Starting phenix.real_space_refine on Sun Mar 10 21:01:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtk_14143/03_2024/7qtk_14143.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtk_14143/03_2024/7qtk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtk_14143/03_2024/7qtk_14143.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtk_14143/03_2024/7qtk_14143.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtk_14143/03_2024/7qtk_14143.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qtk_14143/03_2024/7qtk_14143.pdb" } resolution = 3.84 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= 0.029 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 Residue "B GLU 62": "OE1" <-> "OE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 3.33, per 1000 atoms: 0.66 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 - 3.50 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN D 343 " Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 917.0 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: 0.64 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: 1.39 Time building geometry restraints manager: 2.05 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: 101.02 - 107.63: 196 107.63 - 114.24: 2829 114.24 - 120.85: 2092 120.85 - 127.46: 1815 127.46 - 134.07: 51 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 2.520 nonbonded pdb=" OG SER C 14 " pdb=" OD2 ASP C 17 " model vdw 2.210 2.440 nonbonded pdb=" OE2 GLU D 406 " pdb=" NE2 GLN D 409 " model vdw 2.279 2.520 nonbonded pdb=" O TYR C 192 " pdb=" OG SER C 208 " model vdw 2.287 2.440 nonbonded pdb=" OG SER B 17 " pdb=" ND2 ASN B 84 " model vdw 2.299 2.520 ... (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 ========== 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.750 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 18.770 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.670 ------------------------------------------------------------------------------- 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 5134 Z= 0.264 Angle : 0.731 8.208 6983 Z= 0.420 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 : 9.44 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.34), 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 TRP 0.007 0.001 TRP B 115 HIS 0.003 0.001 HIS C 189 PHE 0.019 0.001 PHE D 392 TYR 0.023 0.002 TYR C 94 ARG 0.010 0.001 ARG C 18 *********************** 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 fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.653 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: 0.2292 time to fit residues: 23.5037 Evaluate side-chains 61 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 49 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 0.0030 chunk 57 optimal weight: 0.2980 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN B 209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5134 Z= 0.169 Angle : 0.607 9.911 6983 Z= 0.308 Chirality : 0.046 0.361 775 Planarity : 0.004 0.033 898 Dihedral : 6.328 58.082 744 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.87 % Favored : 94.98 % Rotamer: Outliers : 0.90 % Allowed : 9.37 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.34), residues: 637 helix: -2.38 (0.91), residues: 26 sheet: 0.91 (0.35), residues: 240 loop : -0.59 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 166 HIS 0.003 0.001 HIS C 198 PHE 0.013 0.001 PHE B 29 TYR 0.021 0.001 TYR D 369 ARG 0.006 0.000 ARG B 67 *********************** 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 78 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: B 89 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7948 (mp0) REVERT: B 156 ASP cc_start: 0.5459 (m-30) cc_final: 0.4537 (t70) REVERT: B 216 ASN cc_start: 0.7742 (m-40) cc_final: 0.6945 (p0) outliers start: 5 outliers final: 4 residues processed: 75 average time/residue: 0.2286 time to fit residues: 21.0617 Evaluate side-chains 68 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain B residue 113 ASP 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 31 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 0.0270 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.7244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5134 Z= 0.226 Angle : 0.624 9.794 6983 Z= 0.316 Chirality : 0.046 0.346 775 Planarity : 0.004 0.033 898 Dihedral : 5.998 52.814 744 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.02 % Favored : 94.82 % Rotamer: Outliers : 1.08 % Allowed : 12.79 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.34), residues: 637 helix: -1.77 (1.03), residues: 26 sheet: 0.81 (0.34), residues: 245 loop : -0.60 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 115 HIS 0.004 0.001 HIS B 101 PHE 0.021 0.001 PHE B 29 TYR 0.014 0.001 TYR B 102 ARG 0.007 0.001 ARG B 67 *********************** 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 73 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.563 Fit side-chains REVERT: D 406 GLU cc_start: 0.8560 (pt0) cc_final: 0.8201 (pt0) REVERT: B 29 PHE cc_start: 0.8387 (t80) cc_final: 0.8149 (t80) REVERT: B 89 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7872 (mp0) REVERT: B 206 TYR cc_start: 0.4963 (m-80) cc_final: 0.4553 (m-80) REVERT: B 216 ASN cc_start: 0.7969 (m-40) cc_final: 0.6977 (p0) REVERT: C 48 ILE cc_start: 0.9392 (tp) cc_final: 0.9072 (tp) outliers start: 6 outliers final: 3 residues processed: 70 average time/residue: 0.2306 time to fit residues: 19.8265 Evaluate side-chains 65 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain B residue 21 SER 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 56 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 38 optimal weight: 0.0010 chunk 57 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 54 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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** B 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5134 Z= 0.147 Angle : 0.573 9.970 6983 Z= 0.286 Chirality : 0.045 0.342 775 Planarity : 0.003 0.032 898 Dihedral : 5.476 52.472 744 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.92 % Favored : 95.92 % Rotamer: Outliers : 1.62 % Allowed : 13.69 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.34), residues: 637 helix: -2.10 (0.89), residues: 32 sheet: 0.97 (0.34), residues: 244 loop : -0.50 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 115 HIS 0.003 0.001 HIS B 101 PHE 0.015 0.001 PHE B 29 TYR 0.020 0.001 TYR D 369 ARG 0.003 0.000 ARG B 100 *********************** 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 79 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: B 28 ARG cc_start: 0.7513 (ttp80) cc_final: 0.6813 (ttp80) REVERT: B 29 PHE cc_start: 0.8383 (t80) cc_final: 0.8129 (t80) REVERT: B 89 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7826 (mp0) REVERT: B 156 ASP cc_start: 0.6059 (m-30) cc_final: 0.4911 (t0) REVERT: B 216 ASN cc_start: 0.8061 (m-40) cc_final: 0.6994 (p0) REVERT: C 48 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.9007 (tp) outliers start: 9 outliers final: 4 residues processed: 75 average time/residue: 0.2200 time to fit residues: 20.3969 Evaluate side-chains 67 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 417 ASN Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain C residue 48 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5134 Z= 0.227 Angle : 0.642 10.121 6983 Z= 0.317 Chirality : 0.046 0.386 775 Planarity : 0.004 0.032 898 Dihedral : 5.512 51.033 744 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.02 % Favored : 94.82 % Rotamer: Outliers : 1.98 % Allowed : 14.41 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.09 (0.35), residues: 637 helix: -2.01 (0.89), residues: 32 sheet: 0.84 (0.35), residues: 239 loop : -0.47 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 115 HIS 0.002 0.001 HIS C 189 PHE 0.014 0.001 PHE D 515 TYR 0.014 0.001 TYR B 102 ARG 0.005 0.001 ARG B 67 *********************** 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 73 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.597 Fit side-chains REVERT: B 28 ARG cc_start: 0.7617 (ttp80) cc_final: 0.6877 (ttp80) REVERT: B 29 PHE cc_start: 0.8335 (t80) cc_final: 0.8011 (t80) REVERT: B 89 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7851 (mp0) REVERT: C 48 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9032 (mm) outliers start: 11 outliers final: 6 residues processed: 68 average time/residue: 0.2307 time to fit residues: 19.3762 Evaluate side-chains 67 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 339 ASP 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 89 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 15 optimal weight: 0.1980 chunk 60 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5134 Z= 0.236 Angle : 0.645 9.940 6983 Z= 0.322 Chirality : 0.047 0.399 775 Planarity : 0.004 0.034 898 Dihedral : 5.665 53.635 744 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.02 % Favored : 94.82 % Rotamer: Outliers : 1.80 % Allowed : 15.68 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.35), residues: 637 helix: -1.88 (0.92), residues: 32 sheet: 0.78 (0.35), residues: 238 loop : -0.57 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 115 HIS 0.002 0.001 HIS B 212 PHE 0.023 0.001 PHE D 515 TYR 0.016 0.001 TYR D 369 ARG 0.004 0.000 ARG B 100 *********************** 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 72 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.617 Fit side-chains REVERT: D 402 ILE cc_start: 0.8327 (mm) cc_final: 0.7886 (pt) REVERT: B 28 ARG cc_start: 0.7685 (ttp80) cc_final: 0.6938 (ttp80) REVERT: B 29 PHE cc_start: 0.8198 (t80) cc_final: 0.7790 (t80) REVERT: B 89 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7829 (mp0) REVERT: B 162 VAL cc_start: 0.7387 (OUTLIER) cc_final: 0.7083 (p) REVERT: B 206 TYR cc_start: 0.4948 (m-80) cc_final: 0.4658 (m-80) REVERT: C 48 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9039 (mm) outliers start: 10 outliers final: 6 residues processed: 70 average time/residue: 0.2534 time to fit residues: 21.5638 Evaluate side-chains 67 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 339 ASP 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 D residue 515 PHE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 89 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5134 Z= 0.201 Angle : 0.627 10.154 6983 Z= 0.312 Chirality : 0.047 0.394 775 Planarity : 0.003 0.034 898 Dihedral : 5.605 52.963 744 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.55 % Favored : 95.29 % Rotamer: Outliers : 1.80 % Allowed : 15.50 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.35), residues: 637 helix: -1.75 (0.94), residues: 32 sheet: 0.82 (0.35), residues: 237 loop : -0.55 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 115 HIS 0.002 0.001 HIS C 189 PHE 0.019 0.001 PHE D 515 TYR 0.014 0.001 TYR B 102 ARG 0.004 0.000 ARG D 403 *********************** 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 69 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.591 Fit side-chains REVERT: D 402 ILE cc_start: 0.8433 (mm) cc_final: 0.7969 (pt) REVERT: B 28 ARG cc_start: 0.7642 (ttp80) cc_final: 0.6920 (ttp80) REVERT: B 29 PHE cc_start: 0.8238 (t80) cc_final: 0.7851 (t80) REVERT: B 89 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7845 (mp0) REVERT: B 162 VAL cc_start: 0.7415 (OUTLIER) cc_final: 0.7124 (p) REVERT: C 48 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9068 (mm) outliers start: 10 outliers final: 5 residues processed: 65 average time/residue: 0.2338 time to fit residues: 18.6996 Evaluate side-chains 65 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 48 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.1980 chunk 38 optimal weight: 0.0070 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 53 optimal weight: 30.0000 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 0.0470 overall best weight: 1.0500 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5134 Z= 0.177 Angle : 0.614 10.174 6983 Z= 0.304 Chirality : 0.046 0.391 775 Planarity : 0.004 0.035 898 Dihedral : 5.508 53.038 744 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.71 % Favored : 95.13 % Rotamer: Outliers : 2.16 % Allowed : 14.77 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.35), residues: 637 helix: -1.69 (0.94), residues: 32 sheet: 0.90 (0.34), residues: 245 loop : -0.63 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 115 HIS 0.001 0.001 HIS C 189 PHE 0.018 0.001 PHE D 515 TYR 0.016 0.001 TYR D 369 ARG 0.005 0.000 ARG D 403 *********************** 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 73 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: D 402 ILE cc_start: 0.8360 (mm) cc_final: 0.7926 (pt) REVERT: B 29 PHE cc_start: 0.8244 (t80) cc_final: 0.7812 (t80) REVERT: B 89 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7827 (mp0) REVERT: B 156 ASP cc_start: 0.6033 (m-30) cc_final: 0.4820 (t0) REVERT: B 162 VAL cc_start: 0.7373 (OUTLIER) cc_final: 0.7072 (p) REVERT: C 48 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.9062 (mm) outliers start: 12 outliers final: 5 residues processed: 70 average time/residue: 0.2409 time to fit residues: 20.7570 Evaluate side-chains 66 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 89 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 53 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.0370 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5134 Z= 0.184 Angle : 0.623 10.249 6983 Z= 0.308 Chirality : 0.046 0.391 775 Planarity : 0.004 0.035 898 Dihedral : 5.531 51.724 744 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.02 % Favored : 94.82 % Rotamer: Outliers : 1.62 % Allowed : 14.