Starting phenix.real_space_refine on Tue Mar 3 13:24:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qtk_14143/03_2026/7qtk_14143.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qtk_14143/03_2026/7qtk_14143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qtk_14143/03_2026/7qtk_14143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qtk_14143/03_2026/7qtk_14143.map" model { file = "/net/cci-nas-00/data/ceres_data/7qtk_14143/03_2026/7qtk_14143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qtk_14143/03_2026/7qtk_14143.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 3171 2.51 5 N 845 2.21 5 O 974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5009 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "C" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.39, per 1000 atoms: 0.28 Number of scatterers: 5009 At special positions: 0 Unit cell: (71.9316, 103.747, 125.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 974 8.00 N 845 7.00 C 3171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.05 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN D 343 " Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 317.5 milliseconds 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1194 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 13 sheets defined 11.7% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'D' and resid 337 through 343 removed outlier: 4.320A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 372 removed outlier: 3.875A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 removed outlier: 4.035A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.756A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.766A pdb=" N ASP B 31 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.853A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 removed outlier: 3.654A pdb=" N LYS C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 189 removed outlier: 3.731A pdb=" N HIS C 189 " --> pdb=" O ASP C 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 354 through 358 removed outlier: 4.132A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'D' and resid 473 through 474 removed outlier: 4.001A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.334A pdb=" N GLY B 10 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 50 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 59 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.334A pdb=" N GLY B 10 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE B 114 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 132 through 136 removed outlier: 3.547A pdb=" N GLY B 151 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 143 through 144 Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 166 removed outlier: 3.650A pdb=" N THR B 163 " --> pdb=" O ASN B 211 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR B 206 " --> pdb=" O VAL B 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.665A pdb=" N VAL C 19 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 13 removed outlier: 7.135A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 114 through 118 removed outlier: 3.804A pdb=" N VAL C 133 " --> pdb=" O PHE C 118 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR C 173 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 153 through 155 removed outlier: 4.260A pdb=" N TRP C 148 " --> pdb=" O GLN C 155 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS C 145 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C 207 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL C 196 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 205 " --> pdb=" O VAL C 196 " (cutoff:3.500A) 164 hydrogen bonds defined for protein. 408 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: 0.82 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 859 1.32 - 1.45: 1457 1.45 - 1.57: 2798 1.57 - 1.69: 0 1.69 - 1.82: 20 Bond restraints: 5134 Sorted by residual: bond pdb=" N VAL C 96 " pdb=" CA VAL C 96 " ideal model delta sigma weight residual 1.457 1.509 -0.052 1.32e-02 5.74e+03 1.53e+01 bond pdb=" CA SER C 93 " pdb=" CB SER C 93 " ideal model delta sigma weight residual 1.530 1.470 0.060 1.69e-02 3.50e+03 1.26e+01 bond pdb=" N THR C 109 " pdb=" CA THR C 109 " ideal model delta sigma weight residual 1.455 1.498 -0.042 1.33e-02 5.65e+03 1.00e+01 bond pdb=" N VAL C 110 " pdb=" CA VAL C 110 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.22e-02 6.72e+03 9.37e+00 bond pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.23e-02 6.61e+03 8.45e+00 ... (remaining 