Starting phenix.real_space_refine on Thu Mar 6 03:12:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kbf_62223/03_2025/9kbf_62223.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kbf_62223/03_2025/9kbf_62223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kbf_62223/03_2025/9kbf_62223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kbf_62223/03_2025/9kbf_62223.map" model { file = "/net/cci-nas-00/data/ceres_data/9kbf_62223/03_2025/9kbf_62223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kbf_62223/03_2025/9kbf_62223.cif" } resolution = 3.74 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 2922 2.51 5 N 763 2.21 5 O 873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4587 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1298 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 10, 'TRANS': 151} Chain: "C" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3289 Classifications: {'peptide': 407} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 385} Time building chain proxies: 4.17, per 1000 atoms: 0.91 Number of scatterers: 4587 At special positions: 0 Unit cell: (66.42, 115.62, 113.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 873 8.00 N 763 7.00 C 2922 6.00 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: 1.05 Conformation dependent library (CDL) restraints added in 537.4 milliseconds 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1080 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 10 sheets defined 43.6% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 24 through 34 Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.549A pdb=" N ASP B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 65 Processing helix chain 'B' and resid 75 through 79 removed outlier: 3.598A pdb=" N GLU B 79 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 93 Processing helix chain 'B' and resid 96 through 111 Processing helix chain 'B' and resid 112 through 126 Processing helix chain 'B' and resid 131 through 139 Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'C' and resid 17 through 27 removed outlier: 3.747A pdb=" N PHE C 27 " --> pdb=" O LEU C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 38 removed outlier: 3.943A pdb=" N TYR C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 48 removed outlier: 3.568A pdb=" N SER C 48 " --> pdb=" O SER C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 56 removed outlier: 3.899A pdb=" N ARG C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N HIS C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 51 through 56' Processing helix chain 'C' and resid 64 through 72 Processing helix chain 'C' and resid 74 through 87 removed outlier: 3.645A pdb=" N ASP C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 107 removed outlier: 4.472A pdb=" N ALA C 94 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ALA C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS C 105 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 118 removed outlier: 4.644A pdb=" N VAL C 115 " --> pdb=" O CYS C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 135 removed outlier: 3.520A pdb=" N LEU C 127 " --> pdb=" O ARG C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 149 Processing helix chain 'C' and resid 176 through 183 Processing helix chain 'C' and resid 244 through 258 Processing helix chain 'C' and resid 347 through 351 removed outlier: 3.906A pdb=" N GLY C 350 " --> pdb=" O GLY C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 415 Processing sheet with id=AA1, first strand: chain 'B' and resid 13 through 17 removed outlier: 9.550A pdb=" N VAL B 45 " --> pdb=" O SER B 3 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LYS B 5 " --> pdb=" O VAL B 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 162 through 164 Processing sheet with id=AA3, first strand: chain 'C' and resid 173 through 174 Processing sheet with id=AA4, first strand: chain 'C' and resid 185 through 186 Processing sheet with id=AA5, first strand: chain 'C' and resid 224 through 226 Processing sheet with id=AA6, first strand: chain 'C' and resid 263 through 264 Processing sheet with id=AA7, first strand: chain 'C' and resid 284 through 285 Processing sheet with id=AA8, first strand: chain 'C' and resid 284 through 285 removed outlier: 3.631A pdb=" N TYR C 363 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.541A