Starting phenix.real_space_refine on Wed Sep 25 11:35:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds6_27684/09_2024/8ds6_27684.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds6_27684/09_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_27684/09_2024/8ds6_27684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds6_27684/09_2024/8ds6_27684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds6_27684/09_2024/8ds6_27684.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds6_27684/09_2024/8ds6_27684.cif" } 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. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 4.25, per 1000 atoms: 0.42 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 741.0 milliseconds 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: 0.91 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: 3.73 Time building geometry restraints manager: 3.45 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: 0.00 - 2.61: 16165 2.61 - 5.21: 1903 5.21 - 7.82: 620 7.82 - 10.43: 16 10.43 - 13.04: 17 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 Time spend for trying shortcut: 0.00 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: 16.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.690 Find NCS groups from input model: 0.300 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.400 ------------------------------------------------------------------------------- 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 : 0.806 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: 0.4503 time to fit residues: 49.3674 Evaluate side-chains 64 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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: 2.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 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: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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: 0.7132 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5172 Z= 0.254 Angle : 0.621 6.036 7088 Z= 0.331 Chirality : 0.037 0.135 799 Planarity : 0.006 0.050 923 Dihedral : 4.338 16.391 722 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: 2.43 (0.27), residues: 326 sheet: -0.53 (0.49), residues: 84 loop : 0.24 (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 0.013 0.001 PHE A 331 TYR 0.008 0.001 TYR B 187 ARG 0.005 0.001 ARG A 156 *********************** 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 : 0.820 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: A 398 LEU cc_start: 0.8895 (tp) cc_final: 0.8618 (tt) REVERT: B 247 TRP cc_start: 0.7479 (p90) cc_final: 0.6966 (p90) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.4807 time to fit residues: 43.3266 Evaluate side-chains 53 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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: 0.4980 chunk 18 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.7125 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5172 Z= 0.168 Angle : 0.540 5.741 7088 Z= 0.275 Chirality : 0.037 0.136 799 Planarity : 0.006 0.051 923 Dihedral : 4.021 14.530 722 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: 1.95 (0.32), residues: 661 helix: 2.59 (0.27), residues: 327 sheet: -0.71 (0.49), residues: 84 loop : 0.34 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 450 HIS 0.003 0.001 HIS A 161 PHE 0.010 0.001 PHE B 171 TYR 0.015 0.001 TYR B 455 ARG 0.003 0.000 ARG A 147 *********************** 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 63 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.798 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: B 464 MET cc_start: 0.7276 (mmm) cc_final: 0.6949 (mmp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.3963 time to fit residues: 32.7910 Evaluate side-chains 52 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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: 10.0000 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.7228 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5172 Z= 0.285 Angle : 0.615 5.833 7088 Z= 0.318 Chirality : 0.037 0.145 799 Planarity : 0.006 0.041 923 Dihedral : 4.162 16.008 722 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.20 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: 1.30 (0.32), residues: 661 helix: 1.98 (0.28), residues: 326 sheet: -1.00 (0.49), residues: 78 loop : 0.13 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 472 HIS 0.007 0.001 HIS B 348 PHE 0.013 0.002 PHE A 331 TYR 0.009 0.002 TYR B 187 ARG 0.003 0.001 ARG B 306 *********************** 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 58 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.728 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: B 219 GLU cc_start: 0.9410 (mt-10) cc_final: 0.8947 (tm-30) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.3657 time to fit residues: 27.4800 Evaluate side-chains 46 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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: 0.6980 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 54 optimal weight: 0.0000 chunk 44 optimal weight: 0.1980 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.0870 chunk 12 optimal weight: 10.0000 overall best weight: 0.3962 ------------------------------------------------------------------------------- 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: 0.7155 moved from start: 0.3449 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= 0.150 Angle : 0.514 5.602 7088 Z= 0.256 Chirality : 0.036 0.139 799 Planarity : 0.006 0.046 923 Dihedral : 3.832 13.761 722 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 1.88 (0.33), residues: 661 helix: 2.60 (0.28), residues: 326 sheet: -1.00 (0.48), residues: 84 loop : 0.33 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 472 HIS 0.008 0.001 HIS B 135 PHE 0.013 0.001 PHE A 331 TYR 0.007 0.001 TYR A 188 ARG 0.002 0.000 ARG A 357 *********************** 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 : 0.797 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: B 188 TYR cc_start: 0.8985 (m-80) cc_final: 0.8259 (m-80) REVERT: B 219 GLU cc_start: 0.9391 (mt-10) cc_final: 0.8967 (tm-30) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.3591 time to fit residues: 28.3251 Evaluate side-chains 51 