Starting phenix.real_space_refine on Mon Jan 20 15:16:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vww_43604/01_2025/8vww_43604.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vww_43604/01_2025/8vww_43604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vww_43604/01_2025/8vww_43604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vww_43604/01_2025/8vww_43604.map" model { file = "/net/cci-nas-00/data/ceres_data/8vww_43604/01_2025/8vww_43604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vww_43604/01_2025/8vww_43604.cif" } resolution = 3.9 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1936 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 28 5.16 5 C 4411 2.51 5 N 1158 2.21 5 O 1349 1.98 5 H 6855 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 13801 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 4013 Classifications: {'peptide': 247} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 239} Chain breaks: 1 Chain: "B" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1866 Classifications: {'peptide': 122} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "C" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1595 Classifications: {'peptide': 107} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3199 Classifications: {'peptide': 217} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain breaks: 1 Chain: "L" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 3128 Classifications: {'peptide': 206} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 194} Chain breaks: 1 Time building chain proxies: 7.33, per 1000 atoms: 0.53 Number of scatterers: 13801 At special positions: 0 Unit cell: (73.3216, 94.1516, 153.309, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 O 1349 8.00 N 1158 7.00 C 4411 6.00 H 6855 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 295 " distance=2.02 Simple disulfide: pdb=" SG CYS A 363 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 479 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.04 Simple disulfide: pdb=" SG CYS H 216 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 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 Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 1.2 seconds 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1660 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 19 sheets defined 10.6% alpha, 37.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 256 through 272 Processing helix chain 'A' and resid 282 through 291 Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 394 through 398 removed outlier: 4.103A pdb=" N ILE A 398 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.505A pdb=" N ASN B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.794A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 185 through 189 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.596A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 355 removed outlier: 6.941A pdb=" N SER A 360 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER A 442 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N CYS A 439 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 436 " --> pdb=" O CYS A 439 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 375 through 376 removed outlier: 3.583A pdb=" N ILE A 375 " --> pdb=" O ILE A 461 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 385 through 386 removed outlier: 6.199A pdb=" N VAL A 385 " --> pdb=" O GLN A 501 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LYS A 503 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.595A pdb=" N SER B 7 " --> pdb=" O SER B 21 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER B 21 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 18 " --> pdb=" O MET B 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.937A pdb=" N MET B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.642A pdb=" N ALA B 100E" --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.302A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP C 50 " --> pdb=" O SER C 53 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.302A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN C 90 " --> pdb=" O THR C 97 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.650A pdb=" N GLN H 5 " --> pdb=" O THR H 23 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR H 23 " --> pdb=" O GLN H 5 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.770A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TRP H 35A" --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N SER H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.770A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.156A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER H 