pdb=" N CYS C 324 " --> pdb=" O ILE C 355 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 340 through 343 removed outlier: 3.837A pdb=" N VAL C 343 " --> pdb=" O TRP C 331 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP C 331 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY C 378 " --> pdb=" O ILE C 396 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 525 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1489 1.34 - 1.46: 872 1.46 - 1.58: 2297 1.58 - 1.69: 0 1.69 - 1.81: 41 Bond restraints: 4699 Sorted by residual: bond pdb=" N MET C 415 " pdb=" CA MET C 415 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.34e-02 5.57e+03 5.42e+00 bond pdb=" N GLU B 161 " pdb=" CA GLU B 161 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.27e-02 6.20e+03 5.10e+00 bond pdb=" N CYS B 160 " pdb=" CA CYS B 160 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.28e-02 6.10e+03 4.54e+00 bond pdb=" N TRP B 159 " pdb=" CA TRP B 159 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.41e-02 5.03e+03 3.91e+00 bond pdb=" N GLY C 416 " pdb=" CA GLY C 416 " ideal model delta sigma weight residual 1.451 1.476 -0.025 1.60e-02 3.91e+03 2.41e+00 ... (remaining 4694 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 6071 1.32 - 2.64: 242 2.64 - 3.96: 43 3.96 - 5.28: 9 5.28 - 6.60: 7 Bond angle restraints: 6372 Sorted by residual: angle pdb=" C VAL C 348 " pdb=" N VAL C 349 " pdb=" CA VAL C 349 " ideal model delta sigma weight residual 121.97 128.21 -6.24 1.80e+00 3.09e-01 1.20e+01 angle pdb=" N CYS B 160 " pdb=" CA CYS B 160 " pdb=" C CYS B 160 " ideal model delta sigma weight residual 111.82 108.03 3.79 1.16e+00 7.43e-01 1.06e+01 angle pdb=" C ASP B 41 " pdb=" N ASP B 42 " pdb=" CA ASP B 42 " ideal model delta sigma weight residual 121.54 127.33 -5.79 1.91e+00 2.74e-01 9.18e+00 angle pdb=" CA MET C 415 " pdb=" C MET C 415 " pdb=" O MET C 415 " ideal model delta sigma weight residual 121.87 118.46 3.41 1.16e+00 7.43e-01 8.66e+00 angle pdb=" N TRP B 159 " pdb=" CA TRP B 159 " pdb=" C TRP B 159 " ideal model delta sigma weight residual 113.18 109.43 3.75 1.33e+00 5.65e-01 7.96e+00 ... (remaining 6367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 2497 16.20 - 32.40: 265 32.40 - 48.60: 55 48.60 - 64.80: 13 64.80 - 81.00: 7 Dihedral angle restraints: 2837 sinusoidal: 1165 harmonic: 1672 Sorted by residual: dihedral pdb=" CA ASP B 42 " pdb=" CB ASP B 42 " pdb=" CG ASP B 42 " pdb=" OD1 ASP B 42 " ideal model delta sinusoidal sigma weight residual -30.00 -88.09 58.09 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP C 327 " pdb=" CB ASP C 327 " pdb=" CG ASP C 327 " pdb=" OD1 ASP C 327 " ideal model delta sinusoidal sigma weight residual -30.00 -87.12 57.12 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA ALA C 95 " pdb=" C ALA C 95 " pdb=" N ILE C 96 " pdb=" CA ILE C 96 " ideal model delta harmonic sigma weight residual -180.00 -163.77 -16.23 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 2834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 543 0.051 - 0.102: 116 0.102 - 0.153: 31 0.153 - 0.204: 2 0.204 - 0.254: 1 Chirality restraints: 693 Sorted by residual: chirality pdb=" CB VAL C 349 " pdb=" CA VAL C 349 " pdb=" CG1 VAL C 349 " pdb=" CG2 VAL C 349 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA CYS B 160 " pdb=" N CYS B 160 " pdb=" C CYS B 160 " pdb=" CB CYS B 160 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA ASN C 72 " pdb=" N ASN C 72 " pdb=" C ASN C 72 " pdb=" CB ASN C 72 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 ... (remaining 690 not shown) Planarity restraints: 825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 158 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.37e+01 pdb=" C GLN B 158 " 0.064 2.00e-02 2.50e+03 pdb=" O GLN B 158 " -0.025 2.00e-02 2.50e+03 pdb=" N TRP B 159 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 356 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO C 357 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 357 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 357 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 50 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO C 51 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 51 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 51 " -0.023 5.00e-02 4.00e+02 ... (remaining 822 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 