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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: 4.9990 chunk 63 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 0.0170 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.9624 ------------------------------------------------------------------------------- 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: 0.7227 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5172 Z= 0.232 Angle : 0.564 5.781 7088 Z= 0.287 Chirality : 0.036 0.145 799 Planarity : 0.006 0.037 923 Dihedral : 3.876 14.304 722 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.20 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: 1.57 (0.34), residues: 661 helix: 2.27 (0.28), residues: 326 sheet: -1.19 (0.49), residues: 78 loop : 0.26 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 472 HIS 0.004 0.001 HIS A 166 PHE 0.010 0.001 PHE A 294 TYR 0.007 0.001 TYR B 187 ARG 0.006 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 51 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.785 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: 51 average time/residue: 0.3624 time to fit residues: 24.3132 Evaluate side-chains 46 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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: 3.9990 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.7190 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 : 0.002 0.036 5172 Z= 0.150 Angle : 0.506 5.668 7088 Z= 0.250 Chirality : 0.036 0.140 799 Planarity : 0.005 0.040 923 Dihedral : 3.720 13.231 722 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: 1.87 (0.34), residues: 661 helix: 2.63 (0.28), residues: 326 sheet: -1.23 (0.49), residues: 78 loop : 0.30 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 472 HIS 0.002 0.000 HIS B 169 PHE 0.007 0.001 PHE A 294 TYR 0.007 0.001 TYR A 188 ARG 0.002 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 54 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.717 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: 0.8926 (m-80) cc_final: 0.8205 (m-80) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.3132 time to fit residues: 22.9522 Evaluate side-chains 46 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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: 10.0000 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 59 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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: 0.7225 moved from start: 0.4114 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= 0.201 Angle : 0.536 5.656 7088 Z= 0.268 Chirality : 0.036 0.141 799 Planarity : 0.006 0.035 923 Dihedral : 3.714 13.226 722 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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: 1.64 (0.34), residues: 661 helix: 2.49 (0.29), residues: 325 sheet: -1.48 (0.52), residues: 69 loop : 0.11 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 472 HIS 0.010 0.001 HIS A 135 PHE 0.020 0.002 PHE B 171 TYR 0.007 0.001 TYR B 187 ARG 0.003 0.000 ARG A 357 *********************** 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 51 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.845 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: 51 average time/residue: 0.3339 time to fit residues: 22.9251 Evaluate side-chains 43 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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: 1.9990 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5172 Z= 0.217 Angle : 0.551 5.697 7088 Z= 0.278 Chirality : 0.037 0.140 799 Planarity : 0.006 0.049 923 Dihedral : 3.781 14.099 722 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 1.53 (0.34), residues: 661 helix: 2.41 (0.29), residues: 327 sheet: -1.59 (0.51), residues: 69 loop : 0.04 (0.41), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 216 HIS 0.005 0.001 HIS B 169 PHE 0.022 0.002 PHE B 171 TYR 0.007 0.001 TYR A 188 ARG 0.003 0.000 ARG A 357 *********************** 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 49 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.829 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: A 234 CYS cc_start: 0.7496 (m) cc_final: 0.7280 (t) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.3475 time to fit residues: 22.7971 Evaluate side-chains 44 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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: 0.9990 chunk 52 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.7208 moved from start: 0.4305 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= 0.152 Angle : 0.510 5.607 7088 Z= 0.250 Chirality : 0.036 0.139 799 Planarity : 0.006 0.036 923 Dihedral : 3.670 13.870 722 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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: 1.78 (0.34), residues: 661 helix: 2.71 (0.29), residues: 325 sheet: -1.57 (0.51), residues: 69 loop : 0.07 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 216 HIS 0.004 0.001 HIS B 348 PHE 0.007 0.001 PHE A 294 TYR 0.008 0.001 TYR A 188 ARG 0.006 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 50 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.764 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: 0.3487 time to fit residues: 23.3240 Evaluate side-chains 44 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 0.0980 chunk 53 optimal weight: 0.6980 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.049831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.038349 restraints weight = 129532.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.040126 restraints weight = 76590.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.041490 restraints weight = 52080.083| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5172 Z= 0.146 Angle : 0.503 5.556 7088 Z= 0.246 Chirality : 0.036 0.138 799 Planarity : 0.005 0.036 923 Dihedral : 3.540 13.669 722 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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: 1.89 (0.34), residues: 661 helix: 2.83 (0.28), residues: 325 sheet: -1.54 (0.48), residues: 75 loop : 0.14 (0.42), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 216 HIS 0.008 0.001 HIS B 135 PHE 0.025 0.001 PHE B 171 TYR 0.007 0.001 TYR A 188 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: 2873.78 seconds wall clock time: 50 minutes 42.42 seconds (3042.42 seconds total)