5129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 6696 1.64 - 3.28: 220 3.28 - 4.92: 50 4.92 - 6.57: 13 6.57 - 8.21: 4 Bond angle restraints: 6983 Sorted by residual: angle pdb=" C VAL C 96 " pdb=" N THR C 97 " pdb=" CA THR C 97 " ideal model delta sigma weight residual 122.39 115.93 6.46 1.48e+00 4.57e-01 1.90e+01 angle pdb=" N PRO C 95 " pdb=" CA PRO C 95 " pdb=" C PRO C 95 " ideal model delta sigma weight residual 112.47 104.26 8.21 2.06e+00 2.36e-01 1.59e+01 angle pdb=" N TYR C 94 " pdb=" CA TYR C 94 " pdb=" CB TYR C 94 " ideal model delta sigma weight residual 110.37 117.38 -7.01 1.78e+00 3.16e-01 1.55e+01 angle pdb=" CA TYR C 94 " pdb=" C TYR C 94 " pdb=" N PRO C 95 " ideal model delta sigma weight residual 118.44 124.39 -5.95 1.59e+00 3.96e-01 1.40e+01 angle pdb=" CA LYS B 129 " pdb=" C LYS B 129 " pdb=" O LYS B 129 " ideal model delta sigma weight residual 121.40 117.32 4.08 1.11e+00 8.12e-01 1.35e+01 ... (remaining 6978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 2781 16.64 - 33.28: 240 33.28 - 49.92: 47 49.92 - 66.56: 13 66.56 - 83.20: 4 Dihedral angle restraints: 3085 sinusoidal: 1216 harmonic: 1869 Sorted by residual: dihedral pdb=" N TYR C 94 " pdb=" C TYR C 94 " pdb=" CA TYR C 94 " pdb=" CB TYR C 94 " ideal model delta harmonic sigma weight residual 122.80 138.48 -15.68 0 2.50e+00 1.60e-01 3.93e+01 dihedral pdb=" C TYR C 94 " pdb=" N TYR C 94 " pdb=" CA TYR C 94 " pdb=" CB TYR C 94 " ideal model delta harmonic sigma weight residual -122.60 -135.93 13.33 0 2.50e+00 1.60e-01 2.84e+01 dihedral pdb=" CB CYS D 391 " pdb=" SG CYS D 391 " pdb=" SG CYS D 525 " pdb=" CB CYS D 525 " ideal model delta sinusoidal sigma weight residual 93.00 50.33 42.67 1 1.00e+01 1.00e-02 2.54e+01 ... (remaining 3082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 755 0.122 - 0.245: 18 0.245 - 0.367: 1 0.367 - 0.489: 0 0.489 - 0.611: 1 Chirality restraints: 775 Sorted by residual: chirality pdb=" CA TYR C 94 " pdb=" N TYR C 94 " pdb=" C TYR C 94 " pdb=" CB TYR C 94 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.34e+00 chirality pdb=" CA VAL B 123 " pdb=" N VAL B 123 " pdb=" C VAL B 123 " pdb=" CB VAL B 123 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA LYS B 129 " pdb=" N LYS B 129 " pdb=" C LYS B 129 " pdb=" CB LYS B 129 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 772 not shown) Planarity restraints: 899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS C 92 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C HIS C 92 " 0.047 2.00e-02 2.50e+03 pdb=" O HIS C 92 " -0.017 2.00e-02 2.50e+03 pdb=" N SER C 93 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 97 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C THR C 97 " -0.033 2.00e-02 2.50e+03 pdb=" O THR C 97 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE C 98 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 94 " 0.018 2.00e-02 2.50e+03 1.06e-02 2.23e+00 pdb=" CG TYR C 94 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR C 94 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 94 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 94 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 94 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 94 " 0.005 2.00e-02 2.50e+03 ... (remaining 896 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 260 2.73 - 3.27: 4783 3.27 - 3.81: 7745 3.81 - 4.36: 9078 4.36 - 4.90: 15883 Nonbonded interactions: 37749 Sorted by model distance: nonbonded pdb=" OD1 ASP B 99 " pdb=" N ARG B 100 " model vdw 2.182 3.120 nonbonded pdb=" OG SER C 14 " pdb=" OD2 ASP C 17 " model vdw 2.210 3.040 nonbonded pdb=" OE2 GLU D 406 " pdb=" NE2 GLN D 409 " model vdw 2.279 3.120 nonbonded pdb=" O TYR C 192 " pdb=" OG SER C 208 " model vdw 2.287 3.040 nonbonded pdb=" OG SER B 17 " pdb=" ND2 ASN B 84 " model vdw 2.299 3.120 ... (remaining 37744 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: 2.670 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.840 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 : 0.004 0.060 5145 Z= 0.238 Angle : 0.739 8.208 7007 Z= 0.421 Chirality : 0.054 0.611 775 Planarity : 0.004 0.033 898 Dihedral : 13.163 83.203 1864 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.87 % Favored : 94.98 % Rotamer: Outliers : 0.54 % Allowed : 1.44 % Favored : 98.02 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.34), residues: 637 helix: -2.54 (0.93), residues: 22 sheet: 0.89 (0.34), residues: 244 loop : -0.47 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 18 TYR 0.023 0.002 TYR C 94 PHE 0.019 0.001 PHE D 392 TRP 0.007 0.001 