Starting phenix.real_space_refine on Sat Dec 9 04:28:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds6_27684/12_2023/8ds6_27684.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds6_27684/12_2023/8ds6_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_27684/12_2023/8ds6_27684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds6_27684/12_2023/8ds6_27684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds6_27684/12_2023/8ds6_27684.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds6_27684/12_2023/8ds6_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-1.21rc1-5172/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: 5.13, per 1000 atoms: 0.51 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: 8.28 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: 0.98 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: 3.96 Time building geometry restraints manager: 8.60 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: 4490 17.82 - 35.63: 135 35.63 - 53.45: 53 53.45 - 71.26: 10 71.26 - 89.08: 4 Dihedral angle restraints: 4692 sinusoidal: 2536 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 4689 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: 2.140 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: 0.160 Extract box with map and model: 6.980 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 37.330 Find NCS groups from input model: 0.440 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.030 ------------------------------------------------------------------------------- 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 : 0.856 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 outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.4794 time to fit residues: 53.2202 Evaluate side-chains 60 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0766 ------------------------------------------------------------------------------- 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: 5.9990 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: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5172 Z= 0.289 Angle : 0.636 6.006 7088 Z= 0.343 Chirality : 0.037 0.137 799 Planarity : 0.006 0.044 923 Dihedral : 4.319 16.423 722 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.53 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: 1.69 (0.31), residues: 661 helix: 2.30 (0.27), residues: 326 sheet: -0.54 (0.49), residues: 78 loop : 0.20 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 216 HIS 0.004 0.001 HIS B 169 PHE 0.012 0.001 PHE A 331 TYR 0.008 0.001 TYR B 187 ARG 0.006 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 66 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.4379 time to fit residues: 36.2884 Evaluate side-chains 52 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.869 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9970 ------------------------------------------------------------------------------- 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: 0.9990 chunk 18 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 0.0370 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 0.0970 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5172 Z= 0.162 Angle : 0.534 5.717 7088 Z= 0.275 Chirality : 0.037 0.137 799 Planarity : 0.006 0.050 923 Dihedral : 4.031 14.742 722 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: 1.98 (0.32), residues: 661 helix: 2.64 (0.27), residues: 326 sheet: -0.76 (0.49), residues: 84 loop : 0.36 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 216 HIS 0.002 0.000 HIS A 199 PHE 0.013 0.001 PHE A 331 TYR 0.007 0.001 TYR B 455 ARG 0.004 0.000 ARG A 156 *********************** 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 61 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.834 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 outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.3428 time to fit residues: 27.8772 Evaluate side-chains 51 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.826 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9899 ------------------------------------------------------------------------------- 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: 1.9990 chunk 6 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 17 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3042 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= 0.170 Angle : 0.528 5.714 7088 Z= 0.263 Chirality : 0.036 0.140 799 Planarity : 0.005 0.048 923 Dihedral : 3.800 15.551 722 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: 2.05 (0.32), residues: 661 helix: 2.72 (0.27), residues: 326 sheet: -0.93 (0.49), residues: 84 loop : 0.44 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 472 HIS 0.002 0.001 HIS A 166 PHE 0.009 0.001 PHE A 331 TYR 0.007 0.001 TYR B 187 ARG 0.001 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 60 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.878 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 outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.3436 time to fit residues: 27.5685 Evaluate side-chains 50 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.815 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9458 ------------------------------------------------------------------------------- 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: 0.1980 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 54 optimal weight: 0.0870 chunk 44 optimal weight: 0.0000 chunk 32 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 0.0170 chunk 12 optimal weight: 8.9990 overall best weight: 0.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.3247 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= 0.137 Angle : 0.497 5.571 7088 Z= 0.242 Chirality : 0.036 0.137 799 Planarity : 0.005 0.052 923 Dihedral : 3.685 14.051 722 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.20 % Allowed : 0.20 % 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: 2.26 (0.33), residues: 661 helix: 2.97 (0.28), residues: 326 sheet: -0.96 (0.49), residues: 84 loop : 0.49 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 472 HIS 0.011 0.001 HIS B 348 PHE 0.007 0.001 PHE A 331 TYR 0.005 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 61 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.867 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: 1 outliers final: 1 residues processed: 60 average time/residue: 0.3865 time to fit residues: 29.9125 Evaluate side-chains 53 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.792 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1775 time to fit residues: 1.2932 ------------------------------------------------------------------------------- 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: 