177 " --> pdb=" O ALA H 168 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA H 168 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N SER H 179 " --> pdb=" O PHE H 166 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.396A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.892A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 14 removed outlier: 3.563A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU L 33 " --> pdb=" O ALA L 50 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA L 50 " --> pdb=" O THR L 53 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 116 through 118 removed outlier: 3.557A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 145 through 149 removed outlier: 3.702A pdb=" N LYS L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 660 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: 5.10 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 6855 1.03 - 1.23: 6 1.23 - 1.42: 3002 1.42 - 1.62: 4058 1.62 - 1.81: 34 Bond restraints: 13955 Sorted by residual: bond pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 1.498 1.473 0.025 3.10e-02 1.04e+03 6.64e-01 bond pdb=" CB CYS A 287 " pdb=" SG CYS A 287 " ideal model delta sigma weight residual 1.808 1.783 0.025 3.30e-02 9.18e+02 5.61e-01 bond pdb=" CB CYS B 92 " pdb=" SG CYS B 92 " ideal model delta sigma weight residual 1.808 1.784 0.024 3.30e-02 9.18e+02 5.34e-01 bond pdb=" CB GLN A 373 " pdb=" CG GLN A 373 " ideal model delta sigma weight residual 1.520 1.499 0.021 3.00e-02 1.11e+03 4.88e-01 bond pdb=" ND2 ASN A 402 " pdb="HD22 ASN A 402 " ideal model delta sigma weight residual 0.860 0.846 0.014 2.00e-02 2.50e+03 4.88e-01 ... (remaining 13950 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 24534 1.49 - 2.98: 573 2.98 - 4.47: 59 4.47 - 5.96: 5 5.96 - 7.45: 2 Bond angle restraints: 25173 Sorted by residual: angle pdb=" N PRO H 149 " pdb=" CA PRO H 149 " pdb=" C PRO H 149 " ideal model delta sigma weight residual 110.21 113.99 -3.78 1.64e+00 3.72e-01 5.31e+00 angle pdb=" N TYR A 359 " pdb=" CA TYR A 359 " pdb=" C TYR A 359 " ideal model delta sigma weight residual 108.79 105.26 3.53 1.53e+00 4.27e-01 5.31e+00 angle pdb=" N HIS A 431 " pdb=" CA HIS A 431 " pdb=" C HIS A 431 " ideal model delta sigma weight residual 108.02 104.04 3.98 1.78e+00 3.16e-01 4.99e+00 angle pdb=" N LYS H 201 " pdb=" CA LYS H 201 " pdb=" C LYS H 201 " ideal model delta sigma weight residual 109.81 114.67 -4.86 2.21e+00 2.05e-01 4.84e+00 angle pdb=" N ILE A 309 " pdb=" CA ILE A 309 " pdb=" C ILE A 309 " ideal model delta sigma weight residual 109.34 113.84 -4.50 2.08e+00 2.31e-01 4.68e+00 ... (remaining 25168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5997 17.82 - 35.63: 425 35.63 - 53.45: 141 53.45 - 71.27: 98 71.27 - 89.08: 7 Dihedral angle restraints: 6668 sinusoidal: 3593 harmonic: 3075 Sorted by residual: dihedral pdb=" CA ALA B 88 " pdb=" C ALA B 88 " pdb=" N VAL B 89 " pdb=" CA VAL B 89 " ideal model delta harmonic sigma weight residual 180.00 153.45 26.55 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA PRO H 98 " pdb=" C PRO H 98 " pdb=" N ASP H 99 " pdb=" CA ASP H 99 " ideal model delta harmonic sigma weight residual 180.00 -153.74 -26.26 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ILE H 69 " pdb=" C ILE H 69 " pdb=" N SER H 70 " pdb=" CA SER H 70 " ideal model delta harmonic sigma weight residual 180.00 154.71 25.29 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 6665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 674 0.032 - 0.065: 260 0.065 - 0.097: 91 0.097 - 0.130: 57 0.130 - 0.162: 9 Chirality restraints: 1091 Sorted by residual: chirality pdb=" CA ILE A 254 " pdb=" N ILE A 254 " pdb=" C ILE A 254 " pdb=" CB ILE A 254 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CA ILE C 48 " pdb=" N ILE C 48 " pdb=" C ILE C 48 " pdb=" CB ILE C 48 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CA VAL A 433 " pdb=" N VAL A 433 " pdb=" C VAL A 433 " pdb=" CB VAL A 433 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 1088 not shown) Planarity restraints: 2068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 496 " 0.029 2.00e-02 2.50e+03 4.99e-02 3.74e+01 pdb=" CD GLN A 496 " -0.057 2.00e-02 2.50e+03 pdb=" OE1 GLN A 496 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 GLN A 496 " 0.086 2.00e-02 2.50e+03 pdb="HE21 GLN A 496 " 0.005 2.00e-02 2.50e+03 pdb="HE22 GLN A 496 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 402 " -0.040 2.00e-02 2.50e+03 4.83e-02 3.49e+01 pdb=" CG ASN A 402 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN A 402 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 402 " 0.075 2.00e-02 2.50e+03 pdb="HD21 ASN A 402 " 0.002 2.00e-02 2.50e+03 pdb="HD22 ASN