Starting phenix.real_space_refine on Thu Mar 14 23:31:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds6_27684/03_2024/8ds6_27684.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds6_27684/03_2024/8ds6_27684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds6_27684/03_2024/8ds6_27684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds6_27684/03_2024/8ds6_27684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds6_27684/03_2024/8ds6_27684.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds6_27684/03_2024/8ds6_27684.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 20 5.16 5 C 3224 2.51 5 N 909 2.21 5 O 875 1.98 5 H 5107 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10135 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5051 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 34, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 5084 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 35, 'TRANS': 299} Chain breaks: 1 Time building chain proxies: 4.95, per 1000 atoms: 0.49 Number of scatterers: 10135 At special positions: 0 Unit cell: (72.645, 101.87, 108.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 O 875 8.00 N 909 7.00 C 3224 6.00 H 5107 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.64 Conformation dependent library (CDL) restraints added in 1.1 seconds 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1218 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 52.6% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 130 through 158 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 262 through 270 removed outlier: 3.812A pdb=" N GLU A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 299 removed outlier: 3.507A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 348 through 361 Processing helix chain 'A' and resid 368 through 384 Processing helix chain 'A' and resid 387 through 400 Processing helix chain 'A' and resid 420 through 440 Processing helix chain 'A' and resid 446 through 459 Processing helix chain 'A' and resid 460 through 473 removed outlier: 3.528A pdb=" N LEU A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 158 Processing helix chain 'B' and resid 214 through 224 removed outlier: 4.115A pdb=" N LEU B 218 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 270 removed outlier: 3.758A pdb=" N GLU B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 298 removed outlier: 3.603A pdb=" N VAL B 281 " --> pdb=" O PHE B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 309 Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 348 through 363 Processing helix chain 'B' and resid 368 through 385 removed outlier: 3.515A pdb=" N ALA B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 Processing helix chain 'B' and resid 415 through 418 Processing helix chain 'B' and resid 419 through 441 Processing helix chain 'B' and resid 446 through 459 Processing helix chain 'B' and resid 460 through 472 Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 173 Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 173 removed outlier: 4.652A pdb=" N ALA A 252 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY A 235 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA4, first strand: chain 'A' and resid 300 through 302 Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 173 removed outlier: 3.614A pdb=" N ALA B 180 " --> pdb=" O TYR B 187 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 173 removed outlier: 5.096A pdb=" N ALA B 252 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY B 235 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 260 through 261 Processing sheet with id=AA8, first strand: chain 'B' and resid 300 through 302 318 hydrogen bonds defined for protein. 909 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: 3.43 Time building geometry restraints manager: 9.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.92 - 1.09: 4677 1.09 - 1.27: 1221 1.27 - 1.45: 1392 1.45 - 1.63: 2965 1.63 - 1.81: 24 Bond restraints: 10279 Sorted by residual: bond pdb=" CD2 PHE B 294 " pdb=" HD2 PHE B 294 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" CD2 HIS B 348 " pdb=" HD2 HIS B 348 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" CD2 HIS A 227 " pdb=" HD2 HIS A 227 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" CZ2 TRP A 450 " pdb=" HZ2 TRP A 450 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" CZ3 TRP A 400 " pdb=" HZ3 TRP A 400 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.48e+01 ... (remaining 10274 not shown) Histogram of bond angle deviations from ideal: 95.96 - 103.53: 136 103.53 - 111.10: 11021 111.10 - 