TRP B 115 HIS 0.003 0.001 HIS C 189 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 5134) covalent geometry : angle 0.73100 ( 6983) SS BOND : bond 0.00509 ( 9) SS BOND : angle 0.50101 ( 18) hydrogen bonds : bond 0.24191 ( 152) hydrogen bonds : angle 9.12790 ( 408) link_BETA1-4 : bond 0.00437 ( 1) link_BETA1-4 : angle 4.18155 ( 3) link_NAG-ASN : bond 0.00062 ( 1) link_NAG-ASN : angle 3.35267 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.184 Fit side-chains REVERT: B 89 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7709 (mp0) REVERT: B 152 CYS cc_start: 0.3391 (m) cc_final: 0.3030 (m) REVERT: B 216 ASN cc_start: 0.7341 (m-40) cc_final: 0.6990 (p0) REVERT: C 49 TYR cc_start: 0.8696 (p90) cc_final: 0.8487 (p90) outliers start: 3 outliers final: 0 residues processed: 84 average time/residue: 0.1018 time to fit residues: 10.3691 Evaluate side-chains 61 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 7.9990 chunk 24 optimal weight: 0.4980 chunk 48 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN B 183 GLN B 209 ASN ** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.122884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.097818 restraints weight = 11986.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.099580 restraints weight = 8166.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.100776 restraints weight = 6364.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.101419 restraints weight = 5400.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.102014 restraints weight = 4897.955| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5145 Z= 0.175 Angle : 0.670 10.876 7007 Z= 0.344 Chirality : 0.048 0.364 775 Planarity : 0.004 0.034 898 Dihedral : 6.066 49.426 744 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 1.08 % Allowed : 9.37 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.34), residues: 637 helix: -2.47 (0.82), residues: 28 sheet: 0.83 (0.34), residues: 243 loop : -0.69 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 67 TYR 0.020 0.002 TYR D 369 PHE 0.015 0.001 PHE B 29 TRP 0.016 0.002 TRP B 166 HIS 0.004 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 5134) covalent geometry : angle 0.66449 ( 6983) SS BOND : bond 0.00413 ( 9) SS BOND : angle 0.83834 ( 18) hydrogen bonds : bond 0.03831 ( 152) hydrogen bonds : angle 6.57399 ( 408) link_BETA1-4 : bond 0.00191 ( 1) link_BETA1-4 : angle 2.82538 ( 3) link_NAG-ASN : bond 0.00337 ( 1) link_NAG-ASN : angle 2.81389 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.199 Fit side-chains REVERT: B 89 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7712 (mp0) REVERT: B 114 ILE cc_start: 0.9074 (mm) cc_final: 0.8757 (mm) REVERT: B 216 ASN cc_start: 0.7016 (m-40) cc_final: 0.6295 (p0) outliers start: 6 outliers final: 2 residues processed: 72 average time/residue: 0.1065 time to fit residues: 9.2472 Evaluate side-chains 64 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 52 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.123247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.098075 restraints weight = 11886.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.100165 restraints weight = 7554.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.101486 restraints weight = 5637.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.102363 restraints weight = 4684.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.102766 restraints weight = 4151.705| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5145 Z= 0.180 Angle : 0.669 10.664 7007 Z= 0.340 Chirality : 0.048 0.377 775 Planarity : 0.004 0.037 898 Dihedral : 5.897 50.041 744 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.49 % Favored : 94.35 % Rotamer: Outliers : 0.90 % Allowed : 12.61 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.34), residues: 637 helix: -2.39 (0.89), residues: 28 sheet: 0.72 (0.34), residues: 243 loop : -0.81 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 100 TYR 0.029 0.002 TYR C 49 PHE 0.022 0.002 PHE B 29 TRP 0.011 0.001 TRP B 115 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 5134) covalent geometry : angle 0.66206 ( 6983) SS BOND : bond 0.00491 ( 9) SS BOND : angle 0.96807 ( 18) hydrogen bonds : bond 0.03570 ( 152) hydrogen bonds : angle 6.15459 ( 408) link_BETA1-4 : bond 0.00215 ( 1) link_BETA1-4 : angle 3.09279 ( 3) link_NAG-ASN : bond 0.00484 ( 1) link_NAG-ASN : angle 2.99841 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.175 Fit side-chains REVERT: D 378 LYS cc_start: 0.9000 (ttpt) cc_final: 0.8657 (pttm) REVERT: D 406 GLU