Starting phenix.real_space_refine on Sat May 10 02:11:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kbf_62223/05_2025/9kbf_62223.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kbf_62223/05_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_62223/05_2025/9kbf_62223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kbf_62223/05_2025/9kbf_62223.map" model { file = "/net/cci-nas-00/data/ceres_data/9kbf_62223/05_2025/9kbf_62223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kbf_62223/05_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-5687/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: 3.89, per 1000 atoms: 0.85 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: 0.98 Conformation dependent library (CDL) restraints added in 497.2 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: 0.57 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: 1.21 Time building geometry restraints manager: 1.17 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: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.100 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.500 ------------------------------------------------------------------------------- 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= 0.198 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 Details of bonding type rmsd hydrogen bonds : bond 0.16134 ( 182) hydrogen bonds : angle 7.99074 ( 525) covalent geometry : bond 0.00423 ( 4699) covalent geometry : angle 0.63913 ( 6372) *********************** 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 : 0.529 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: 0.2028 time to fit residues: 40.3120 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 : 0.504 ------------------------------------------------------------------------------- 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: 0.0970 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: 0.6276 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.153827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124880 restraints weight = 7269.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.127457 restraints weight = 5218.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.129239 restraints weight = 4166.245| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 4699 Z= 0.161 Angle : 0.602 6.173 6372 Z= 0.312 Chirality : 0.044 0.146 693 Planarity : 0.004 0.036 825 Dihedral : 4.336 18.463 620 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.18 % Allowed : 11.18 % Favored : 87.65 % 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: -0.78 (0.35), residues: 565 helix: -0.08 (0.34), residues: 227 sheet: -1.41 (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 C 61 HIS 0.004 0.001 HIS C 49 PHE 0.011 0.002 PHE C 306 TYR 0.011 0.001 TYR C 380 ARG 0.004 0.000 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.03576 ( 182) hydrogen bonds : angle 5.84968 ( 525) covalent geometry : bond 0.00387 ( 4699) covalent geometry : angle 0.60242 ( 6372) *********************** 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 122 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 81 ARG cc_start: 0.8116 (ptp-110) cc_final: 0.7569 (mtm110) REVERT: B 125 ASN cc_start: 0.8706 (m-40) cc_final: 0.8443 (m-40) REVERT: B 158 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7267 (tm-30) REVERT: C 15 SER cc_start: 0.8570 (p) cc_final: 0.8225 (t) REVERT: C 229 MET cc_start: 0.7362 (tmm) cc_final: 0.6818 (tmm) REVERT: C 270 ARG cc_start: 0.8340 (mtt-85) cc_final: 0.8071 (ttm-80) REVERT: C 325 GLN cc_start: 0.7588 (tt0) cc_final: 0.7005 (tt0) REVERT: C 352 PHE cc_start: 0.8480 (m-80) cc_final: 0.8268 (m-80) outliers start: 6 outliers final: 4 residues processed: 119 average time/residue: 0.1455 time to fit residues: 22.4188 Evaluate side-chains 100 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 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: 0.0970 chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 42 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 GLN C 267 GLN C 303 HIS C 325 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.151996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121993 restraints weight = 7455.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.124563 restraints weight = 5393.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.126386 restraints weight = 4340.742| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 4699 Z= 0.180 Angle : 0.586 6.614 6372 Z= 0.302 Chirality : 0.045 0.148 693 Planarity : 0.004 0.033 825 Dihedral : 4.295 15.502 620 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.55 % Allowed : 14.12 % Favored : 83.33 % 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: -0.67 (0.35), residues: 565 helix: 0.14 (0.34), residues: 226 sheet: -1.54 (0.58), residues: 77 loop : -0.45 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 248 HIS 0.002 0.001 HIS B 65 PHE 0.011 0.001 PHE C 399 TYR 0.016 0.001 TYR C 252 ARG 0.002 0.000 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 182) hydrogen bonds : angle 5.45672 ( 525) covalent geometry : bond 0.00434 ( 4699) covalent geometry : angle 0.58567 ( 6372) *********************** 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 116 