118.66: 3365 118.66 - 126.23: 4016 126.23 - 133.80: 183 Bond angle restraints: 18721 Sorted by residual: angle pdb=" N ALA A 291 " pdb=" CA ALA A 291 " pdb=" C ALA A 291 " ideal model delta sigma weight residual 111.28 103.64 7.64 1.09e+00 8.42e-01 4.91e+01 angle pdb=" N PRO B 338 " pdb=" CA PRO B 338 " pdb=" C PRO B 338 " ideal model delta sigma weight residual 110.70 119.16 -8.46 1.22e+00 6.72e-01 4.81e+01 angle pdb=" C GLY A 322 " pdb=" N PRO A 323 " pdb=" CA PRO A 323 " ideal model delta sigma weight residual 119.66 124.05 -4.39 7.20e-01 1.93e+00 3.72e+01 angle pdb=" CA PRO B 338 " pdb=" C PRO B 338 " pdb=" N PRO B 339 " ideal model delta sigma weight residual 117.93 124.66 -6.73 1.20e+00 6.94e-01 3.14e+01 angle pdb=" CA GLU B 132 " pdb=" C GLU B 132 " pdb=" O GLU B 132 " ideal model delta sigma weight residual 120.55 114.88 5.67 1.06e+00 8.90e-01 2.86e+01 ... (remaining 18716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4554 17.82 - 35.63: 156 35.63 - 53.45: 106 53.45 - 71.26: 34 71.26 - 89.08: 4 Dihedral angle restraints: 4854 sinusoidal: 2698 harmonic: 2156 Sorted by residual: dihedral pdb=" CA PRO B 273 " pdb=" C PRO B 273 " pdb=" N PRO B 274 " pdb=" CA PRO B 274 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA THR B 329 " pdb=" C THR B 329 " pdb=" N ASP B 330 " pdb=" CA ASP B 330 " ideal model delta harmonic sigma weight residual -180.00 -160.44 -19.56 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA GLY B 343 " pdb=" C GLY B 343 " pdb=" N SER B 344 " pdb=" CA SER B 344 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 4851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 514 0.051 - 0.102: 230 0.102 - 0.152: 33 0.152 - 0.203: 20 0.203 - 0.254: 2 Chirality restraints: 799 Sorted by residual: chirality pdb=" CA ASP A 473 " pdb=" N ASP A 473 " pdb=" C ASP A 473 " pdb=" CB ASP A 473 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA VAL A 237 " pdb=" N VAL A 237 " pdb=" C VAL A 237 " pdb=" CB VAL A 237 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA VAL B 237 " pdb=" N VAL B 237 " pdb=" C VAL B 237 " pdb=" CB VAL B 237 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.75e-01 ... (remaining 796 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 325 " 0.298 9.50e-02 1.11e+02 1.22e-01 1.21e+02 pdb=" NE ARG B 325 " 0.043 2.00e-02 2.50e+03 pdb=" CZ ARG B 325 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 325 " 0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG B 325 " -0.062 2.00e-02 2.50e+03 pdb="HH11 ARG B 325 " -0.006 2.00e-02 2.50e+03 pdb="HH12 ARG B 325 " -0.080 2.00e-02 2.50e+03 pdb="HH21 ARG B 325 " -0.084 2.00e-02 2.50e+03 pdb="HH22 ARG B 325 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 325 " -0.413 9.50e-02 1.11e+02 1.48e-01 8.69e+01 pdb=" NE ARG A 325 " -0.053 2.00e-02 2.50e+03 pdb=" CZ ARG A 325 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 325 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG A 325 " 0.049 2.00e-02 2.50e+03 pdb="HH11 ARG A 325 " 0.051 2.00e-02 2.50e+03 pdb="HH12 ARG A 325 " 0.018 2.00e-02 2.50e+03 pdb="HH21 ARG A 325 " 0.080 2.00e-02 2.50e+03 pdb="HH22 ARG A 325 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 192 " 0.171 9.50e-02 1.11e+02 6.96e-02 3.91e+01 pdb=" NE ARG B 192 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 192 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 192 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 192 " -0.033 2.00e-02 2.50e+03 pdb="HH11 ARG B 192 " 0.024 2.00e-02 2.50e+03 pdb="HH12 ARG B 192 " -0.049 2.00e-02 2.50e+03 pdb="HH21 ARG B 192 " -0.034 2.00e-02 2.50e+03 pdb="HH22 ARG B 192 " 0.092 2.00e-02 2.50e+03 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 995 2.24 - 2.83: 20752 2.83 - 3.42: 28654 3.42 - 4.01: 37970 4.01 - 4.60: 55049 Nonbonded interactions: 143420 Sorted by model distance: nonbonded pdb=" O TRP B 450 " pdb=" HG CYS B 453 " model vdw 1.650 2.620 nonbonded pdb=" O TRP A 450 " pdb=" HG CYS A 453 " model vdw 1.689 2.620 nonbonded pdb="HG23 THR A 368 " pdb=" H ALA A 371 " model vdw 1.707 2.270 nonbonded pdb=" HD2 ARG A 156 " pdb="HH11 ARG A 156 " model vdw 1.716 2.270 nonbonded pdb=" O LEU A 266 " pdb=" HG CYS A 270 " model vdw 1.728 2.620 ... (remaining 143415 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 130 through 472) selection = (chain 'B' and (resid 130 through 406 or resid 419 through 472)) } 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: 1.420 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: 0.140 Extract box with map and model: 7.020 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 35.530 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 