Starting phenix.real_space_refine on Tue Aug 6 05:02:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vww_43604/08_2024/8vww_43604.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vww_43604/08_2024/8vww_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vww_43604/08_2024/8vww_43604.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vww_43604/08_2024/8vww_43604.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vww_43604/08_2024/8vww_43604.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vww_43604/08_2024/8vww_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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 7.56, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 11.32 Conformation dependent library (CDL) restraints added in 1.6 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: 1.54 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: 5.62 Time building geometry restraints manager: 11.86 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: 100.04 - 106.83: 240 106.83 - 113.62: 16573 113.62 - 120.40: 4299 120.40 - 127.19: 3980 127.19 - 133.98: 81 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: 10.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.230 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 48.780 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.810 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 16 poor density : 222 time to evaluate : 1.132 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: 0.5050 time to fit residues: 147.7875 Evaluate side-chains 151 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 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 fitting. rotamer outliers: 21 poor density : 155 time to evaluate : 1.088 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: 0.7165 (OUTLIER) cc_final: 0.6701 (pmm) REVERT: A 286 TRP cc_start: 0.8514 (t60) cc_final: 0.8088 (t60) REVERT: A 475 LEU cc_start: 0.9082 (mt) cc_final: 0.8880 (mt) REVERT: A 480 THR cc_start: 0.7697 (m) cc_final: 0.7486 (p) REVERT: B 13 GLN cc_start: 0.8286 (mp10) cc_final: 0.8045 (mp10) REVERT: C 18 ARG cc_start: 0.5974 (OUTLIER) cc_final: 0.5685 (ttt-90) REVERT: C 39 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6774 (mtpt) REVERT: H 6 GLU cc_start: 0.8639 (mp0) cc_final: 0.8206 (mp0) REVERT: H 16 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.7022 (tp30) REVERT: H 199 ASN cc_start: 0.8914 (t0) cc_final: 0.8674 (t0) REVERT: L 190 LYS cc_start: 0.8547 (tptp) cc_final: 0.8203 (tptp) outliers start: 21 outliers final: 11 residues processed: 165 average time/residue: 0.4288 time to fit residues: 92.9353 Evaluate side-chains 143 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 16 GLU 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 43 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 79 optimal weight: 0.0870 chunk 85 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 78 optimal weight: 0.1980 chunk 26 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7100 Z= 0.219 Angle : 0.606 7.982 9637 Z= 0.315 Chirality : 0.043 0.156 1091 Planarity : 0.003 0.033 1219 Dihedral : 5.714 47.825 976 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.92 % Allowed : 15.22 % Favored : 82.86 % 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: -0.21 (0.29), residues: 883 helix: 0.86 (0.70), residues: 55 sheet: 0.05 (0.28), residues: 343 loop : -0.31 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 148 HIS 0.004 0.001 HIS L 198 PHE 0.008 0.001 PHE L 209 TYR 0.013 0.002 TYR L 87 ARG 0.005 0.000 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 153 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 1.064 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 251 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6868 (pmm) REVERT: A 286 TRP cc_start: 0.8346 (t60) cc_final: 0.7859 (t60) REVERT: B 13 GLN cc_start: 0.8303 (mp10) cc_final: 0.8081 (mp10) REVERT: C 79 GLN cc_start: 0.8195 (mm110) cc_final: 0.7888 (mp10) REVERT: H 6 GLU cc_start: 0.8675 (mp0) cc_final: 0.8218 (mp0) REVERT: H 122 PHE cc_start: 0.8566 (m-80) cc_final: 0.8051 (m-80) REVERT: H 199 ASN cc_start: 0.8876 (t0) cc_final: 0.8621 (t0) REVERT: L 167 ASP cc_start: 0.7858 (t70) cc_final: 0.6791 (m-30) outliers start: 15 outliers final: 9 residues processed: 148 average time/residue: 0.3901 time to fit residues: 77.2756 Evaluate side-chains 145 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 78 