Starting phenix.real_space_refine on Thu Jun 5 00:55:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f2m_28822/06_2025/8f2m_28822.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f2m_28822/06_2025/8f2m_28822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f2m_28822/06_2025/8f2m_28822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f2m_28822/06_2025/8f2m_28822.map" model { file = "/net/cci-nas-00/data/ceres_data/8f2m_28822/06_2025/8f2m_28822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f2m_28822/06_2025/8f2m_28822.cif" } resolution = 3.7 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= 0.001 sd= 0.010 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 9 5.16 5 C 2970 2.51 5 N 794 2.21 5 O 923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 4696 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3425 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 11, 'TRANS': 422} Chain breaks: 1 Chain: "F" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 589 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "B" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 589 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 93 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Time building chain proxies: 3.16, per 1000 atoms: 0.67 Number of scatterers: 4696 At special positions: 0 Unit cell: (101.556, 108.108, 126.672, 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 9 16.00 O 923 8.00 N 794 7.00 C 2970 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: 1.00 Conformation dependent library (CDL) restraints added in 515.5 milliseconds 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1124 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 6 sheets defined 45.6% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'D' and resid 14 through 18 removed outlier: 3.748A pdb=" N TYR D 18 " --> pdb=" O THR D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 52 Processing helix chain 'D' and resid 54 through 78 removed outlier: 3.625A pdb=" N ILE D 69 " --> pdb=" O LEU D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 111 through 118 removed outlier: 3.743A pdb=" N GLN D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 152 Processing helix chain 'D' and resid 157 through 192 removed outlier: 3.703A pdb=" N ASN D 172 " --> pdb=" O ASN D 168 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER D 173 " --> pdb=" O ALA D 169 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA D 174 " --> pdb=" O ILE D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 225 removed outlier: 3.548A pdb=" N THR D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'D' and resid 253 through 259 removed outlier: 3.673A pdb=" N GLU D 258 " --> pdb=" O ASP D 254 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 268 removed outlier: 4.554A pdb=" N LEU D 264 " --> pdb=" O ASP D 260 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LYS D 266 " --> pdb=" O ASP D 262 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'F' and resid 4 through 15 removed outlier: 3.601A pdb=" N ASP F 10 " --> pdb=" O GLU F 6 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE F 11 " --> pdb=" O GLU F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 74 removed outlier: 3.789A pdb=" N LEU F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU F 46 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA F 55 " --> pdb=" O GLU F 51 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR F 74 " --> pdb=" O GLN F 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.649A pdb=" N ILE B 11 " --> pdb=" O GLU B 7 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 12 " --> pdb=" O HIS B 8 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN B 13 " --> pdb=" O GLU B 9 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP B 17 " --> pdb=" O ASN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 73 removed outlier: 3.954A pdb=" N THR B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 52 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 54 " --> pdb=" O HIS B 50 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 87 through 90 removed outlier: 5.044A pdb=" N ASP D 304 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLN D 90 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N LEU D 306 " --> pdb=" O GLN D 90 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP D 327 " --> pdb=" O ASN D 305 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS D 307 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N HIS D 325 " --> pdb=" O HIS D 307 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY D 138 " --> pdb=" O