cc_start: 0.8336 (pt0) cc_final: 0.8010 (pt0) REVERT: B 28 ARG cc_start: 0.7643 (ttp80) cc_final: 0.7174 (ttp80) REVERT: B 29 PHE cc_start: 0.8329 (t80) cc_final: 0.8120 (t80) REVERT: B 89 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7764 (mp0) REVERT: B 209 ASN cc_start: 0.6909 (OUTLIER) cc_final: 0.6563 (m-40) REVERT: C 18 ARG cc_start: 0.7024 (tpp80) cc_final: 0.6653 (mmm-85) REVERT: C 48 ILE cc_start: 0.9388 (tp) cc_final: 0.9111 (tp) outliers start: 5 outliers final: 2 residues processed: 72 average time/residue: 0.0933 time to fit residues: 8.3195 Evaluate side-chains 60 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 34 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.122530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.097638 restraints weight = 11806.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.099649 restraints weight = 7548.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.101007 restraints weight = 5697.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.101853 restraints weight = 4738.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.102311 restraints weight = 4222.668| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5145 Z= 0.164 Angle : 0.652 10.806 7007 Z= 0.330 Chirality : 0.048 0.376 775 Planarity : 0.004 0.034 898 Dihedral : 5.811 50.465 744 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.49 % Favored : 94.35 % Rotamer: Outliers : 1.80 % Allowed : 14.41 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.34), residues: 637 helix: -2.38 (0.94), residues: 26 sheet: 0.57 (0.34), residues: 232 loop : -0.82 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 67 TYR 0.026 0.002 TYR C 49 PHE 0.017 0.002 PHE D 515 TRP 0.010 0.001 TRP B 115 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 5134) covalent geometry : angle 0.64492 ( 6983) SS BOND : bond 0.00445 ( 9) SS BOND : angle 0.93808 ( 18) hydrogen bonds : bond 0.03228 ( 152) hydrogen bonds : angle 5.88513 ( 408) link_BETA1-4 : bond 0.00310 ( 1) link_BETA1-4 : angle 3.32613 ( 3) link_NAG-ASN : bond 0.00492 ( 1) link_NAG-ASN : angle 3.05395 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.255 Fit side-chains REVERT: D 378 LYS cc_start: 0.8976 (ttpt) cc_final: 0.8735 (pttm) REVERT: B 28 ARG cc_start: 0.7624 (ttp80) cc_final: 0.7048 (ttp80) REVERT: B 29 PHE cc_start: 0.8253 (t80) cc_final: 0.8019 (t80) REVERT: B 32 TYR cc_start: 0.8705 (m-80) cc_final: 0.8043 (m-80) REVERT: B 89 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7736 (mp0) REVERT: C 18 ARG cc_start: 0.7018 (tpp80) cc_final: 0.6734 (mmm-85) REVERT: C 48 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.8994 (mm) outliers start: 10 outliers final: 5 residues processed: 72 average time/residue: 0.1050 time to fit residues: 9.2862 Evaluate side-chains 66 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 417 ASN Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 0.0170 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.120134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.094791 restraints weight = 12243.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.096663 restraints weight = 8329.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.097866 restraints weight = 6457.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.098387 restraints weight = 5483.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.098971 restraints weight = 5024.836| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5145 Z= 0.143 Angle : 0.659 11.292 7007 Z= 0.326 Chirality : 0.047 0.366 775 Planarity : 0.004 0.033 898 Dihedral : 5.741 48.985 744 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.55 % Favored : 95.29 % Rotamer: Outliers : 1.80 % Allowed : 14.77 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.34), residues: 637 helix: -2.66 (0.78), residues: 32 sheet: 0.60 (0.34), residues: 232 loop : -0.86 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 67 TYR 0.028 0.002 TYR C 49 PHE 0.015 0.001 PHE D 515 TRP 0.009 0.001 TRP B 115 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 5134) covalent geometry : angle 0.65119 ( 6983) SS BOND : bond 0.00313 ( 9) SS BOND : angle 0.92055 ( 18) hydrogen bonds : bond 0.02957 ( 152) hydrogen bonds : angle 5.69536 ( 408) link_BETA1-4 : bond 0.00388 ( 1) link_BETA1-4 : angle 3.41284 ( 3) link_NAG-ASN : bond 0.00486 ( 1) link_NAG-ASN : angle 3.00910 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.168 Fit side-chains REVERT: B 29 PHE cc_start: 0.8121 (t80) cc_final: 0.7766 (t80) REVERT: B 32 TYR cc_start: 0.8673 (m-80) cc_final: 