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7100 Z= 0.250 Angle : 0.595 7.869 9637 Z= 0.310 Chirality : 0.043 0.151 1091 Planarity : 0.004 0.048 1219 Dihedral : 5.229 21.445 970 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.92 % Allowed : 15.73 % 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: -0.23 (0.29), residues: 883 helix: 1.01 (0.71), residues: 55 sheet: 0.01 (0.28), residues: 342 loop : -0.32 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 154 HIS 0.004 0.001 HIS A 456 PHE 0.014 0.002 PHE L 209 TYR 0.013 0.002 TYR L 49 ARG 0.006 0.001 ARG A 490 *********************** 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 147 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 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: A 251 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6884 (pmm) REVERT: A 286 TRP cc_start: 0.8386 (t60) cc_final: 0.7875 (t60) REVERT: B 13 GLN cc_start: 0.8339 (mp10) cc_final: 0.8132 (mp10) REVERT: C 70 ASP cc_start: 0.7424 (t70) cc_final: 0.7032 (m-30) REVERT: C 79 GLN cc_start: 0.8201 (mm110) cc_final: 0.7896 (mp10) REVERT: C 92 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.8019 (t0) REVERT: H 6 GLU cc_start: 0.8640 (mp0) cc_final: 0.8197 (mp0) REVERT: H 199 ASN cc_start: 0.8866 (t0) cc_final: 0.8629 (t0) REVERT: L 167 ASP cc_start: 0.7803 (t70) cc_final: 0.6622 (m-30) REVERT: L 170 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7745 (m-30) outliers start: 15 outliers final: 10 residues processed: 143 average time/residue: 0.4053 time to fit residues: 80.0408 Evaluate side-chains 139 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 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 180 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 71 optimal weight: 0.0870 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN L 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7100 Z= 0.241 Angle : 0.579 7.522 9637 Z= 0.301 Chirality : 0.043 0.151 1091 Planarity : 0.003 0.050 1219 Dihedral : 5.054 21.056 970 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.30 % Allowed : 16.24 % Favored : 81.46 % 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: -0.19 (0.29), residues: 883 helix: 1.16 (0.70), residues: 55 sheet: -0.02 (0.29), residues: 329 loop : -0.26 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 154 HIS 0.007 0.001 HIS L 198 PHE 0.011 0.001 PHE L 209 TYR 0.013 0.001 TYR L 49 ARG 0.007 0.001 ARG C 18 *********************** 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 151 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 1.054 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: 0.7164 (OUTLIER) cc_final: 0.6901 (pmm) REVERT: A 286 TRP cc_start: 0.8395 (t60) cc_final: 0.7888 (t60) REVERT: C 39 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6878 (mtpt) REVERT: C 70 ASP cc_start: 0.7370 (t70) cc_final: 0.7071 (m-30) REVERT: C 79 GLN cc_start: 0.8156 (mm110) cc_final: 0.7871 (mp10) REVERT: H 6 GLU cc_start: 0.8623 (mp0) cc_final: 0.8108 (mp0) REVERT: H 199 ASN cc_start: 0.8868 (t0) cc_final: 0.8628 (t0) REVERT: L 167 ASP cc_start: 0.7926 (t70) cc_final: 0.6515 (m-30) REVERT: L 170 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7763 (m-30) outliers start: 18 outliers final: 12 residues processed: 145 average time/residue: 0.4225 time to fit residues: 81.7181 Evaluate side-chains 141 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 99 SER Chi-restraints excluded: chain C residue 11 LEU 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 170 ASP 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 75 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 C 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7100 Z= 0.285 Angle : 0.592 7.677 9637 Z= 0.308 Chirality : 0.043 0.150 1091 Planarity : 0.004 0.039 1219 Dihedral : 5.036 21.578 970 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.56 % Allowed : 16.50 % 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: -0.28 (0.29), residues: 883 helix: 1.19 (0.71), residues: 55 sheet: -0.09 (0.29), residues: 329 loop : -0.33 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 100A HIS 0.005 0.001 HIS L 198 PHE 0.011 0.002 PHE L 209 TYR 0.016 0.002 TYR L 49 ARG 0.005 0.001 ARG B 38 *********************** 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 151 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.124 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 251 