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 99 THR cc_start: 0.8360 (p) cc_final: 0.7918 (t) REVERT: B 125 ASN cc_start: 0.8707 (m-40) cc_final: 0.8491 (m-40) REVERT: C 15 SER cc_start: 0.8578 (p) cc_final: 0.8212 (t) REVERT: C 229 MET cc_start: 0.7400 (tmm) cc_final: 0.6792 (tmm) REVERT: C 274 ASP cc_start: 0.7247 (t70) cc_final: 0.6808 (t0) REVERT: C 310 ILE cc_start: 0.7916 (mp) cc_final: 0.7633 (mm) REVERT: C 401 MET cc_start: 0.8192 (mmm) cc_final: 0.7932 (mmt) outliers start: 13 outliers final: 9 residues processed: 109 average time/residue: 0.1273 time to fit residues: 18.6335 Evaluate side-chains 102 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 40 SER 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: 4.9990 chunk 40 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.152302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.123007 restraints weight = 7436.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.125517 restraints weight = 5383.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.127298 restraints weight = 4316.713| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 4699 Z= 0.152 Angle : 0.549 5.258 6372 Z= 0.286 Chirality : 0.043 0.152 693 Planarity : 0.004 0.034 825 Dihedral : 4.221 13.874 620 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.76 % Allowed : 16.27 % Favored : 81.96 % 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: -0.52 (0.36), residues: 565 helix: 0.30 (0.34), residues: 227 sheet: -1.52 (0.59), residues: 77 loop : -0.40 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 248 HIS 0.003 0.001 HIS C 303 PHE 0.011 0.001 PHE C 399 TYR 0.014 0.001 TYR C 252 ARG 0.002 0.000 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.03046 ( 182) hydrogen bonds : angle 5.24513 ( 525) covalent geometry : bond 0.00372 ( 4699) covalent geometry : angle 0.54887 ( 6372) *********************** 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 105 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: B 99 THR cc_start: 0.8288 (p) cc_final: 0.7825 (t) REVERT: B 125 ASN cc_start: 0.8671 (m-40) cc_final: 0.8461 (m-40) REVERT: C 15 SER cc_start: 0.8594 (p) cc_final: 0.8210 (t) REVERT: C 229 MET cc_start: 0.7362 (tmm) cc_final: 0.6803 (tmm) REVERT: C 274 ASP cc_start: 0.7238 (t70) cc_final: 0.6780 (t0) REVERT: C 310 ILE cc_start: 0.7956 (mp) cc_final: 0.7628 (mm) REVERT: C 333 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6755 (mp) outliers start: 9 outliers final: 5 residues processed: 102 average time/residue: 0.1317 time to fit residues: 17.9993 Evaluate side-chains 95 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 16 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 394 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: 0.9990 chunk 54 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 34 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.163395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.131746 restraints weight = 7875.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.135641 restraints weight = 4988.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138265 restraints weight = 3688.685| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 4699 Z= 0.168 Angle : 0.562 5.703 6372 Z= 0.290 Chirality : 0.043 0.158 693 Planarity : 0.004 0.034 825 Dihedral : 4.182 14.563 620 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.35 % Allowed : 17.25 % 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: -0.46 (0.36), residues: 565 helix: 0.40 (0.35), residues: 228 sheet: -1.46 (0.60), residues: 77 loop : -0.42 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 248 HIS 0.002 0.001 HIS B 64 PHE 0.011 0.001 PHE C 399 TYR 0.015 0.001 TYR C 252 ARG 0.007 0.000 ARG C 55 Details of bonding type rmsd hydrogen bonds : bond 0.02952 ( 182) hydrogen bonds : angle 5.16457 ( 525) covalent geometry : bond 0.00407 ( 4699) covalent geometry : angle 0.56172 ( 6372) *********************** 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 103 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: B 125 ASN cc_start: 0.8732 (m-40) cc_final: 0.8486 (m-40) REVERT: C 15 SER cc_start: 0.8723 (p) cc_final: 0.8521 (t) REVERT: C 229 MET cc_start: 0.7671 (tmm) cc_final: 0.7024 (tmm) REVERT: C 274 ASP cc_start: 0.7330 (t70) cc_final: 0.6748 (t0) REVERT: C 310 ILE cc_start: 0.7827 (mp) cc_final: 0.7527 (mm) REVERT: C 333 ILE cc_start: 0.6908 (OUTLIER) cc_final: 0.6500 (mp) outliers start: 12 outliers final: 7 residues processed: 100 average time/residue: 0.1301 time to fit residues: 17.4229 Evaluate side-chains 96 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 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 160 LEU Chi-restraints excluded: chain C residue 177 VAL 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: 0.5980 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 0.3980 chunk 54 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 185 GLN C 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.166534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.136246 restraints weight = 7560.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.140146 restraints weight = 4516.