A 402 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 248 " 0.024 2.00e-02 2.50e+03 2.95e-02 1.31e+01 pdb=" CG ASN A 248 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 248 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 248 " -0.047 2.00e-02 2.50e+03 pdb="HD21 ASN A 248 " -0.000 2.00e-02 2.50e+03 pdb="HD22 ASN A 248 " 0.045 2.00e-02 2.50e+03 ... (remaining 2065 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 509 2.15 - 2.76: 26284 2.76 - 3.37: 37766 3.37 - 3.99: 49393 3.99 - 4.60: 76250 Nonbonded interactions: 190202 Sorted by model distance: nonbonded pdb=" HG1 THR A 367 " pdb=" OG SER A 370 " model vdw 1.533 2.450 nonbonded pdb=" O GLY A 350 " pdb=" H SER A 365 " model vdw 1.562 2.450 nonbonded pdb=" OE1 GLN L 6 " pdb=" H GLY L 101 " model vdw 1.587 2.450 nonbonded pdb=" O GLN L 124 " pdb=" HG SER L 127 " model vdw 1.595 2.450 nonbonded pdb=" H GLN L 79 " pdb=" OD2 ASP L 82 " model vdw 1.600 2.450 ... (remaining 190197 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 26.140 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 29.950 Find NCS groups from input model: 0.110 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7100 Z= 0.226 Angle : 0.634 7.449 9637 Z= 0.342 Chirality : 0.045 0.162 1091 Planarity : 0.006 0.063 1219 Dihedral : 13.699 89.083 2558 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.53 % Favored : 95.36 % Rotamer: Outliers : 2.05 % Allowed : 7.67 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.82 (0.27), residues: 883 helix: -1.07 (0.56), residues: 57 sheet: -0.13 (0.28), residues: 340 loop : -0.72 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP B 100A HIS 0.009 0.003 HIS A 453 PHE 0.015 0.002 PHE A 408 TYR 0.035 0.005 TYR C 87 ARG 0.014 0.002 ARG L 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 222 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TRP cc_start: 0.8376 (t60) cc_final: 0.7900 (t60) REVERT: A 480 THR cc_start: 0.8008 (m) cc_final: 0.7795 (p) REVERT: B 13 GLN cc_start: 0.8050 (mp10) cc_final: 0.7681 (mp10) REVERT: B 33 TYR cc_start: 0.8155 (m-10) cc_final: 0.7904 (m-10) REVERT: B 75 LYS cc_start: 0.8772 (mmtm) cc_final: 0.8565 (mmtt) REVERT: B 101 ASP cc_start: 0.7671 (p0) cc_final: 0.7431 (p0) REVERT: C 106 ILE cc_start: 0.6146 (mm) cc_final: 0.5819 (mm) REVERT: H 194 TYR cc_start: 0.8112 (m-80) cc_final: 0.7898 (m-80) REVERT: H 199 ASN cc_start: 0.8846 (t0) cc_final: 0.8636 (t0) REVERT: L 70 ASP cc_start: 0.8145 (t70) cc_final: 0.7817 (t0) REVERT: L 92 TYR cc_start: 0.8689 (t80) cc_final: 0.8377 (t80) REVERT: L 145 LYS cc_start: 0.8201 (ttmm) cc_final: 0.7939 (mtmm) REVERT: L 167 ASP cc_start: 0.8535 (t70) cc_final: 0.7189 (m-30) outliers start: 16 outliers final: 3 residues processed: 233 average time/residue: 0.5293 time to fit residues: 155.0366 Evaluate side-chains 151 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 148 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain L residue 135 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 422 GLN H 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.143420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.117952 restraints weight = 28537.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.122403 restraints weight = 15608.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.125368 restraints weight = 10276.292| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 7100 Z= 0.418 Angle : 0.731 8.129 9637 Z= 0.390 Chirality : 0.046 0.158 1091 Planarity : 0.004 0.034 1219 Dihedral : 6.460 49.704 979 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.69 % Allowed : 13.17 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.56 (0.28), residues: 883 helix: 0.21 (0.69), residues: 53 sheet: -0.13 (0.28), residues: 342 loop : -0.54 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 100A HIS 0.006 0.002 HIS A 456 PHE 0.015 0.002 PHE H 100B TYR 0.019 0.002 TYR A 465 ARG 0.007 0.001 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6691 (pmm) REVERT: A 286 TRP cc_start: 0.8549 (t60) cc_final: 0.8177 (t60) REVERT: C 18 ARG cc_start: 0.5905 (OUTLIER) cc_final: 0.5559 (ttt-90) REVERT: C 39 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6851 (mtpt) REVERT: H 6 GLU cc_start: 0.8593 (mp0) cc_final: 0.8236 (mp0) REVERT: H 199 ASN cc_start: 0.8912 (t0) cc_final: 0.8700 (t0) REVERT: L 190 LYS cc_start: 0.8474 (tptp) cc_final: 0.8220 (tptp) outliers start: 21 outliers final: 11 residues processed: 165 average time/residue: 0.4390 time to fit residues: 95.5371 Evaluate side-chains 142 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 85 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 78 optimal weight: 0.0870 chunk 44 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN H 164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.144869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.118062 restraints weight = 28602.