VAL D 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 143 through 145 removed outlier: 3.684A pdb=" N TYR D 319 " --> pdb=" O ASN D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 279 through 282 Processing sheet with id=AA4, first strand: chain 'D' and resid 349 through 354 removed outlier: 4.419A pdb=" N GLN D 351 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG D 374 " --> pdb=" O GLN D 351 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 358 through 361 removed outlier: 5.988A pdb=" N ALA D 359 " --> pdb=" O SER D 436 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL D 429 " --> pdb=" O VAL D 418 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 366 through 368 removed outlier: 3.632A pdb=" N ALA D 395 " --> pdb=" O SER D 403 " (cutoff:3.500A) 224 hydrogen bonds defined for protein. 654 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: 1.19 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1563 1.34 - 1.46: 693 1.46 - 1.57: 2500 1.57 - 1.69: 1 1.69 - 1.81: 18 Bond restraints: 4775 Sorted by residual: bond pdb=" CB PRO D 356 " pdb=" CG PRO D 356 " ideal model delta sigma weight residual 1.492 1.581 -0.089 5.00e-02 4.00e+02 3.13e+00 bond pdb=" C SER D 355 " pdb=" N PRO D 356 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.89e+00 bond pdb=" CG PRO B 18 " pdb=" CD PRO B 18 " ideal model delta sigma weight residual 1.503 1.544 -0.041 3.40e-02 8.65e+02 1.43e+00 bond pdb=" CG PRO D 356 " pdb=" CD PRO D 356 " ideal model delta sigma weight residual 1.503 1.544 -0.041 3.40e-02 8.65e+02 1.43e+00 bond pdb=" CB LYS D 215 " pdb=" CG LYS D 215 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.26e+00 ... (remaining 4770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 6221 1.49 - 2.98: 191 2.98 - 4.48: 39 4.48 - 5.97: 11 5.97 - 7.46: 5 Bond angle restraints: 6467 Sorted by residual: angle pdb=" CA PRO D 356 " pdb=" N PRO D 356 " pdb=" CD PRO D 356 " ideal model delta sigma weight residual 112.00 106.76 5.24 1.40e+00 5.10e-01 1.40e+01 angle pdb=" CA LYS D 223 " pdb=" CB LYS D 223 " pdb=" CG LYS D 223 " ideal model delta sigma weight residual 114.10 120.94 -6.84 2.00e+00 2.50e-01 1.17e+01 angle pdb=" CB LYS D 215 " pdb=" CG LYS D 215 " pdb=" CD LYS D 215 " ideal model delta sigma weight residual 111.30 118.76 -7.46 2.30e+00 1.89e-01 1.05e+01 angle pdb=" N SER D 34 " pdb=" CA SER D 34 " pdb=" C SER D 34 " ideal model delta sigma weight residual 114.39 109.85 4.54 1.45e+00 4.76e-01 9.81e+00 angle pdb=" C TYR D 18 " pdb=" N ASP D 19 " pdb=" CA ASP D 19 " ideal model delta sigma weight residual 121.54 127.34 -5.80 1.91e+00 2.74e-01 9.21e+00 ... (remaining 6462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 2491 17.70 - 35.41: 306 35.41 - 53.11: 81 53.11 - 70.81: 12 70.81 - 88.52: 2 Dihedral angle restraints: 2892 sinusoidal: 1160 harmonic: 1732 Sorted by residual: dihedral pdb=" CA TYR D 18 " pdb=" C TYR D 18 " pdb=" N ASP D 19 " pdb=" CA ASP D 19 " ideal model delta harmonic sigma weight residual 180.00 153.29 26.71 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA SER D 355 " pdb=" C SER D 355 " pdb=" N PRO D 356 " pdb=" CA PRO D 356 " ideal model delta harmonic sigma weight residual 180.00 -157.43 -22.57 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ILE D 170 " pdb=" C ILE D 170 " pdb=" N TYR D 171 " pdb=" CA TYR D 171 " ideal model delta harmonic sigma weight residual 180.00 -161.67 -18.33 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 2889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 534 0.038 - 0.075: 154 0.075 - 0.112: 46 0.112 - 0.150: 10 0.150 - 0.187: 2 Chirality restraints: 746 Sorted by residual: chirality pdb=" CA PRO D 356 " pdb=" N PRO D 356 " pdb=" C PRO D 356 " pdb=" CB PRO D 356 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" CA PRO B 18 " pdb=" N PRO B 18 " pdb=" C PRO B 18 " pdb=" CB PRO B 18 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ASP D 19 " pdb=" N ASP D 19 " pdb=" C ASP D 19 " pdb=" CB ASP D 19 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 743 not shown) Planarity restraints: 834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 355 " 0.082 5.00e-02 4.00e+02 1.24e-01 2.47e+01 pdb=" N PRO D 356 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO D 356 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO D 356 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 226 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO D 227 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 227 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 227 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 4 