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.142767 restraints weight = 3227.171| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 4699 Z= 0.131 Angle : 0.530 5.289 6372 Z= 0.277 Chirality : 0.042 0.164 693 Planarity : 0.004 0.035 825 Dihedral : 4.078 15.521 620 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.16 % Allowed : 18.82 % Favored : 79.02 % 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: -0.29 (0.36), residues: 565 helix: 0.55 (0.34), residues: 227 sheet: -1.13 (0.58), residues: 81 loop : -0.41 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.007 0.000 ARG C 55 Details of bonding type rmsd hydrogen bonds : bond 0.02804 ( 182) hydrogen bonds : angle 5.00951 ( 525) covalent geometry : bond 0.00318 ( 4699) covalent geometry : angle 0.52959 ( 6372) *********************** 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 103 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: B 125 ASN cc_start: 0.8769 (m-40) cc_final: 0.8494 (m-40) REVERT: C 15 SER cc_start: 0.8731 (p) cc_final: 0.8518 (t) REVERT: C 185 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7778 (mt0) REVERT: C 229 MET cc_start: 0.7664 (tmm) cc_final: 0.7055 (tmm) REVERT: C 274 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.6706 (t0) REVERT: C 291 SER cc_start: 0.8882 (t) cc_final: 0.8489 (m) REVERT: C 310 ILE cc_start: 0.7800 (mp) cc_final: 0.7464 (mm) REVERT: C 333 ILE cc_start: 0.6866 (OUTLIER) cc_final: 0.6445 (mp) REVERT: C 352 PHE cc_start: 0.8374 (m-80) cc_final: 0.7996 (m-10) outliers start: 11 outliers final: 7 residues processed: 100 average time/residue: 0.1294 time to fit residues: 17.4862 Evaluate side-chains 99 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 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 185 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.0570 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 10 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.166733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.137408 restraints weight = 7542.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.141001 restraints weight = 4710.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.143549 restraints weight = 3444.807| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 4699 Z= 0.129 Angle : 0.529 5.287 6372 Z= 0.276 Chirality : 0.042 0.167 693 Planarity : 0.003 0.034 825 Dihedral : 4.042 15.512 620 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.16 % Allowed : 20.59 % Favored : 77.25 % 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: -0.24 (0.36), residues: 565 helix: 0.64 (0.35), residues: 227 sheet: -1.32 (0.57), residues: 82 loop : -0.35 (0.41), residues: 256 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 0.026 0.001 PHE C 399 TYR 0.007 0.001 TYR C 142 ARG 0.005 0.000 ARG C 55 Details of bonding type rmsd hydrogen bonds : bond 0.02732 ( 182) hydrogen bonds : angle 4.91090 ( 525) covalent geometry : bond 0.00311 ( 4699) covalent geometry : angle 0.52881 ( 6372) *********************** 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 98 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: B 125 ASN cc_start: 0.8762 (m-40) cc_final: 0.8509 (m-40) REVERT: C 15 SER cc_start: 0.8695 (p) cc_final: 0.8444 (t) REVERT: C 229 MET cc_start: 0.7577 (tmm) cc_final: 0.7002 (tmm) REVERT: C 274 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6729 (t0) REVERT: C 352 PHE cc_start: 0.8329 (m-80) cc_final: 0.7967 (m-10) outliers start: 11 outliers final: 6 residues processed: 95 average time/residue: 0.1271 time to fit residues: 16.4900 Evaluate side-chains 89 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 7 optimal weight: 0.0020 chunk 35 optimal weight: 0.6980 chunk 44 optimal weight: 0.1980 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.169168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.136102 restraints weight = 7790.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.140044 restraints weight = 4865.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.142703 restraints weight = 3588.842| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 4699 Z= 0.125 Angle : 0.533 5.277 6372 Z= 0.278 Chirality : 0.042 0.169 693 Planarity : 0.003 0.034 825 Dihedral : 3.979 17.086 620 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.96 % Allowed : 20.59 % 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: -0.17 (0.36), residues: 565 helix: 0.69 (0.35), residues: 227 sheet: -1.27 (0.57), residues: 81 loop : -0.30 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 248 HIS 0.003 0.001 HIS B 64 PHE 0.029 0.001 PHE C 399 TYR 0.007 0.001 TYR C 142 ARG 0.005 0.000 ARG C 55 Details of bonding type rmsd hydrogen bonds : bond 0.02711 ( 182) hydrogen bonds : angle 4.83067 ( 525) covalent geometry : bond 0.00304 ( 4699) covalent geometry : angle 0.53344 ( 6372) *********************** 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 95 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: B 81 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7319 (mtm110) REVERT: C 219 ASN cc_start: 0.8683 (t0) cc_final: 0.8464 (t0) REVERT: C 229 MET cc_start: 0.7761 (tmm) cc_final: 0.7176 (tmm) REVERT: C 274 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.6693 (t0) REVERT: C 333 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6495 (mp) REVERT: C 352 PHE cc_start: 0.8309 (m-80) cc_final: 0.7878 (m-10) outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 0.1305 time to fit residues: 16.3029 Evaluate side-chains 90 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 81 ARG 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 49 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3973 r_free = 0.3973 target = 0.163626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.131498 restraints weight = 7793.