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122985 restraints weight = 14786.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126242 restraints weight = 9382.847| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7100 Z= 0.206 Angle : 0.608 7.983 9637 Z= 0.316 Chirality : 0.043 0.157 1091 Planarity : 0.004 0.041 1219 Dihedral : 5.725 47.927 976 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.92 % Allowed : 15.35 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.23 (0.29), residues: 883 helix: 0.88 (0.69), residues: 55 sheet: 0.04 (0.28), residues: 348 loop : -0.32 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 100A HIS 0.004 0.001 HIS L 198 PHE 0.009 0.001 PHE L 209 TYR 0.012 0.001 TYR C 93 ARG 0.003 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.6733 (pmm) REVERT: A 286 TRP cc_start: 0.8369 (t60) cc_final: 0.7936 (t60) REVERT: A 395 LEU cc_start: 0.7853 (tp) cc_final: 0.7603 (tp) REVERT: B 13 GLN cc_start: 0.7988 (mp10) cc_final: 0.7664 (mp10) REVERT: H 6 GLU cc_start: 0.8620 (mp0) cc_final: 0.8241 (mp0) REVERT: H 122 PHE cc_start: 0.8460 (m-80) cc_final: 0.7925 (m-80) REVERT: H 199 ASN cc_start: 0.8866 (t0) cc_final: 0.8639 (t0) REVERT: L 167 ASP cc_start: 0.7608 (t70) cc_final: 0.6668 (m-30) outliers start: 15 outliers final: 9 residues processed: 147 average time/residue: 0.4262 time to fit residues: 84.9748 Evaluate side-chains 144 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 41 optimal weight: 0.0370 chunk 75 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN L 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.143176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.116340 restraints weight = 28522.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.121204 restraints weight = 14772.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.124424 restraints weight = 9444.195| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7100 Z= 0.218 Angle : 0.585 8.607 9637 Z= 0.304 Chirality : 0.043 0.152 1091 Planarity : 0.004 0.052 1219 Dihedral : 5.138 21.256 970 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.05 % Allowed : 15.60 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.18 (0.29), residues: 883 helix: 1.15 (0.71), residues: 55 sheet: 0.03 (0.28), residues: 347 loop : -0.29 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 154 HIS 0.004 0.001 HIS L 198 PHE 0.016 0.001 PHE L 209 TYR 0.012 0.001 TYR L 49 ARG 0.005 0.000 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.6771 (pmm) REVERT: A 286 TRP cc_start: 0.8406 (t60) cc_final: 0.7953 (t60) REVERT: B 13 GLN cc_start: 0.8041 (mp10) cc_final: 0.7647 (mp10) REVERT: C 70 ASP cc_start: 0.7376 (t70) cc_final: 0.7157 (m-30) REVERT: C 92 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8220 (t0) REVERT: H 6 GLU cc_start: 0.8584 (mp0) cc_final: 0.8185 (mp0) REVERT: H 199 ASN cc_start: 0.8838 (t0) cc_final: 0.8630 (t0) REVERT: L 167 ASP cc_start: 0.7631 (t70) cc_final: 0.6474 (m-30) REVERT: L 170 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7334 (m-30) outliers start: 16 outliers final: 12 residues processed: 141 average time/residue: 0.3886 time to fit residues: 74.2701 Evaluate side-chains 138 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 174 SER Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 105 GLN L 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.142451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.116070 restraints weight = 29509.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.120440 restraints weight = 16328.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.123374 restraints weight = 10834.990| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7100 Z= 0.281 Angle : 0.592 7.633 9637 Z= 0.309 Chirality : 0.043 0.147 1091 Planarity : 0.003 0.036 1219 Dihedral : 5.072 21.533 970 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.05 % Allowed : 16.88 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.22 (0.29), residues: 883 helix: 1.12 (0.70), residues: 55 sheet: -0.04 (0.28), residues: 334 loop : -0.27 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 100A HIS 0.007 0.001 HIS L 198 PHE 0.011 0.002 PHE L 209 TYR 0.015 0.002 TYR L 49 ARG 0.004 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6870 (pmm) REVERT: A 286 TRP cc_start: 0.8476 (t60) cc_final: 0.8036 (t60) REVERT: C 39 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.7037 (mtpt) REVERT: H 6 GLU cc_start: 0.8562 (mp0) cc_final: 0.8192 (mp0) REVERT: L 167 ASP cc_start: 0.7665 (t70) cc_final: 0.6303 (m-30) REVERT: L 170 ASP cc_start: 0.7590 (m-30) cc_final: 0.7203 (m-30) outliers start: 16 outliers final: 12 residues processed: 140 average time/residue: 0.4293 time to fit residues: 80.0255 Evaluate side-chains 134 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 187 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 61 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN L 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.144264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.117587 restraints weight = 29317.