Starting phenix.real_space_refine on Thu May 1 05:14:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ds6_27684/05_2025/8ds6_27684.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ds6_27684/05_2025/8ds6_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/cci-nas-00/data/ceres_data/8ds6_27684/05_2025/8ds6_27684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ds6_27684/05_2025/8ds6_27684.map" model { file = "/net/cci-nas-00/data/ceres_data/8ds6_27684/05_2025/8ds6_27684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ds6_27684/05_2025/8ds6_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-5669/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: 6.27, per 1000 atoms: 0.62 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: 3.11 Conformation dependent library (CDL) restraints added in 809.2 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: 1.05 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: 3.62 Time building geometry restraints manager: 3.69 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: 2.700 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.340 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.230 ------------------------------------------------------------------------------- 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= 0.837 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 Details of bonding type rmsd hydrogen bonds : bond 0.20831 ( 310) hydrogen bonds : angle 6.85343 ( 909) covalent geometry : bond 0.01234 ( 5172) covalent geometry : angle 1.43355 ( 7088) *********************** 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 to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.008 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: 0.4852 time to fit residues: 53.6783 Evaluate side-chains 64 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.050069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.038271 restraints weight = 119545.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.040088 restraints weight = 70510.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.041436 restraints weight = 48106.547| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 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= 0.187 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 Details of bonding type rmsd hydrogen bonds : bond 0.07135 ( 310) hydrogen bonds : angle 5.37932 ( 909) covalent geometry : bond 0.00376 ( 5172) covalent geometry : angle 0.62078 ( 7088) *********************** 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 to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 2.631 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: 0.8459 (tp) cc_final: 0.8119 (tt) REVERT: B 247 TRP cc_start: 0.7629 (p90) cc_final: 0.6974 (p90) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.6096 time to fit residues: 57.1344 Evaluate side-chains 53 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 50 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 3 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.051323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.039006 restraints weight = 119620.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.040930 restraints weight = 69320.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.042369 restraints weight = 46956.647| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.2708 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= 0.124 Angle : 0.534 5.706 7088 Z= 0.271 Chirality : 0.037 0.136 799 Planarity : 0.006 0.050 923 Dihedral : 4.005 14.358 722 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: 2.00 (0.32), residues: 661 helix: 2.64 (0.27), residues: 327 sheet: -0.72 (0.49), residues: 84 loop : 0.38 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 216 HIS 0.002 0.001 HIS A 161 PHE 0.009 0.001 PHE B 171 TYR 0.016 0.001 TYR B 455 ARG 0.003 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.05722 ( 310) hydrogen bonds : angle 4.88579 ( 909) covalent geometry : bond 0.00241 ( 5172) covalent geometry : angle 0.53418 ( 7088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.801 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: B 464 MET cc_start: 0.7485 (mmm) cc_final: 0.7193 (mmp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.3627 time to fit residues: 30.4058 Evaluate side-chains 53 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 30 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 54 optimal weight: 0.0040 chunk 41 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 21 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.051297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.039407 restraints weight = 121355.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.041264 restraints weight = 71427.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.042689 restraints weight = 48833.941| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.2980 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= 0.123 Angle : 0.518 5.669 7088 Z= 0.262 Chirality : 0.036 0.139 799 Planarity : 0.006 0.049 923 Dihedral : 3.919 14.203 722 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: 2.02 (0.33), residues: 661 helix: 2.73 (0.27), residues: 326 sheet: -0.93 (0.47), residues: 84 loop : 0.37 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 472 HIS 0.005 0.001 HIS B 348 PHE 0.012 0.001 PHE A 331 TYR 0.010 0.001 TYR A 455 ARG 0.002 0.000 ARG B 306 Details of bonding type rmsd hydrogen bonds : bond 0.05109 ( 310) hydrogen bonds : angle 4.73920 ( 909) covalent geometry : bond 0.00244 ( 5172) covalent geometry : angle 0.51780 ( 7088) *********************** 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 63 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.737 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: 63 average time/residue: 0.3649 time to fit residues: 29.9871 Evaluate side-chains 50 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.050039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.038529 restraints weight = 127172.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.040340 restraints weight = 74488.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.041739 restraints weight = 50595.331| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5172 Z= 0.122 Angle : 0.512 5.595 7088 Z= 0.257 Chirality : 0.036 0.138 799 Planarity : 0.006 0.047 923 Dihedral : 3.720 14.147 722 Min Nonbonded Distance : 2.319 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: 2.03 (0.33), residues: 661 helix: 2.83 (0.28), residues: 326 sheet: -1.21 (0.47), residues: 78 loop : 0.30 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 472 HIS 0.003 0.001 HIS A 166 PHE 0.012 0.001 PHE B 171 TYR 0.007 0.001 TYR A 455 ARG 0.002 0.000 ARG A 438 Details of bonding type rmsd hydrogen bonds : bond 0.04670 ( 310) hydrogen bonds : angle 4.57850 ( 909) covalent geometry : bond 0.00243 ( 5172) covalent geometry : angle 0.51225 ( 7088) *********************** 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 to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 TYR cc_start: 0.9004 (m-80) cc_final: 0.8453 (m-80) REVERT: B 219 GLU cc_start: 0.9468 (mt-10) cc_final: 0.9084 (tm-30) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.3604 time to fit residues: 28.5372 Evaluate side-chains 50 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 39 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.049128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.038136 restraints weight = 131301.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.039849 restraints weight = 77584.