0.5980 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.7152 moved from start: 0.3464 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= 0.158 Angle : 0.504 5.582 7088 Z= 0.248 Chirality : 0.036 0.138 799 Planarity : 0.005 0.046 923 Dihedral : 3.555 13.951 722 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.81 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: 2.22 (0.33), residues: 661 helix: 2.97 (0.28), residues: 326 sheet: -1.03 (0.49), residues: 84 loop : 0.43 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 472 HIS 0.004 0.001 HIS B 348 PHE 0.012 0.001 PHE A 331 TYR 0.007 0.001 TYR B 187 ARG 0.002 0.000 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 56 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 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 outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.3504 time to fit residues: 26.1115 Evaluate side-chains 50 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.746 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9567 ------------------------------------------------------------------------------- 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: 4.9990 chunk 36 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 19 optimal weight: 0.0870 overall best weight: 1.5562 ------------------------------------------------------------------------------- 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: 0.7189 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5172 Z= 0.181 Angle : 0.522 5.600 7088 Z= 0.260 Chirality : 0.036 0.138 799 Planarity : 0.005 0.043 923 Dihedral : 3.587 12.863 722 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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: 2.04 (0.33), residues: 661 helix: 2.69 (0.28), residues: 334 sheet: -1.04 (0.49), residues: 84 loop : 0.45 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 472 HIS 0.004 0.001 HIS B 348 PHE 0.011 0.001 PHE A 331 TYR 0.007 0.001 TYR B 187 ARG 0.003 0.000 ARG B 156 *********************** 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 56 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.861 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 outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.3549 time to fit residues: 26.6394 Evaluate side-chains 48 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.839 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0338 ------------------------------------------------------------------------------- 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: 7.9990 chunk 43 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.4142 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= 0.226 Angle : 0.566 5.607 7088 Z= 0.283 Chirality : 0.037 0.140 799 Planarity : 0.006 0.059 923 Dihedral : 3.761 13.620 722 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: 1.57 (0.33), residues: 661 helix: 2.26 (0.28), residues: 336 sheet: -1.21 (0.51), residues: 75 loop : 0.18 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 247 HIS 0.004 0.001 HIS B 169 PHE 0.008 0.001 PHE A 294 TYR 0.008 0.001 TYR B 187 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 53 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.876 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: 53 average time/residue: 0.3948 time to fit residues: 27.2687 Evaluate side-chains 43 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.894 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0471 ------------------------------------------------------------------------------- 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: 7.9990 chunk 46 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5172 Z= 0.210 Angle : 0.548 5.656 7088 Z= 0.276 Chirality : 0.036 0.140 799 Planarity : 0.005 0.034 923 Dihedral : 3.746 14.313 722 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: 1.55 (0.33), residues: 661 helix: 2.28 (0.28), residues: 336 sheet: -1.27 (0.51), residues: 75 loop : 0.12 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 0.003 0.000 ARG B 390 *********************** 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 : 0.805 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 outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.3428 time to fit residues: 22.5819 Evaluate side-chains 43 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.764 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9159 ------------------------------------------------------------------------------- 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: 0.2980 chunk 52 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.4347 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 : 0.508 5.563 7088 Z= 0.247 Chirality : 0.036 0.138 799 Planarity : 0.005 0.035 923 Dihedral : 3.613 13.892 722 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: 1.94 (0.34), residues: 661 helix: 2.74 (0.28), residues: 333 sheet: -1.31 (0.50), residues: 75 loop : 0.21 (0.42), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 216 HIS 0.006 0.001 HIS B 135 PHE 0.006 0.001 PHE A 294 TYR 0.008 0.001 TYR A 188 ARG 0.002 0.000 ARG A 357 ********************** 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 : 0.889 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 outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.3552 time to fit residues: 23.9048 Evaluate side-chains 43 residues out of total 509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.914 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0432 ------------------------------------------------------------------------------- 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: 8.9990 chunk 21 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.049630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.038494 restraints weight = 132710.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.040197 restraints weight = 79796.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.041464 restraints weight = 54581.655| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.4483 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= 0.191 Angle : 0.533 5.633 7088 Z= 0.264 Chirality : 0.036 0.137 799 Planarity : 0.005 0.035 923 Dihedral : 3.650 14.202 722 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.67 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: 1.81 (0.33), residues: 661 helix: 2.62 (0.28), residues: 333 sheet: -1.29 (0.50), residues: 73 loop : 0.12 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 216 HIS 0.004 0.001 HIS B 135 PHE 0.008 0.001 PHE A 294 TYR 0.008 0.001 TYR A 188 ARG 0.003 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2901.96 seconds wall clock time: 51 minutes 51.52 seconds (3111.52 seconds total)