mmtt) cc_final: 0.8296 (ttpt) REVERT: B 146 GLN cc_start: 0.8782 (tp40) cc_final: 0.8309 (tt0) outliers start: 22 outliers final: 19 residues processed: 159 average time/residue: 0.2335 time to fit residues: 49.5624 Evaluate side-chains 162 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 57 LYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 144 THR 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 200 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: 2.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.121630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.080584 restraints weight = 12401.774| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.64 r_work: 0.2735 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8205 Z= 0.240 Angle : 0.604 8.209 11184 Z= 0.313 Chirality : 0.044 0.181 1245 Planarity : 0.005 0.072 1438 Dihedral : 4.683 35.459 1167 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.14 % Allowed : 17.16 % Favored : 80.70 % 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: -2.26 (0.63), residues: 49 sheet: 1.26 (0.25), residues: 420 loop : -0.78 (0.27), 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 H 95 TYR 0.023 0.001 TYR H 151 ARG 0.003 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 166 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.849 Fit side-chains REVERT: A 462 LYS cc_start: 0.8683 (mmtp) cc_final: 0.8318 (mtpt) REVERT: H 80 TYR cc_start: 0.9127 (m-10) cc_final: 0.8745 (m-10) REVERT: H 123 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8772 (ttmm) REVERT: H 203 ASN cc_start: 0.8447 (m110) cc_final: 0.8036 (m-40) REVERT: H 207 LYS cc_start: 0.8795 (mtpt) cc_final: 0.8430 (ttmt) REVERT: L 78 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7811 (mt-10) REVERT: L 108 LEU cc_start: 0.7344 (mm) cc_final: 0.7068 (mm) REVERT: L 110 GLN cc_start: 0.8550 (mm110) cc_final: 0.8244 (mt0) REVERT: L 127 LEU cc_start: 0.9229 (mt) cc_final: 0.8962 (mm) REVERT: C 20 GLU cc_start: 0.8557 (mp0) cc_final: 0.8249 (mp0) REVERT: C 87 ASP cc_start: 0.8405 (t0) cc_final: 0.8100 (t0) REVERT: C 238 LYS cc_start: 0.8613 (tttp) cc_final: 0.8404 (tptm) REVERT: B 17 ASP cc_start: 0.8336 (m-30) cc_final: 0.7765 (m-30) REVERT: B 77 SER cc_start: 0.8236 (t) cc_final: 0.7857 (p) REVERT: B 144 LYS cc_start: 0.8673 (mmtt) cc_final: 0.8281 (ttpt) REVERT: B 146 GLN cc_start: 0.8809 (tp40) cc_final: 0.8297 (tt0) outliers start: 19 outliers final: 17 residues processed: 159 average time/residue: 0.2346 time to fit residues: 48.3709 Evaluate side-chains 162 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 144 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 12 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 36 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.122826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.085794 restraints weight = 12363.402| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.68 r_work: 0.2779 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.4368 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= 0.205 Angle : 0.593 7.689 11184 Z= 0.307 Chirality : 0.044 0.168 1245 Planarity : 0.005 0.071 1438 Dihedral : 4.585 33.818 1167 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.48 % Allowed : 16.70 % 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: 0.07 (0.26), residues: 1038 helix: -2.15 (0.65), residues: 49 sheet: 1.24 (0.25), residues: 425 loop : -0.71 (0.27), residues: 564 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 0.010 0.001 PHE B 138 TYR 0.023 0.001 TYR H 151 ARG 0.006 0.000 ARG H 16 =============================================================================== Job complete usr+sys time: 4655.53 seconds wall clock time: 83 minutes 7.83 seconds (4987.83 seconds total)