0.8021 (m-80) REVERT: B 89 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7753 (mp0) REVERT: B 162 VAL cc_start: 0.7354 (OUTLIER) cc_final: 0.7047 (p) REVERT: C 1 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8070 (p0) REVERT: C 18 ARG cc_start: 0.6988 (tpp80) cc_final: 0.6737 (mmm-85) REVERT: C 48 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9015 (mm) outliers start: 10 outliers final: 5 residues processed: 73 average time/residue: 0.0958 time to fit residues: 8.5341 Evaluate side-chains 67 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 89 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 46 optimal weight: 0.2980 chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.115141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.095312 restraints weight = 12544.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.093573 restraints weight = 12673.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.094870 restraints weight = 13724.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.094851 restraints weight = 9164.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.095075 restraints weight = 9413.281| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 5145 Z= 0.308 Angle : 0.807 11.263 7007 Z= 0.410 Chirality : 0.051 0.384 775 Planarity : 0.005 0.046 898 Dihedral : 6.351 46.075 744 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.01 % Favored : 91.84 % Rotamer: Outliers : 3.06 % Allowed : 15.32 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.33), residues: 637 helix: -2.88 (0.73), residues: 32 sheet: 0.33 (0.34), residues: 232 loop : -1.19 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 67 TYR 0.016 0.002 TYR C 87 PHE 0.017 0.002 PHE D 515 TRP 0.012 0.002 TRP B 115 HIS 0.005 0.002 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00713 ( 5134) covalent geometry : angle 0.79925 ( 6983) SS BOND : bond 0.00372 ( 9) SS BOND : angle 1.23424 ( 18) hydrogen bonds : bond 0.04255 ( 152) hydrogen bonds : angle 6.33703 ( 408) link_BETA1-4 : bond 0.00339 ( 1) link_BETA1-4 : angle 3.41757 ( 3) link_NAG-ASN : bond 0.00633 ( 1) link_NAG-ASN : angle 3.68681 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 353 TRP cc_start: 0.8773 (OUTLIER) cc_final: 0.8086 (p-90) REVERT: B 29 PHE cc_start: 0.8279 (t80) cc_final: 0.7902 (t80) REVERT: B 32 TYR cc_start: 0.8824 (m-80) cc_final: 0.8364 (m-80) REVERT: B 83 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.6824 (mmm) REVERT: B 162 VAL cc_start: 0.7280 (OUTLIER) cc_final: 0.6947 (p) REVERT: B 191 SER cc_start: 0.7813 (m) cc_final: 0.7591 (t) REVERT: C 18 ARG cc_start: 0.7414 (tpp80) cc_final: 0.6940 (mmm-85) REVERT: C 48 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.9042 (mm) outliers start: 17 outliers final: 9 residues processed: 71 average time/residue: 0.0952 time to fit residues: 8.4207 Evaluate side-chains 68 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 353 TRP Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 136 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 14 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 394 ASN ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.116333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.093873 restraints weight = 12263.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.093189 restraints weight = 11356.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.093593 restraints weight = 10006.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.093729 restraints weight = 9058.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.094510 restraints weight = 8312.997| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5145 Z= 0.219 Angle : 0.744 11.452 7007 Z= 0.374 Chirality : 0.049 0.394 775 Planarity : 0.004 0.035 898 Dihedral : 6.156 45.485 744 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.34 % Favored : 94.51 % Rotamer: Outliers : 3.78 % Allowed : 15.14 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.33), residues: 637 helix: -2.82 (0.75), residues: 32 sheet: 0.40 (0.34), residues: 230 loop : -1.22 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 100 TYR 0.019 0.002 TYR C 49 PHE 0.013 0.002 PHE D 515 TRP 0.012 0.001 TRP B 115 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 5134) covalent geometry : angle 0.73661 ( 6983) SS BOND : bond 0.00320 ( 9) SS BOND : angle 1.03694 ( 18) hydrogen bonds : bond 0.03597 ( 152) hydrogen bonds : angle 6.07882 ( 408) link_BETA1-4 : bond 0.00456 ( 1) link_BETA1-4 : angle 3.37260 ( 3) link_NAG-ASN : bond 0.00575 ( 1) link_NAG-ASN : angle 3.54917 