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 5 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 5 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 5 " -0.021 5.00e-02 4.00e+02 ... (remaining 831 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1022 2.78 - 3.31: 4429 3.31 - 3.84: 7211 3.84 - 4.37: 8206 4.37 - 4.90: 13799 Nonbonded interactions: 34667 Sorted by model distance: nonbonded pdb=" NZ LYS D 87 " pdb=" OE2 GLU D 178 " model vdw 2.253 3.120 nonbonded pdb=" OG SER D 11 " pdb=" OG SER D 17 " model vdw 2.255 3.040 nonbonded pdb=" OG SER D 405 " pdb=" OE2 GLU D 408 " model vdw 2.262 3.040 nonbonded pdb=" O GLY D 390 " pdb=" ND2 ASN D 410 " model vdw 2.266 3.120 nonbonded pdb=" OG1 THR D 15 " pdb=" OE2 GLU D 160 " model vdw 2.268 3.040 ... (remaining 34662 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'F' } 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: 0.780 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.620 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 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 : 0.003 0.089 4775 Z= 0.147 Angle : 0.671 7.461 6467 Z= 0.380 Chirality : 0.040 0.187 746 Planarity : 0.006 0.124 834 Dihedral : 16.382 88.515 1768 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 1.03 % Allowed : 4.98 % Favored : 93.99 % Rotamer: Outliers : 0.38 % Allowed : 24.18 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.34), residues: 582 helix: 0.70 (0.32), residues: 256 sheet: -0.62 (0.47), residues: 115 loop : -2.10 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 320 HIS 0.003 0.001 HIS D 248 PHE 0.019 0.001 PHE D 162 TYR 0.019 0.002 TYR D 324 ARG 0.008 0.001 ARG D 239 Details of bonding type rmsd hydrogen bonds : bond 0.23061 ( 224) hydrogen bonds : angle 7.46775 ( 654) covalent geometry : bond 0.00326 ( 4775) covalent geometry : angle 0.67136 ( 6467) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 25 ARG cc_start: 0.5800 (mtm180) cc_final: 0.4943 (mtp-110) REVERT: F 46 LEU cc_start: 0.8103 (tp) cc_final: 0.7801 (mm) REVERT: B 25 ARG cc_start: 0.6595 (ttt-90) cc_final: 0.5887 (tpt-90) outliers start: 2 outliers final: 2 residues processed: 88 average time/residue: 0.2058 time to fit residues: 22.5878 Evaluate side-chains 72 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 279 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 30.0000 chunk 43 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 45 optimal weight: 30.0000 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN F 22 GLN F 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.165766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.138574 restraints weight = 7044.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.135970 restraints weight = 16644.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.135673 restraints weight = 16040.066| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 4775 Z= 0.286 Angle : 0.785 9.368 6467 Z= 0.426 Chirality : 0.048 0.241 746 Planarity : 0.007 0.132 834 Dihedral : 5.855 32.351 636 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.86 % Allowed : 6.19 % Favored : 92.96 % Rotamer: Outliers : 3.65 % Allowed : 21.11 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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: -1.01 (0.33), residues: 582 helix: 0.63 (0.31), residues: 263 sheet: -0.82 (0.45), residues: 126 loop : -2.34 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 299 HIS 0.008 0.002 HIS D 141 PHE 0.039 0.003 PHE F 68 TYR 0.019 0.003 TYR D 324 ARG 0.003 0.001 ARG F 33 Details of bonding type rmsd hydrogen bonds : bond 0.07851 ( 224) hydrogen bonds : angle 5.10611 ( 654) covalent geometry : bond 0.00669 ( 4775) covalent geometry : angle 0.78505 ( 6467) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: D 74 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7929 (mt) REVERT: D 80 ASN cc_start: 0.7749 (p0) cc_final: 0.7259 (p0) REVERT: F 22 GLN cc_start: 0.6067 (OUTLIER) cc_final: 0.5771 (tp-100) REVERT: B 43 TYR cc_start: 0.6835 (t80) cc_final: 0.6506 (t80) outliers start: 19 outliers final: 9 residues processed: 100 average time/residue: 0.1695 time to fit residues: 21.6155 Evaluate side-chains 81 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain F residue 22 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 41 optimal weight: 20.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 248 HIS D 271 ASN F 8 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.164513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.132748 restraints weight = 7073.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.132305 restraints weight = 14596.