397 2.74 - 3.28: 4598 3.28 - 3.82: 7739 3.82 - 4.36: 8909 4.36 - 4.90: 15241 Nonbonded interactions: 36884 Sorted by model distance: nonbonded pdb=" OG SER C 298 " pdb=" O PRO C 301 " model vdw 2.199 3.040 nonbonded pdb=" O LYS B 130 " pdb=" ND2 ASN C 35 " model vdw 2.229 3.120 nonbonded pdb=" OE1 GLN C 185 " pdb=" OH TYR C 207 " model vdw 2.283 3.040 nonbonded pdb=" OD1 ASP C 85 " pdb=" NH2 ARG C 147 " model vdw 2.309 3.120 nonbonded pdb=" O MET C 114 " pdb=" OG SER C 117 " model vdw 2.323 3.040 ... (remaining 36879 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.970 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4699 Z= 0.282 Angle : 0.639 6.603 6372 Z= 0.351 Chirality : 0.047 0.254 693 Planarity : 0.005 0.046 825 Dihedral : 14.543 80.996 1757 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.20 % Allowed : 0.78 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.16 (0.35), residues: 565 helix: -0.62 (0.32), residues: 220 sheet: -1.10 (0.54), residues: 96 loop : -0.56 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 159 HIS 0.006 0.001 HIS C 49 PHE 0.012 0.002 PHE C 306 TYR 0.010 0.002 TYR C 142 ARG 0.002 0.000 ARG C 332 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7946 (tm-30) REVERT: C 40 SER cc_start: 0.8457 (t) cc_final: 0.8257 (m) REVERT: C 100 TRP cc_start: 0.8636 (m100) cc_final: 0.7667 (m100) REVERT: C 101 ASP cc_start: 0.7780 (t70) cc_final: 0.7148 (t0) REVERT: C 270 ARG cc_start: 0.8276 (mtt-85) cc_final: 0.8021 (ttm-80) REVERT: C 274 ASP cc_start: 0.7487 (t70) cc_final: 0.6590 (t70) REVERT: C 325 GLN cc_start: 0.7425 (tt0) cc_final: 0.6909 (tt0) REVERT: C 406 PHE cc_start: 0.8156 (p90) cc_final: 0.7844 (p90) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.2065 time to fit residues: 41.0169 Evaluate side-chains 103 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.9980 chunk 42 optimal weight: 0.0470 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 HIS C 152 GLN C 267 GLN C 325 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.152666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.123411 restraints weight = 7296.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.126047 restraints weight = 5286.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.127799 restraints weight = 4226.084| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 4699 Z= 0.288 Angle : 0.621 6.304 6372 Z= 0.320 Chirality : 0.044 0.144 693 Planarity : 0.004 0.036 825 Dihedral : 4.395 19.151 620 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.18 % Allowed : 12.55 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.35), residues: 565 helix: -0.10 (0.34), residues: 227 sheet: -1.45 (0.58), residues: 77 loop : -0.46 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 88 HIS 0.004 0.001 HIS C 49 PHE 0.012 0.002 PHE C 249 TYR 0.011 0.001 TYR C 380 ARG 0.004 0.000 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 81 ARG cc_start: 0.8125 (ptp-110) cc_final: 0.7581 (mtm110) REVERT: B 125 ASN cc_start: 0.8724 (m-40) cc_final: 0.8465 (m-40) REVERT: B 158 GLN cc_start: 0.7848 (tm-30) cc_final: 0.7238 (tm-30) REVERT: C 15 SER cc_start: 0.8606 (p) cc_final: 0.8252 (t) REVERT: C 229 MET cc_start: 0.7352 (tmm) cc_final: 0.6789 (tmm) outliers start: 6 outliers final: 5 residues processed: 114 average time/residue: 0.1452 time to fit residues: 21.6201 Evaluate side-chains 103 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 394 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 chunk 49 optimal weight: 0.0970 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.153188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.123512 restraints weight = 7437.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.126161 restraints weight = 5332.