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.122135 restraints weight = 15733.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.125183 restraints weight = 10333.291| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7100 Z= 0.186 Angle : 0.555 7.770 9637 Z= 0.285 Chirality : 0.043 0.149 1091 Planarity : 0.003 0.035 1219 Dihedral : 4.852 19.854 970 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.17 % Allowed : 16.88 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.12 (0.29), residues: 883 helix: 1.37 (0.72), residues: 55 sheet: 0.02 (0.29), residues: 333 loop : -0.23 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 100A HIS 0.004 0.001 HIS L 198 PHE 0.011 0.001 PHE L 209 TYR 0.010 0.001 TYR L 49 ARG 0.004 0.000 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6805 (pmm) REVERT: A 286 TRP cc_start: 0.8438 (t60) cc_final: 0.7946 (t60) REVERT: H 6 GLU cc_start: 0.8535 (mp0) cc_final: 0.8114 (mp0) REVERT: H 16 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6481 (tp30) REVERT: H 122 PHE cc_start: 0.7652 (m-80) cc_final: 0.7236 (m-10) REVERT: H 142 VAL cc_start: 0.9207 (m) cc_final: 0.8823 (p) REVERT: L 167 ASP cc_start: 0.7643 (t70) cc_final: 0.6217 (m-30) outliers start: 17 outliers final: 12 residues processed: 142 average time/residue: 0.4583 time to fit residues: 89.2320 Evaluate side-chains 139 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 187 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 72 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 GLN B 105 GLN L 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.142801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.116402 restraints weight = 29555.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.120784 restraints weight = 16266.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.123691 restraints weight = 10786.597| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7100 Z= 0.256 Angle : 0.582 7.749 9637 Z= 0.300 Chirality : 0.043 0.149 1091 Planarity : 0.003 0.034 1219 Dihedral : 4.881 20.796 970 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.05 % Allowed : 16.75 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.24 (0.29), residues: 883 helix: 1.34 (0.73), residues: 55 sheet: -0.09 (0.29), residues: 333 loop : -0.29 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 148 HIS 0.004 0.001 HIS L 198 PHE 0.013 0.002 PHE H 122 TYR 0.015 0.001 TYR L 49 ARG 0.005 0.001 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TRP cc_start: 0.8459 (t60) cc_final: 0.7938 (t60) REVERT: H 6 GLU cc_start: 0.8552 (mp0) cc_final: 0.8105 (mp0) REVERT: H 16 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6491 (tp30) REVERT: H 142 VAL cc_start: 0.9227 (m) cc_final: 0.8854 (p) REVERT: L 167 ASP cc_start: 0.7584 (t70) cc_final: 0.6119 (m-30) outliers start: 16 outliers final: 12 residues processed: 139 average time/residue: 0.4300 time to fit residues: 79.4161 Evaluate side-chains 136 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 187 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.142367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.116054 restraints weight = 29435.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.120403 restraints weight = 16200.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.123265 restraints weight = 10774.214| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7100 Z= 0.241 Angle : 0.570 7.796 9637 Z= 0.293 Chirality : 0.043 0.150 1091 Planarity : 0.003 0.034 1219 Dihedral : 4.864 20.580 970 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.56 % Allowed : 16.37 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.31 (0.29), residues: 883 helix: 1.43 (0.73), residues: 55 sheet: -0.10 (0.29), residues: 331 loop : -0.39 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 100A HIS 0.003 0.001 HIS L 198 PHE 0.010 0.002 PHE L 209 TYR 0.013 0.001 TYR L 49 ARG 0.005 0.000 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 GLU cc_start: 0.8186 (tt0) cc_final: 0.7921 (mt-10) REVERT: H 6 GLU cc_start: 0.8548 (mp0) cc_final: 0.8084 (mp0) REVERT: H 16 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6580 (tp30) REVERT: H 142 VAL cc_start: 0.9221 (m) cc_final: 0.8854 (p) REVERT: L 167 ASP cc_start: 0.7652 (t70) cc_final: 0.6078 (m-30) outliers start: 20 outliers final: 14 residues processed: 141 average time/residue: 0.4299 time to fit residues: 81.7400 Evaluate side-chains 138 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 187 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 76 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 GLN A 476 ASN B 105 GLN L 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.142691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.116173 restraints weight = 29235.