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.133462 restraints weight = 13480.779| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 4775 Z= 0.161 Angle : 0.627 9.274 6467 Z= 0.343 Chirality : 0.044 0.194 746 Planarity : 0.006 0.128 834 Dihedral : 5.242 31.930 634 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 1.03 % Allowed : 5.67 % Favored : 93.30 % Rotamer: Outliers : 3.26 % Allowed : 21.69 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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: -0.63 (0.34), residues: 582 helix: 1.00 (0.31), residues: 262 sheet: -0.65 (0.45), residues: 126 loop : -2.21 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 299 HIS 0.004 0.001 HIS D 307 PHE 0.023 0.002 PHE F 68 TYR 0.016 0.002 TYR D 324 ARG 0.003 0.000 ARG D 239 Details of bonding type rmsd hydrogen bonds : bond 0.06606 ( 224) hydrogen bonds : angle 4.71017 ( 654) covalent geometry : bond 0.00358 ( 4775) covalent geometry : angle 0.62683 ( 6467) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: D 80 ASN cc_start: 0.7797 (p0) cc_final: 0.7393 (p0) REVERT: D 216 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7915 (mtpt) REVERT: D 326 VAL cc_start: 0.9273 (OUTLIER) cc_final: 0.8992 (p) REVERT: F 22 GLN cc_start: 0.5978 (pp30) cc_final: 0.5671 (tp-100) REVERT: B 43 TYR cc_start: 0.7001 (t80) cc_final: 0.6448 (t80) outliers start: 17 outliers final: 9 residues processed: 91 average time/residue: 0.1590 time to fit residues: 18.7177 Evaluate side-chains 76 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain B residue 16 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 35 optimal weight: 50.0000 chunk 15 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 23 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.165502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.133745 restraints weight = 7155.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.133175 restraints weight = 14392.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.134431 restraints weight = 12622.792| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 4775 Z= 0.140 Angle : 0.600 8.955 6467 Z= 0.329 Chirality : 0.043 0.193 746 Planarity : 0.006 0.125 834 Dihedral : 4.936 30.692 634 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 1.03 % Allowed : 5.67 % Favored : 93.30 % Rotamer: Outliers : 2.30 % Allowed : 22.07 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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: -0.39 (0.35), residues: 582 helix: 1.21 (0.31), residues: 262 sheet: -0.47 (0.47), residues: 126 loop : -2.17 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 299 HIS 0.004 0.001 HIS F 8 PHE 0.018 0.001 PHE D 162 TYR 0.015 0.001 TYR D 140 ARG 0.002 0.000 ARG F 25 Details of bonding type rmsd hydrogen bonds : bond 0.05972 ( 224) hydrogen bonds : angle 4.56982 ( 654) covalent geometry : bond 0.00305 ( 4775) covalent geometry : angle 0.59989 ( 6467) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.530 Fit side-chains REVERT: D 80 ASN cc_start: 0.7707 (p0) cc_final: 0.7424 (p0) REVERT: D 212 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7161 (tm-30) REVERT: D 216 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7934 (mtpp) REVERT: D 326 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.8968 (p) REVERT: B 43 TYR cc_start: 0.7023 (t80) cc_final: 0.6561 (t80) outliers start: 12 outliers final: 5 residues processed: 82 average time/residue: 0.1717 time to fit residues: 18.1504 Evaluate side-chains 69 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain B residue 16 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 55 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 35 optimal weight: 40.0000 chunk 39 optimal weight: 0.0030 chunk 44 optimal weight: 20.0000 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 overall best weight: 5.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 GLN ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 ASN D 337 ASN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.157565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.123986 restraints weight = 7174.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.122050 restraints weight = 14442.