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.35), residues: 637 helix: -1.76 (0.91), residues: 32 sheet: 0.95 (0.35), residues: 244 loop : -0.64 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 115 HIS 0.002 0.001 HIS C 189 PHE 0.018 0.001 PHE D 515 TYR 0.013 0.001 TYR D 508 ARG 0.004 0.000 ARG C 142 *********************** 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 68 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: D 402 ILE cc_start: 0.8398 (mm) cc_final: 0.7967 (pt) REVERT: B 29 PHE cc_start: 0.8270 (t80) cc_final: 0.7832 (t80) REVERT: B 89 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7806 (mp0) REVERT: B 156 ASP cc_start: 0.6346 (m-30) cc_final: 0.5033 (t0) REVERT: B 162 VAL cc_start: 0.7371 (OUTLIER) cc_final: 0.7072 (p) REVERT: C 48 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9073 (mm) outliers start: 9 outliers final: 7 residues processed: 64 average time/residue: 0.2632 time to fit residues: 20.3687 Evaluate side-chains 67 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 162 VAL 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 62 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 38 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 46 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5134 Z= 0.183 Angle : 0.628 10.257 6983 Z= 0.310 Chirality : 0.046 0.392 775 Planarity : 0.004 0.034 898 Dihedral : 5.521 51.529 744 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.02 % Favored : 94.82 % Rotamer: Outliers : 1.62 % Allowed : 15.14 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.14 (0.35), residues: 637 helix: -1.91 (0.89), residues: 32 sheet: 0.93 (0.34), residues: 244 loop : -0.64 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 115 HIS 0.001 0.001 HIS B 212 PHE 0.016 0.001 PHE D 515 TYR 0.017 0.001 TYR D 369 ARG 0.004 0.000 ARG C 142 ********************** 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 67 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: D 402 ILE cc_start: 0.8409 (mm) cc_final: 0.7957 (pt) REVERT: B 16 ARG cc_start: 0.7430 (tpp-160) cc_final: 0.7088 (tpp80) REVERT: B 29 PHE cc_start: 0.8274 (t80) cc_final: 0.7842 (t80) REVERT: B 89 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7800 (mp0) REVERT: B 156 ASP cc_start: 0.6320 (m-30) cc_final: 0.5018 (t0) REVERT: B 162 VAL cc_start: 0.7368 (OUTLIER) cc_final: 0.7069 (p) REVERT: C 48 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9049 (mm) outliers start: 9 outliers final: 7 residues processed: 63 average time/residue: 0.2399 time to fit residues: 18.5653 Evaluate side-chains 66 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 162 VAL 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 13 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 43 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 409 GLN ** 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 = 0.3801 r_free = 0.3801 target = 0.121129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.096833 restraints weight = 12486.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.098366 restraints weight = 8978.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.099390 restraints weight = 7254.976| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5134 Z= 0.175 Angle : 0.621 10.249 6983 Z= 0.305 Chirality : 0.046 0.387 775 Planarity : 0.003 0.031 898 Dihedral : 5.469 51.572 744 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.02 % Favored : 94.82 % Rotamer: Outliers : 1.80 % Allowed : 14.95 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.35), residues: 637 helix: -2.01 (0.87), residues: 32 sheet: 0.96 (0.34), residues: 244 loop : -0.61 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 115 HIS 0.001 0.001 HIS C 189 PHE 0.018 0.001 PHE D 515 TYR 0.014 0.001 TYR D 508 ARG 0.004 0.000 ARG C 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1350.17 seconds wall clock time: 25 minutes 13.21 seconds (1513.21 seconds total)