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.120710 restraints weight = 15742.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123658 restraints weight = 10323.962| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.5572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7100 Z= 0.205 Angle : 0.565 7.829 9637 Z= 0.289 Chirality : 0.043 0.158 1091 Planarity : 0.003 0.033 1219 Dihedral : 4.773 19.665 970 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.79 % Allowed : 17.39 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.26 (0.29), residues: 883 helix: 1.57 (0.73), residues: 55 sheet: -0.12 (0.29), residues: 334 loop : -0.33 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 100A HIS 0.003 0.001 HIS L 198 PHE 0.010 0.001 PHE L 209 TYR 0.011 0.001 TYR A 465 ARG 0.005 0.000 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 GLU cc_start: 0.8145 (tt0) cc_final: 0.7899 (mt-10) REVERT: C 42 ARG cc_start: 0.7727 (tpp80) cc_final: 0.7323 (tpp80) REVERT: H 6 GLU cc_start: 0.8534 (mp0) cc_final: 0.8081 (mp0) REVERT: H 16 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6556 (tp30) outliers start: 14 outliers final: 13 residues processed: 137 average time/residue: 0.4256 time to fit residues: 77.7955 Evaluate side-chains 137 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 187 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 72 optimal weight: 0.0050 chunk 8 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN B 105 GLN L 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.142380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.115727 restraints weight = 29623.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.120275 restraints weight = 15935.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.123255 restraints weight = 10463.376| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7100 Z= 0.224 Angle : 0.569 7.838 9637 Z= 0.291 Chirality : 0.043 0.156 1091 Planarity : 0.003 0.033 1219 Dihedral : 4.774 20.047 970 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.66 % Allowed : 17.77 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.33 (0.29), residues: 883 helix: 1.58 (0.74), residues: 55 sheet: -0.19 (0.29), residues: 334 loop : -0.36 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 100A HIS 0.003 0.001 HIS L 198 PHE 0.025 0.002 PHE H 122 TYR 0.012 0.001 TYR L 49 ARG 0.005 0.000 ARG C 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1766 Ramachandran restraints generated. 883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 GLU cc_start: 0.8151 (tt0) cc_final: 0.7925 (mt-10) REVERT: A 432 VAL cc_start: 0.9397 (t) cc_final: 0.9185 (p) REVERT: C 42 ARG cc_start: 0.7744 (tpp80) cc_final: 0.7369 (tpp80) REVERT: H 6 GLU cc_start: 0.8514 (mp0) cc_final: 0.8058 (mp0) REVERT: H 16 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6518 (tp30) REVERT: H 212 GLU cc_start: 0.7418 (pt0) cc_final: 0.7180 (pt0) outliers start: 13 outliers final: 12 residues processed: 138 average time/residue: 0.4311 time to fit residues: 79.5371 Evaluate side-chains 139 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 187 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.140957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.114509 restraints weight = 29670.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.118981 restraints weight = 16076.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.121919 restraints weight = 10599.676| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7100 Z= 0.276 Angle : 0.587 7.835 9637 Z= 0.303 Chirality : 0.043 0.155 1091 Planarity : 0.003 0.034 1219 Dihedral : 4.871 21.097 970 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.66 % Allowed : 18.29 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.46 (0.29), residues: 883 helix: 1.42 (0.73), residues: 55 sheet: -0.22 (0.29), residues: 330 loop : -0.49 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 100A HIS 0.003 0.001 HIS L 198 PHE 0.011 0.002 PHE C 71 TYR 0.015 0.002 TYR L 49 ARG 0.006 0.001 ARG C 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5003.94 seconds wall clock time: 90 minutes 30.66 seconds (5430.66 seconds total)