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 : 0.012 0.075 5172 Z= 0.820 Angle : 1.434 8.458 7088 Z= 1.063 Chirality : 0.062 0.254 799 Planarity : 0.010 0.119 923 Dihedral : 10.651 89.081 1879 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: 1.06 (0.30), residues: 661 helix: 1.33 (0.26), residues: 322 sheet: 0.06 (0.51), residues: 62 loop : 0.26 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 400 HIS 0.004 0.000 HIS A 135 PHE 0.014 0.001 PHE B 331 TYR 0.001 0.000 TYR A 188 ARG 0.007 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 ARG cc_start: 0.8421 (mtt180) cc_final: 0.8081 (tpp80) REVERT: B 268 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8733 (mp0) REVERT: B 398 LEU cc_start: 0.8050 (mt) cc_final: 0.7797 (mt) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.4394 time to fit residues: 48.3373 Evaluate side-chains 64 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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: 0.7124 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5172 Z= 0.241 Angle : 0.605 5.943 7088 Z= 0.323 Chirality : 0.037 0.133 799 Planarity : 0.006 0.045 923 Dihedral : 4.301 16.214 722 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 1.80 (0.31), residues: 661 helix: 2.47 (0.27), residues: 326 sheet: -0.55 (0.49), residues: 84 loop : 0.20 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 216 HIS 0.003 0.001 HIS B 169 PHE 0.012 0.001 PHE A 331 TYR 0.007 0.001 TYR B 187 ARG 0.005 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 247 TRP cc_start: 0.7418 (p90) cc_final: 0.6969 (p90) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.4592 time to fit residues: 41.4085 Evaluate side-chains 55 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 64 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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: 0.7113 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5172 Z= 0.153 Angle : 0.531 5.762 7088 Z= 0.272 Chirality : 0.036 0.136 799 Planarity : 0.006 0.051 923 Dihedral : 3.994 15.029 722 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.95 (0.32), residues: 661 helix: 2.63 (0.27), residues: 327 sheet: -0.80 (0.48), residues: 84 loop : 0.33 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 216 HIS 0.002 0.000 HIS A 199 PHE 0.012 0.001 PHE A 331 TYR 0.013 0.001 TYR B 455 ARG 0.003 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.3652 time to fit residues: 30.3276 Evaluate side-chains 54 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 53 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7128 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5172 Z= 0.152 Angle : 0.505 5.689 7088 Z= 0.251 Chirality : 0.035 0.138 799 Planarity : 0.005 0.051 923 Dihedral : 3.737 13.454 722 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 2.10 (0.32), residues: 661 helix: 2.86 (0.27), residues: 326 sheet: -1.09 (0.47), residues: 84 loop : 0.39 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 472 HIS 0.003 0.001 HIS B 169 PHE 0.010 0.001 PHE A 331 TYR 0.008 0.001 TYR B 455 ARG 0.002 0.000 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 TYR cc_start: 0.8963 (m-80) cc_final: 0.8210 (m-80) REVERT: B 219 GLU cc_start: 0.9391 (mt-10) cc_final: 0.9047 (tm-30) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.3764 time to fit residues: 30.8361 Evaluate side-chains 53 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.0670 chunk 12 optimal weight: 10.0000 overall best weight: 1.1322 ------------------------------------------------------------------------------- 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: 0.7148 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5172 Z= 0.158 Angle : 0.506 5.596 7088 Z= 0.251 Chirality : 0.036 0.138 799 Planarity : 0.005 0.050 923 Dihedral : 3.686 13.731 722 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.18 (0.33), residues: 661 helix: 2.92 (0.27), residues: 326 sheet: -1.05 (0.48), residues: 84 loop : 0.43 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 472 HIS 0.014 0.001 HIS B 348 PHE 0.007 0.001 PHE A 331 TYR 0.006 0.001 TYR B 187 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 TYR cc_start: 0.8956 (m-80) cc_final: 0.8251 (m-80) REVERT: B 219 GLU cc_start: 0.9388 (mt-10) cc_final: 0.9007 (tm-30) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.3647 time to fit residues: 28.4473 Evaluate side-chains 53 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 21 optimal weight: 0.0000 chunk 33 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.9992 ------------------------------------------------------------------------------- 