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.7042 (pmm) REVERT: A 286 TRP cc_start: 0.8413 (t60) cc_final: 0.7903 (t60) REVERT: C 70 ASP cc_start: 0.7373 (t70) cc_final: 0.7166 (m-30) REVERT: C 79 GLN cc_start: 0.8116 (mm110) cc_final: 0.7847 (mp10) REVERT: H 6 GLU cc_start: 0.8630 (mp0) cc_final: 0.8108 (mp0) REVERT: H 142 VAL cc_start: 0.9095 (m) cc_final: 0.8705 (p) REVERT: H 192 GLN cc_start: 0.6882 (tt0) cc_final: 0.6338 (mt0) REVERT: H 199 ASN cc_start: 0.8880 (t0) cc_final: 0.8655 (t0) REVERT: L 167 ASP cc_start: 0.7927 (t70) cc_final: 0.6428 (m-30) REVERT: L 170 ASP cc_start: 0.8159 (m-30) cc_final: 0.7787 (t0) outliers start: 20 outliers final: 13 residues processed: 146 average time/residue: 0.4208 time to fit residues: 82.6759 Evaluate side-chains 141 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASN 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 386 ASP 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 24 VAL Chi-restraints excluded: chain H residue 96 ASP 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 9 optimal weight: 0.0770 chunk 47 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 52 optimal weight: 0.0170 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7100 Z= 0.179 Angle : 0.561 7.881 9637 Z= 0.286 Chirality : 0.043 0.154 1091 Planarity : 0.003 0.036 1219 Dihedral : 4.802 19.052 970 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.66 % Allowed : 17.26 % 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: -0.17 (0.29), residues: 883 helix: 1.46 (0.72), residues: 55 sheet: -0.08 (0.28), residues: 341 loop : -0.23 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 148 HIS 0.004 0.001 HIS L 198 PHE 0.013 0.001 PHE H 122 TYR 0.009 0.001 TYR L 49 ARG 0.004 0.000 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 143 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 1.051 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: A 251 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6984 (pmm) REVERT: A 306 GLU cc_start: 0.7910 (tt0) cc_final: 0.7659 (mt-10) REVERT: C 79 GLN cc_start: 0.8089 (mm110) cc_final: 0.7678 (mp10) REVERT: H 6 GLU cc_start: 0.8623 (mp0) cc_final: 0.8065 (mp0) REVERT: H 192 GLN cc_start: 0.6892 (tt0) cc_final: 0.6204 (mt0) REVERT: H 199 ASN cc_start: 0.8875 (t0) cc_final: 0.8653 (t0) REVERT: L 167 ASP cc_start: 0.7894 (t70) cc_final: 0.6364 (m-30) REVERT: L 170 ASP cc_start: 0.8108 (m-30) cc_final: 0.7790 (t0) outliers start: 13 outliers final: 8 residues processed: 139 average time/residue: 0.4024 time to fit residues: 74.6469 Evaluate side-chains 132 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 24 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 47 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7100 Z= 0.192 Angle : 0.555 7.819 9637 Z= 0.284 Chirality : 0.043 0.155 1091 Planarity : 0.003 0.035 1219 Dihedral : 4.747 19.540 970 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.41 % Allowed : 17.77 % 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: -0.18 (0.29), residues: 883 helix: 1.57 (0.73), residues: 55 sheet: -0.08 (0.28), residues: 340 loop : -0.25 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 0.004 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 137 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 1.131 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 251 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.7044 (pmm) REVERT: A 306 GLU cc_start: 0.7911 (tt0) cc_final: 0.7672 (mt-10) REVERT: C 79 GLN cc_start: 0.8094 (mm110) cc_final: 0.7672 (mp10) REVERT: H 6 GLU cc_start: 0.8599 (mp0) cc_final: 0.8004 (mp0) REVERT: H 192 GLN cc_start: 0.6813 (tt0) cc_final: 0.6183 (mt0) REVERT: H 199 ASN cc_start: 0.8881 (t0) cc_final: 0.8647 (t0) REVERT: L 70 ASP cc_start: 0.7668 (t0) cc_final: 0.7433 (p0) REVERT: L 167 ASP cc_start: 0.7897 (t70) cc_final: 0.6364 (m-30) REVERT: L 170 ASP cc_start: 0.8105 (m-30) cc_final: 0.7873 (t0) outliers start: 11 outliers final: 9 residues processed: 135 average time/residue: 0.4229 time to fit residues: 75.6112 Evaluate side-chains 133 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 24 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 96 ASP 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 34 optimal weight: 0.0270 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7100 Z= 0.183 Angle : 0.551 7.848 9637 Z= 0.280 Chirality : 0.043 0.155 1091 Planarity : 0.003 0.035 1219 Dihedral : 4.635 18.963 970 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.41 % Allowed : 18.16 % Favored : 80.43 % 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: -0.16 (0.29), residues: 883 helix: 1.73 (0.74), residues: 55 sheet: -0.10 (0.28), residues: 341 loop : -0.23 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 154 HIS 0.003 0.001 HIS L 198 PHE 0.011 0.001 PHE L 209 TYR 0.010 0.001 TYR A 465 ARG 0.008 0.000 ARG B 94 *********************** 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 139 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 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: A 306 GLU cc_start: 0.7894 (tt0) cc_final: 0.7676 (mt-10) REVERT: B 31 SER cc_start: 0.8387 (t) cc_final: 0.8047 (p) REVERT: B 34 MET cc_start: 0.8401 (mmm) cc_final: 0.7860 (mmp) REVERT: B 82 MET cc_start: 0.7974 (mmm) cc_final: 0.7658 (mmm) REVERT: B 105 GLN cc_start: 0.8580 (mm-40) cc_final: 0.7388 (pp30) REVERT: C 79 GLN cc_start: 0.8098 (mm110) cc_final: 0.7703 (mp10) REVERT: H 6 GLU cc_start: 0.8585 (mp0) cc_final: 0.7981 (mp0) REVERT: H 192 GLN cc_start: 0.6748 (tt0) cc_final: 0.6289 (mt0) REVERT: H 212 GLU cc_start: 0.7567 (pt0) cc_final: 0.7262 (pt0) REVERT: L 167 ASP cc_start: 0.7845 (t70) cc_final: 0.6298 (m-30) REVERT: L 170 ASP cc_start: 0.8112 (m-30) cc_final: 0.7852 (t0) outliers start: 11 outliers final: 9 residues processed: 137 average time/residue: 0.4222 time to fit residues: 78.4067 Evaluate side-chains 134 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 24 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 54 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 63 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7100 Z= 0.207 Angle : 0.557 7.876 9637 Z= 0.284 Chirality : 0.043 0.155 1091 Planarity : 0.003 0.035 1219 Dihedral : 4.647 19.758 970 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.28 % Allowed : 18.41 % Favored : 80.31 % 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: 1.60 (0.73), residues: 55 sheet: -0.16 (0.28), residues: 341 loop : -0.24 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 0.001 ARG B 94 ********************** 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 138 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 1.129 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: 0.7904 (tt0) cc_final: 0.7699 (mt-10) REVERT: A 432 VAL cc_start: 0.9291 (t) cc_final: 0.9045 (p) REVERT: B 31 SER cc_start: 0.8359 (t) cc_final: 0.8067 (p) REVERT: B 82 MET cc_start: 0.7993 (mmm) cc_final: 0.7691 (mmm) REVERT: C 79 GLN cc_start: 0.8158 (mm110) cc_final: 0.7736 (mp10) REVERT: H 6 GLU cc_start: 0.8568 (mp0) cc_final: 0.7987 (mp0) REVERT: H 192 GLN cc_start: 0.6798 (tt0) cc_final: 0.6357 (mt0) REVERT: H 212 GLU cc_start: 0.7572 (pt0) cc_final: 0.7271 (pt0) REVERT: L 167 ASP cc_start: 0.7859 (t70) cc_final: 0.6300 (m-30) REVERT: L 170 ASP cc_start: 0.8123 (m-30) cc_final: 0.7841 (t0) outliers start: 10 outliers final: 9 residues processed: 136 average time/residue: 0.3985 time to fit residues: 72.9918 Evaluate side-chains 137 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 24 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.9990 chunk 69 optimal weight: 0.0570 chunk 28 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.0870 chunk 60 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.5876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN B 32 ASN B 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.141838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114251 restraints weight = 29257.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119133 restraints weight = 15174.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122337 restraints weight = 9693.074| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7100 Z= 0.199 Angle : 0.558 7.877 9637 Z= 0.283 Chirality : 0.043 0.157 1091 Planarity : 0.003 0.035 1219 Dihedral : 4.616 19.261 970 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.28 % Allowed : 18.29 % Favored : 80.43 % 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: 1.60 (0.73), residues: 55 sheet: -0.15 (0.29), residues: 341 loop : -0.26 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 100A HIS 0.004 0.001 HIS L 198 PHE 0.010 0.001 PHE L 209 TYR 0.011 0.001 TYR A 465 ARG 0.006 0.001 ARG B 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4065.43 seconds wall clock time: 71 minutes 34.12 seconds (4294.12 seconds total)