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135398 restraints weight = 4864.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.138121 restraints weight = 3593.074| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 4699 Z= 0.184 Angle : 0.582 5.311 6372 Z= 0.301 Chirality : 0.045 0.171 693 Planarity : 0.004 0.035 825 Dihedral : 4.102 14.348 620 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.16 % Allowed : 20.78 % 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: -0.20 (0.36), residues: 565 helix: 0.52 (0.35), residues: 228 sheet: -1.12 (0.55), residues: 94 loop : -0.17 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 248 HIS 0.003 0.001 HIS B 64 PHE 0.018 0.002 PHE C 399 TYR 0.009 0.001 TYR C 142 ARG 0.004 0.000 ARG C 55 Details of bonding type rmsd hydrogen bonds : bond 0.02960 ( 182) hydrogen bonds : angle 5.02045 ( 525) covalent geometry : bond 0.00440 ( 4699) covalent geometry : angle 0.58217 ( 6372) *********************** 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 96 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: B 125 ASN cc_start: 0.8762 (m-40) cc_final: 0.8428 (m-40) REVERT: C 229 MET cc_start: 0.7653 (tmm) cc_final: 0.7088 (tmm) REVERT: C 274 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.6775 (t0) REVERT: C 333 ILE cc_start: 0.7053 (OUTLIER) cc_final: 0.6682 (mp) REVERT: C 352 PHE cc_start: 0.8301 (m-80) cc_final: 0.7922 (m-10) outliers start: 11 outliers final: 6 residues processed: 93 average time/residue: 0.1302 time to fit residues: 16.7764 Evaluate side-chains 89 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 25 optimal weight: 0.8980 chunk 6 optimal weight: 0.0970 chunk 2 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 0.0570 chunk 50 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 37 optimal weight: 0.0370 chunk 39 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 HIS C 303 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.167286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.137238 restraints weight = 7711.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.140858 restraints weight = 4984.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143433 restraints weight = 3748.940| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 4699 Z= 0.114 Angle : 0.546 5.888 6372 Z= 0.285 Chirality : 0.043 0.176 693 Planarity : 0.003 0.036 825 Dihedral : 3.998 15.410 620 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.37 % Allowed : 21.76 % Favored : 76.86 % 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: -0.09 (0.36), residues: 565 helix: 0.63 (0.35), residues: 227 sheet: -1.10 (0.58), residues: 83 loop : -0.17 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 61 HIS 0.002 0.001 HIS B 64 PHE 0.015 0.001 PHE C 399 TYR 0.006 0.001 TYR C 142 ARG 0.003 0.000 ARG C 55 Details of bonding type rmsd hydrogen bonds : bond 0.02685 ( 182) hydrogen bonds : angle 4.84213 ( 525) covalent geometry : bond 0.00268 ( 4699) covalent geometry : angle 0.54607 ( 6372) ********************** 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 89 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: B 81 ARG cc_start: 0.7861 (ptp-110) cc_final: 0.7325 (mtm110) REVERT: C 229 MET cc_start: 0.7522 (tmm) cc_final: 0.7011 (tmm) REVERT: C 274 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.6771 (t0) REVERT: C 352 PHE cc_start: 0.8273 (m-80) cc_final: 0.7903 (m-10) outliers start: 7 outliers final: 6 residues processed: 87 average time/residue: 0.1179 time to fit residues: 14.3356 Evaluate side-chains 86 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 5 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.164931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.133407 restraints weight = 7696.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.137238 restraints weight = 4839.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.140034 restraints weight = 3580.180| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 4699 Z= 0.149 Angle : 0.580 7.412 6372 Z= 0.297 Chirality : 0.044 0.172 693 Planarity : 0.004 0.043 825 Dihedral : 4.059 15.171 620 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.76 % Allowed : 21.57 % Favored : 76.67 % 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: -0.03 (0.37), residues: 565 helix: 0.64 (0.35), residues: 226 sheet: -0.78 (0.57), residues: 90 loop : -0.17 (0.42), residues: 249 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 0.013 0.001 PHE C 399 TYR 0.008 0.001 TYR C 142 ARG 0.003 0.000 ARG C 55 Details of bonding type rmsd hydrogen bonds : bond 0.02793 ( 182) hydrogen bonds : angle 4.96773 ( 525) covalent geometry : bond 0.00357 ( 4699) covalent geometry : angle 0.57968 ( 6372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2039.39 seconds wall clock time: 36 minutes 28.35 seconds (2188.35 seconds total)