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.127994 restraints weight = 4237.385| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 4699 Z= 0.256 Angle : 0.560 5.235 6372 Z= 0.290 Chirality : 0.044 0.148 693 Planarity : 0.004 0.034 825 Dihedral : 4.239 16.218 620 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.76 % Allowed : 15.10 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.35), residues: 565 helix: 0.06 (0.34), residues: 226 sheet: -1.51 (0.57), residues: 77 loop : -0.46 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 88 HIS 0.002 0.001 HIS C 383 PHE 0.011 0.001 PHE C 399 TYR 0.012 0.001 TYR C 380 ARG 0.006 0.000 ARG C 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 99 THR cc_start: 0.8366 (p) cc_final: 0.7917 (t) REVERT: B 125 ASN cc_start: 0.8710 (m-40) cc_final: 0.8492 (m-40) REVERT: C 15 SER cc_start: 0.8592 (p) cc_final: 0.8245 (t) REVERT: C 229 MET cc_start: 0.7492 (tmm) cc_final: 0.6920 (tmm) REVERT: C 248 TRP cc_start: 0.8154 (t60) cc_final: 0.7930 (t60) REVERT: C 274 ASP cc_start: 0.7291 (t70) cc_final: 0.6791 (t0) REVERT: C 401 MET cc_start: 0.8228 (mmm) cc_final: 0.7953 (mmt) outliers start: 9 outliers final: 8 residues processed: 108 average time/residue: 0.1303 time to fit residues: 18.9786 Evaluate side-chains 102 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 394 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 44 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 303 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 = 0.3803 r_free = 0.3803 target = 0.152828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.123247 restraints weight = 7425.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125811 restraints weight = 5328.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.127519 restraints weight = 4259.649| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 4699 Z= 0.249 Angle : 0.558 5.234 6372 Z= 0.290 Chirality : 0.043 0.150 693 Planarity : 0.004 0.038 825 Dihedral : 4.209 17.128 620 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.57 % Allowed : 16.08 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.36), residues: 565 helix: 0.30 (0.34), residues: 227 sheet: -1.54 (0.59), residues: 77 loop : -0.40 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 88 HIS 0.004 0.001 HIS C 303 PHE 0.010 0.001 PHE C 399 TYR 0.011 0.001 TYR C 380 ARG 0.005 0.000 ARG C 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: B 99 THR cc_start: 0.8300 (p) cc_final: 0.7842 (t) REVERT: C 15 SER cc_start: 0.8607 (p) cc_final: 0.8229 (t) REVERT: C 134 ILE cc_start: 0.8756 (mt) cc_final: 0.8333 (mt) REVERT: C 229 MET cc_start: 0.7381 (tmm) cc_final: 0.6830 (tmm) REVERT: C 274 ASP cc_start: 0.7240 (t70) cc_final: 0.6753 (t0) outliers start: 8 outliers final: 6 residues processed: 103 average time/residue: 0.1305 time to fit residues: 18.2283 Evaluate side-chains 97 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 177 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 54 optimal weight: 0.0970 chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.164521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.133476 restraints weight = 7852.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.137181 restraints weight = 5035.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.139790 restraints weight = 3763.806| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 4699 Z= 0.272 Angle : 0.566 5.489 6372 Z= 0.293 Chirality : 0.043 0.155 693 Planarity : 0.004 0.036 825 Dihedral : 4.186 16.531 620 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.55 % Allowed : 17.06 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.36), residues: 565 helix: 0.33 (0.35), residues: 229 sheet: -1.45 (0.60), residues: 77 loop : -0.38 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 88 HIS 0.002 0.001 HIS B 64 PHE 0.011 0.001 PHE C 399 TYR 0.022 0.001 TYR C 252 ARG 0.012 0.001 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: B 81 ARG cc_start: 0.7864 (ptp-110) cc_final: 0.7302 (mtm110) REVERT: B 99 THR cc_start: 0.8554 (p) cc_final: 0.8110 (t) REVERT: C 15 SER cc_start: 0.8703 (p) cc_final: 0.8467 (t) REVERT: C 229 MET cc_start: 0.7627 (tmm) cc_final: 0.7008 (tmm) REVERT: C 274 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6739 (t0) REVERT: C 333 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6681 (mp) outliers start: 13 outliers final: 8 residues processed: 96 average time/residue: 0.1259 time to fit residues: 16.6621 Evaluate side-chains 94 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 394 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 42 optimal weight: 0.2980 chunk 54 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 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 = 0.3996 r_free = 0.3996 target = 0.165542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.133782 restraints weight = 7732.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.137874 restraints weight = 4787.