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.120 Fit side-chains REVERT: D 418 ILE cc_start: 0.7975 (mp) cc_final: 0.7597 (mt) REVERT: B 29 PHE cc_start: 0.8257 (t80) cc_final: 0.7975 (t80) REVERT: B 32 TYR cc_start: 0.8734 (m-80) cc_final: 0.8189 (m-80) REVERT: B 83 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.6999 (mmm) REVERT: B 162 VAL cc_start: 0.7354 (OUTLIER) cc_final: 0.7032 (p) REVERT: B 191 SER cc_start: 0.7916 (m) cc_final: 0.7669 (t) REVERT: B 209 ASN cc_start: 0.7016 (OUTLIER) cc_final: 0.6766 (m-40) REVERT: C 18 ARG cc_start: 0.7329 (tpp80) cc_final: 0.6881 (mmm-85) REVERT: C 48 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.9033 (mm) outliers start: 21 outliers final: 11 residues processed: 73 average time/residue: 0.0892 time to fit residues: 8.0910 Evaluate side-chains 70 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 89 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 25 optimal weight: 0.0020 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.119277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.096418 restraints weight = 12347.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.096718 restraints weight = 9909.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.096647 restraints weight = 8169.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.096876 restraints weight = 7828.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.096973 restraints weight = 7368.958| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5145 Z= 0.118 Angle : 0.682 11.579 7007 Z= 0.335 Chirality : 0.048 0.376 775 Planarity : 0.004 0.034 898 Dihedral : 5.721 45.717 744 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.87 % Favored : 94.98 % Rotamer: Outliers : 2.16 % Allowed : 16.58 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.33), residues: 637 helix: -2.53 (0.81), residues: 32 sheet: 0.58 (0.34), residues: 231 loop : -1.09 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 142 TYR 0.025 0.001 TYR C 49 PHE 0.013 0.001 PHE D 515 TRP 0.010 0.001 TRP B 115 HIS 0.002 0.001 HIS C 189 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 5134) covalent geometry : angle 0.67488 ( 6983) SS BOND : bond 0.00355 ( 9) SS BOND : angle 0.86939 ( 18) hydrogen bonds : bond 0.02792 ( 152) hydrogen bonds : angle 5.58654 ( 408) link_BETA1-4 : bond 0.00491 ( 1) link_BETA1-4 : angle 3.49720 ( 3) link_NAG-ASN : bond 0.00446 ( 1) link_NAG-ASN : angle 3.29391 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: B 32 TYR cc_start: 0.8575 (m-80) cc_final: 0.7957 (m-80) REVERT: B 83 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7193 (mmm) REVERT: B 162 VAL cc_start: 0.7316 (OUTLIER) cc_final: 0.6997 (p) REVERT: C 1 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.7996 (p0) REVERT: C 18 ARG cc_start: 0.7194 (tpp80) cc_final: 0.6921 (mmm-85) REVERT: C 48 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9005 (mm) outliers start: 12 outliers final: 7 residues processed: 69 average time/residue: 0.1019 time to fit residues: 8.6336 Evaluate side-chains 64 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 60 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.118989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.093348 restraints weight = 12394.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.095307 restraints weight = 8212.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.096533 restraints weight = 6310.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.097438 restraints weight = 5331.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.097887 restraints weight = 4760.315| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5145 Z= 0.127 Angle : 0.697 13.000 7007 Z= 0.341 Chirality : 0.047 0.368 775 Planarity : 0.004 0.041 898 Dihedral : 5.423 32.717 744 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.18 % Favored : 94.66 % Rotamer: Outliers : 2.70 % Allowed : 15.32 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.34), residues: 637 helix: -2.31 (0.84), residues: 32 sheet: 0.62 (0.35), residues: 233 loop : -1.01 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 142 TYR 0.023 0.001 TYR C 49 PHE 0.013 0.001 PHE D 515 TRP 0.009 0.001 TRP B 115 HIS 0.005 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 5134) covalent geometry : angle 0.68973 ( 6983) SS BOND : bond 0.00323 ( 9) SS BOND : angle 0.88194 ( 18) hydrogen bonds : bond 0.02777 ( 152) hydrogen bonds : angle 5.41814 ( 408) link_BETA1-4 : bond 0.00765 ( 1) link_BETA1-4 : angle 3.20143 ( 3) link_NAG-ASN : bond 0.00616 ( 1) link_NAG-ASN : angle 3.29127 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.140 Fit side-chains REVERT: B 32 TYR cc_start: 0.8654 (m-80) cc_final: 0.7994 (m-80) REVERT: B 83 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7253 (mmm) REVERT: B 156 ASP cc_start: 0.6122 (m-30) cc_final: 0.5258 (t0) REVERT: B 162 VAL cc_start: 0.7355 (OUTLIER) cc_final: 0.7030 (p) REVERT: C 1 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8033 (p0) REVERT: C 18 ARG cc_start: 0.7198 (tpp80) cc_final: 0.6888 (mmm-85) REVERT: C 48 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9057 (mm) outliers start: 15 outliers final: 9 residues processed: 68 average time/residue: 0.0916 time to fit residues: 7.6231 Evaluate side-chains 65 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 45 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 57 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.118591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.096368 restraints weight = 12374.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.095159 restraints weight = 9591.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.095438 restraints weight = 10035.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.095660 restraints weight = 8148.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.095879 restraints weight = 7690.913| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5145 Z= 0.149 Angle : 0.715 12.646 7007 Z= 0.354 Chirality : 0.048 0.389 775 Planarity : 0.005 0.084 898 Dihedral : 5.577 37.770 744 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.49 % Favored : 94.35 % Rotamer: Outliers : 2.70 % Allowed : 16.04 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.34), residues: 637 helix: -2.37 (0.83), residues: 32 sheet: 0.65 (0.35), residues: 231 loop : -1.04 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 142 TYR 0.021 0.001 TYR C 49 PHE 0.033 0.001 PHE B 29 TRP 0.007 0.001 TRP B 115 HIS 0.002 0.001 HIS C 189 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 5134) covalent geometry : angle 0.70826 ( 6983) SS BOND : bond 0.00319 ( 9) SS BOND : angle 0.94849 ( 18) hydrogen bonds : bond 0.02931 ( 152) hydrogen bonds : angle 5.50246 ( 408) link_BETA1-4 : bond 0.00420 ( 1) link_BETA1-4 : angle 3.32326 ( 3) link_NAG-ASN : bond 0.00599 ( 1) link_NAG-ASN : angle 3.08224 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.201 Fit side-chains REVERT: D 468 ILE cc_start: 0.8475 (pt) cc_final: 0.8267 (pt) REVERT: B 32 TYR cc_start: 0.8612 (m-80) cc_final: 0.7969 (m-80) REVERT: B 83 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7277 (mmm) REVERT: B 162 VAL cc_start: 0.7323 (OUTLIER) cc_final: 0.7007 (p) REVERT: C 18 ARG cc_start: 0.7288 (tpp80) cc_final: 0.6939 (mmm-85) REVERT: C 48 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.8995 (mm) outliers start: 15 outliers final: 9 residues processed: 66 average time/residue: 0.1027 time to fit residues: 8.3698 Evaluate side-chains 65 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.116644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.095147 restraints weight = 12510.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.094432 restraints weight = 11142.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.095705 restraints weight = 11367.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.095570 restraints weight = 7875.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.095817 restraints weight = 8509.076| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5145 Z= 0.195 Angle : 0.745 12.400 7007 Z= 0.373 Chirality : 0.049 0.402 775 Planarity : 0.005 0.071 898 Dihedral : 5.895 40.309 744 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.44 % Favored : 93.41 % Rotamer: Outliers : 2.88 % Allowed : 15.68 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.33), residues: 637 helix: -2.28 (0.91), residues: 26 sheet: 0.50 (0.35), residues: 224 loop : -1.13 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 142 TYR 0.018 0.002 TYR C 49 PHE 0.026 0.002 PHE B 29 TRP 0.008 0.001 TRP B 115 HIS 0.002 0.001 HIS C 189 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 5134) covalent geometry : angle 0.73817 ( 6983) SS BOND : bond 0.00328 ( 9) SS BOND : angle 1.03984 ( 18) hydrogen bonds : bond 0.03317 ( 152) hydrogen bonds : angle 5.74702 ( 408) link_BETA1-4 : bond 0.00438 ( 1) link_BETA1-4 : angle 3.23605 ( 3) link_NAG-ASN : bond 0.00633 ( 1) link_NAG-ASN : angle 3.39070 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 946.55 seconds wall clock time: 17 minutes 2.58 seconds (1022.58 seconds total)