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: 0.7272 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5172 Z= 0.302 Angle : 0.642 5.779 7088 Z= 0.333 Chirality : 0.038 0.148 799 Planarity : 0.006 0.039 923 Dihedral : 4.059 14.629 722 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 1.00 (0.32), residues: 661 helix: 1.62 (0.27), residues: 336 sheet: -1.23 (0.53), residues: 69 loop : 0.06 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 472 HIS 0.006 0.002 HIS A 166 PHE 0.013 0.002 PHE A 331 TYR 0.009 0.002 TYR B 187 ARG 0.018 0.001 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.3577 time to fit residues: 23.2266 Evaluate side-chains 39 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 6.9990 chunk 36 optimal weight: 0.0470 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- 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: 0.7191 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5172 Z= 0.151 Angle : 0.521 5.503 7088 Z= 0.258 Chirality : 0.036 0.142 799 Planarity : 0.005 0.043 923 Dihedral : 3.786 13.753 722 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: 1.79 (0.33), residues: 661 helix: 2.50 (0.28), residues: 328 sheet: -1.14 (0.51), residues: 75 loop : 0.29 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 472 HIS 0.002 0.001 HIS B 348 PHE 0.008 0.001 PHE B 171 TYR 0.015 0.002 TYR A 455 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.3390 time to fit residues: 23.5251 Evaluate side-chains 44 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.7273 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5172 Z= 0.323 Angle : 0.639 5.719 7088 Z= 0.332 Chirality : 0.038 0.141 799 Planarity : 0.006 0.036 923 Dihedral : 4.004 14.306 722 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 0.90 (0.32), residues: 661 helix: 1.58 (0.27), residues: 335 sheet: -1.32 (0.53), residues: 69 loop : -0.02 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 216 HIS 0.005 0.001 HIS A 166 PHE 0.013 0.002 PHE A 294 TYR 0.017 0.002 TYR A 455 ARG 0.005 0.001 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.3426 time to fit residues: 22.6612 Evaluate side-chains 42 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 0.0670 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5172 Z= 0.166 Angle : 0.528 5.558 7088 Z= 0.263 Chirality : 0.036 0.142 799 Planarity : 0.006 0.052 923 Dihedral : 3.847 14.474 722 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.49 (0.33), residues: 661 helix: 2.18 (0.28), residues: 333 sheet: -1.22 (0.51), residues: 75 loop : 0.17 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 216 HIS 0.005 0.001 HIS B 135 PHE 0.033 0.002 PHE B 171 TYR 0.027 0.002 TYR A 455 ARG 0.004 0.000 ARG B 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.3450 time to fit residues: 23.0472 Evaluate side-chains 44 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 0.0040 chunk 52 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5172 Z= 0.149 Angle : 0.507 5.565 7088 Z= 0.249 Chirality : 0.036 0.138 799 Planarity : 0.005 0.039 923 Dihedral : 3.679 13.679 722 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.84 (0.33), residues: 661 helix: 2.61 (0.28), residues: 327 sheet: -1.31 (0.51), residues: 73 loop : 0.27 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 216 HIS 0.012 0.001 HIS B 135 PHE 0.009 0.001 PHE A 294 TYR 0.015 0.001 TYR A 455 ARG 0.005 0.000 ARG B 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.3444 time to fit residues: 23.5672 Evaluate side-chains 44 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 7.9990 chunk 21 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** 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 = 0.3519 r_free = 0.3519 target = 0.049898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.038609 restraints weight = 130517.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.040411 restraints weight = 76490.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.041741 restraints weight = 51590.578| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5172 Z= 0.183 Angle : 0.525 5.572 7088 Z= 0.262 Chirality : 0.036 0.138 799 Planarity : 0.005 0.037 923 Dihedral : 3.672 14.270 722 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.67 (0.33), residues: 661 helix: 2.47 (0.28), residues: 327 sheet: -1.52 (0.51), residues: 67 loop : 0.19 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 472 HIS 0.006 0.001 HIS A 135 PHE 0.010 0.001 PHE A 294 TYR 0.034 0.002 TYR A 455 ARG 0.005 0.000 ARG B 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2722.02 seconds wall clock time: 48 minutes 21.15 seconds (2901.15 seconds total)