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.140748 restraints weight = 3490.099| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 4699 Z= 0.232 Angle : 0.545 5.284 6372 Z= 0.284 Chirality : 0.043 0.165 693 Planarity : 0.004 0.033 825 Dihedral : 4.099 15.668 620 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.57 % Allowed : 18.82 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.36), residues: 565 helix: 0.51 (0.35), residues: 227 sheet: -1.21 (0.57), residues: 82 loop : -0.40 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 88 HIS 0.003 0.001 HIS B 64 PHE 0.010 0.001 PHE C 399 TYR 0.009 0.001 TYR C 380 ARG 0.006 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: B 81 ARG cc_start: 0.7815 (ptp-110) cc_final: 0.7303 (mtm110) REVERT: C 229 MET cc_start: 0.7664 (tmm) cc_final: 0.7044 (tmm) REVERT: C 274 ASP cc_start: 0.7338 (t70) cc_final: 0.6719 (t0) REVERT: C 333 ILE cc_start: 0.6963 (OUTLIER) cc_final: 0.6521 (mp) REVERT: C 352 PHE cc_start: 0.8370 (m-80) cc_final: 0.7948 (m-10) outliers start: 8 outliers final: 5 residues processed: 92 average time/residue: 0.1254 time to fit residues: 16.2142 Evaluate side-chains 88 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 333 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.0060 chunk 19 optimal weight: 0.2980 chunk 26 optimal weight: 0.0770 chunk 50 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 10 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 HIS C 185 GLN C 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.169176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.137607 restraints weight = 7702.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.141801 restraints weight = 4785.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.144693 restraints weight = 3479.359| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 4699 Z= 0.182 Angle : 0.550 9.294 6372 Z= 0.283 Chirality : 0.042 0.163 693 Planarity : 0.004 0.040 825 Dihedral : 4.037 16.528 620 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.76 % Allowed : 19.80 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.36), residues: 565 helix: 0.66 (0.35), residues: 227 sheet: -1.27 (0.56), residues: 81 loop : -0.31 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 61 HIS 0.003 0.001 HIS B 64 PHE 0.035 0.001 PHE C 399 TYR 0.007 0.001 TYR C 380 ARG 0.004 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: B 81 ARG cc_start: 0.7744 (ptp-110) cc_final: 0.7222 (mtm110) REVERT: B 99 THR cc_start: 0.8498 (p) cc_final: 0.7973 (t) REVERT: C 229 MET cc_start: 0.7616 (tmm) cc_final: 0.7072 (tmm) REVERT: C 274 ASP cc_start: 0.7284 (OUTLIER) cc_final: 0.6683 (t0) REVERT: C 333 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6467 (mp) REVERT: C 352 PHE cc_start: 0.8337 (m-80) cc_final: 0.7921 (m-10) outliers start: 9 outliers final: 6 residues processed: 91 average time/residue: 0.1171 time to fit residues: 14.9861 Evaluate side-chains 90 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 380 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.169115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.135466 restraints weight = 7804.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.139388 restraints weight = 4930.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.142023 restraints weight = 3652.650| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 4699 Z= 0.266 Angle : 0.573 7.379 6372 Z= 0.295 Chirality : 0.043 0.166 693 Planarity : 0.004 0.034 825 Dihedral : 4.042 16.574 620 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.35 % Allowed : 20.20 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.37), residues: 565 helix: 0.66 (0.35), residues: 227 sheet: -0.94 (0.57), residues: 90 loop : -0.22 (0.42), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 248 HIS 0.003 0.001 HIS B 64 PHE 0.021 0.001 PHE C 399 TYR 0.009 0.001 TYR C 142 ARG 0.004 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: B 81 ARG cc_start: 0.7883 (ptp-110) cc_final: 0.7325 (mtm110) REVERT: C 229 MET cc_start: 0.7663 (tmm) cc_final: 0.7111 (tmm) REVERT: C 274 ASP cc_start: 0.7323 (OUTLIER) cc_final: 0.6703 (t0) REVERT: C 333 ILE cc_start: 0.7004 (OUTLIER) cc_final: 0.6444 (mp) REVERT: C 352 PHE cc_start: 0.8309 (m-80) cc_final: 0.7886 (m-10) outliers start: 12 outliers final: 9 residues processed: 92 average time/residue: 0.1258 time to fit residues: 16.3090 Evaluate side-chains 93 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 303 HIS Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 380 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 49 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.167315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.134441 restraints weight = 7841.