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.041147 restraints weight = 52634.259| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5172 Z= 0.183 Angle : 0.573 5.691 7088 Z= 0.295 Chirality : 0.037 0.146 799 Planarity : 0.006 0.039 923 Dihedral : 3.886 13.967 722 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.33), residues: 661 helix: 2.29 (0.28), residues: 326 sheet: -1.21 (0.48), residues: 78 loop : 0.23 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 472 HIS 0.006 0.001 HIS A 166 PHE 0.010 0.002 PHE A 294 TYR 0.008 0.001 TYR B 187 ARG 0.005 0.001 ARG B 156 Details of bonding type rmsd hydrogen bonds : bond 0.04696 ( 310) hydrogen bonds : angle 4.62136 ( 909) covalent geometry : bond 0.00363 ( 5172) covalent geometry : angle 0.57293 ( 7088) *********************** 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 53 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.800 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 outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.3732 time to fit residues: 25.8583 Evaluate side-chains 42 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 9 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.049589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.038539 restraints weight = 132390.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.040314 restraints weight = 77893.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.041628 restraints weight = 52852.603| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.3827 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= 0.115 Angle : 0.516 5.622 7088 Z= 0.257 Chirality : 0.036 0.141 799 Planarity : 0.006 0.039 923 Dihedral : 3.719 13.081 722 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.33 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: 1.88 (0.34), residues: 661 helix: 2.68 (0.28), residues: 325 sheet: -1.26 (0.49), residues: 78 loop : 0.27 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 472 HIS 0.006 0.001 HIS A 135 PHE 0.013 0.001 PHE A 331 TYR 0.007 0.001 TYR A 188 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 310) hydrogen bonds : angle 4.38957 ( 909) covalent geometry : bond 0.00238 ( 5172) covalent geometry : angle 0.51589 ( 7088) *********************** 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 55 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.848 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: 55 average time/residue: 0.3115 time to fit residues: 23.5892 Evaluate side-chains 44 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 7 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.049386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.038200 restraints weight = 132047.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.039935 restraints weight = 76910.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.041283 restraints weight = 52145.029| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.4070 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= 0.139 Angle : 0.528 5.678 7088 Z= 0.264 Chirality : 0.036 0.143 799 Planarity : 0.006 0.036 923 Dihedral : 3.691 13.054 722 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.34), residues: 661 helix: 2.67 (0.29), residues: 325 sheet: -1.30 (0.49), residues: 78 loop : 0.17 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 472 HIS 0.004 0.001 HIS A 166 PHE 0.017 0.002 PHE B 171 TYR 0.006 0.001 TYR B 187 ARG 0.003 0.000 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.04296 ( 310) hydrogen bonds : angle 4.36308 ( 909) covalent geometry : bond 0.00283 ( 5172) covalent geometry : angle 0.52757 ( 7088) *********************** 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 50 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.3312 time to fit residues: 22.4832 Evaluate side-chains 42 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 19 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.049749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.038383 restraints weight = 130156.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.040144 restraints weight = 76114.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.041493 restraints weight = 51967.336| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.4151 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= 0.110 Angle : 0.511 5.602 7088 Z= 0.251 Chirality : 0.036 0.139 799 Planarity : 0.006 0.039 923 Dihedral : 3.622 13.385 722 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.34), residues: 661 helix: 2.88 (0.29), residues: 325 sheet: -1.23 (0.48), residues: 84 loop : 0.27 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 216 HIS 0.002 0.001 HIS A 166 PHE 0.008 0.001 PHE A 331 TYR 0.007 0.001 TYR A 188 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 310) hydrogen bonds : angle 4.28769 ( 909) covalent geometry : bond 0.00230 ( 5172) covalent geometry : angle 0.51092 ( 7088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.3385 time to fit residues: 23.1872 Evaluate side-chains 43 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 57 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 166 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 = 0.3475 r_free = 0.3475 target = 0.048789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.038139 restraints weight = 136704.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.039827 restraints weight = 81313.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.041115 restraints weight = 55188.922| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5172 Z= 0.202 Angle : 0.607 5.773 7088 Z= 0.311 Chirality : 0.037 0.142 799 Planarity : 0.006 0.038 923 Dihedral : 3.880 14.110 722 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % 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: 1.14 (0.33), residues: 661 helix: 2.05 (0.28), residues: 327 sheet: -1.65 (0.52), residues: 69 loop : -0.14 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 472 HIS 0.015 0.002 HIS B 135 PHE 0.016 0.002 PHE B 171 TYR 0.008 0.002 TYR A 150 ARG 0.007 0.001 ARG B 156 Details of bonding type rmsd hydrogen bonds : bond 0.04488 ( 310) hydrogen bonds : angle 4.52267 ( 909) covalent geometry : bond 0.00404 ( 5172) covalent geometry : angle 0.60654 ( 7088) ********************** 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 45 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.846 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: 45 average time/residue: 0.3354 time to fit residues: 20.4692 Evaluate side-chains 40 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 0.0670 chunk 7 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.049596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.038387 restraints weight = 131396.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.040151 restraints weight = 78425.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.041471 restraints weight = 53273.942| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.4459 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= 0.105 Angle : 0.514 5.560 7088 Z= 0.252 Chirality : 0.036 0.139 799 Planarity : 0.006 0.034 923 Dihedral : 3.690 14.625 722 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.32 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: 1.73 (0.34), residues: 661 helix: 2.69 (0.29), residues: 327 sheet: -1.49 (0.49), residues: 75 loop : 0.01 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 216 HIS 0.003 0.001 HIS B 135 PHE 0.007 0.001 PHE A 294 TYR 0.008 0.001 TYR A 188 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 310) hydrogen bonds : angle 4.27614 ( 909) covalent geometry : bond 0.00224 ( 5172) covalent geometry : angle 0.51357 ( 7088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3927.21 seconds wall clock time: 68 minutes 21.16 seconds (4101.16 seconds total)