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.138177 restraints weight = 5041.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.140772 restraints weight = 3779.930| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 4699 Z= 0.277 Angle : 0.590 7.007 6372 Z= 0.302 Chirality : 0.044 0.172 693 Planarity : 0.004 0.036 825 Dihedral : 4.120 17.144 620 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.16 % Allowed : 20.00 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.37), residues: 565 helix: 0.59 (0.35), residues: 228 sheet: -0.87 (0.57), residues: 89 loop : -0.15 (0.42), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 248 HIS 0.003 0.001 HIS B 64 PHE 0.014 0.001 PHE C 399 TYR 0.009 0.001 TYR C 142 ARG 0.005 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: C 229 MET cc_start: 0.7712 (tmm) cc_final: 0.7147 (tmm) REVERT: C 274 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.6745 (t0) REVERT: C 333 ILE cc_start: 0.6876 (OUTLIER) cc_final: 0.6401 (mp) REVERT: C 352 PHE cc_start: 0.8303 (m-80) cc_final: 0.7930 (m-10) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 0.1222 time to fit residues: 15.4783 Evaluate side-chains 90 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 380 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 25 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.166213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.135153 restraints weight = 7702.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.138815 restraints weight = 4999.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.141316 restraints weight = 3762.522| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 4699 Z= 0.237 Angle : 0.589 7.379 6372 Z= 0.300 Chirality : 0.044 0.175 693 Planarity : 0.004 0.035 825 Dihedral : 4.110 17.266 620 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.96 % Allowed : 20.98 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.37), residues: 565 helix: 0.60 (0.35), residues: 226 sheet: -0.62 (0.57), residues: 87 loop : -0.19 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 248 HIS 0.003 0.001 HIS B 64 PHE 0.009 0.001 PHE C 399 TYR 0.008 0.001 TYR C 142 ARG 0.004 0.000 ARG C 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: B 81 ARG cc_start: 0.7856 (ptp-110) cc_final: 0.7319 (mtm110) REVERT: C 176 ASP cc_start: 0.7776 (p0) cc_final: 0.7213 (p0) REVERT: C 229 MET cc_start: 0.7534 (tmm) cc_final: 0.7058 (tmm) REVERT: C 274 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.6751 (t0) REVERT: C 333 ILE cc_start: 0.6987 (OUTLIER) cc_final: 0.6534 (mp) REVERT: C 352 PHE cc_start: 0.8292 (m-80) cc_final: 0.7927 (m-10) outliers start: 10 outliers final: 8 residues processed: 87 average time/residue: 0.1137 time to fit residues: 13.9137 Evaluate side-chains 90 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 380 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 5 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 12 optimal weight: 0.0980 chunk 14 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.165837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.134215 restraints weight = 7663.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137988 restraints weight = 4883.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.140651 restraints weight = 3647.152| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 4699 Z= 0.237 Angle : 0.585 7.203 6372 Z= 0.300 Chirality : 0.044 0.172 693 Planarity : 0.004 0.036 825 Dihedral : 4.112 17.495 620 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.96 % Allowed : 20.98 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.37), residues: 565 helix: 0.58 (0.35), residues: 226 sheet: -0.68 (0.57), residues: 91 loop : -0.08 (0.42), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 248 HIS 0.003 0.001 HIS B 64 PHE 0.008 0.001 PHE C 249 TYR 0.008 0.001 TYR C 142 ARG 0.004 0.000 ARG C 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2036.56 seconds wall clock time: 36 minutes 11.93 seconds (2171.93 seconds total)