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.123337 restraints weight = 13577.137| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 4775 Z= 0.261 Angle : 0.717 7.884 6467 Z= 0.395 Chirality : 0.047 0.197 746 Planarity : 0.007 0.128 834 Dihedral : 5.474 34.313 633 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 1.03 % Allowed : 7.04 % Favored : 91.92 % Rotamer: Outliers : 4.41 % Allowed : 20.92 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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: -0.81 (0.34), residues: 582 helix: 0.77 (0.31), residues: 270 sheet: -0.54 (0.47), residues: 123 loop : -2.44 (0.41), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 299 HIS 0.006 0.002 HIS D 141 PHE 0.028 0.002 PHE D 162 TYR 0.014 0.002 TYR D 140 ARG 0.005 0.001 ARG D 136 Details of bonding type rmsd hydrogen bonds : bond 0.07336 ( 224) hydrogen bonds : angle 4.75055 ( 654) covalent geometry : bond 0.00621 ( 4775) covalent geometry : angle 0.71690 ( 6467) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: D 80 ASN cc_start: 0.7971 (p0) cc_final: 0.7550 (p0) REVERT: D 212 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7390 (tm-30) REVERT: D 216 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7943 (mtpt) REVERT: F 22 GLN cc_start: 0.5767 (pp30) cc_final: 0.5316 (tp-100) REVERT: B 43 TYR cc_start: 0.7289 (t80) cc_final: 0.6568 (t80) outliers start: 23 outliers final: 12 residues processed: 91 average time/residue: 0.1763 time to fit residues: 20.7879 Evaluate side-chains 76 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain F residue 46 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 0.0870 chunk 41 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 271 ASN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.163622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.137611 restraints weight = 7045.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.136722 restraints weight = 15695.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.137147 restraints weight = 14213.699| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 4775 Z= 0.141 Angle : 0.602 7.711 6467 Z= 0.330 Chirality : 0.042 0.170 746 Planarity : 0.006 0.125 834 Dihedral : 4.934 32.691 633 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 1.03 % Allowed : 5.15 % Favored : 93.81 % Rotamer: Outliers : 3.26 % Allowed : 21.31 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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 (0.35), residues: 582 helix: 1.21 (0.31), residues: 264 sheet: -0.23 (0.49), residues: 122 loop : -2.21 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 320 HIS 0.003 0.001 HIS F 8 PHE 0.015 0.001 PHE D 162 TYR 0.017 0.001 TYR D 140 ARG 0.001 0.000 ARG F 25 Details of bonding type rmsd hydrogen bonds : bond 0.06038 ( 224) hydrogen bonds : angle 4.44206 ( 654) covalent geometry : bond 0.00303 ( 4775) covalent geometry : angle 0.60232 ( 6467) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.495 Fit side-chains REVERT: D 19 ASP cc_start: 0.6669 (OUTLIER) cc_final: 0.6151 (m-30) REVERT: D 212 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7058 (tm-30) REVERT: D 216 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7994 (mtpt) REVERT: F 22 GLN cc_start: 0.6001 (pp30) cc_final: 0.5529 (tp-100) REVERT: B 43 TYR cc_start: 0.6924 (t80) cc_final: 0.6497 (t80) outliers start: 17 outliers final: 8 residues processed: 84 average time/residue: 0.1776 time to fit residues: 19.6709 Evaluate side-chains 71 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain F residue 46 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 9 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 ASN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.158441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.135201 restraints weight = 7040.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.129989 restraints weight = 13567.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.127988 restraints weight = 15400.685| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4775 Z= 0.228 Angle : 0.737 15.581 6467 Z= 0.391 Chirality : 0.046 0.211 746 Planarity : 0.006 0.126 834 Dihedral : 5.313 34.035 633 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 1.03 % Allowed : 7.04 % Favored : 91.92 % Rotamer: Outliers : 3.26 % Allowed : 22.65 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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: -0.57 (0.36), residues: 582 helix: 0.97 (0.32), residues: 267 sheet: -0.34 (0.49), residues: 122 loop : -2.33 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 299 HIS 0.005 0.001 HIS D 141 PHE 0.027 0.002 PHE D 162 TYR 0.019 0.002 TYR D 35 ARG 0.005 0.000 ARG D 272 Details of bonding type rmsd hydrogen bonds : bond 0.07033 ( 224) hydrogen bonds : angle 4.73324 ( 654) covalent geometry : bond 0.00539 ( 4775) covalent geometry : angle 0.73718 ( 6467) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.501 Fit side-chains REVERT: D 19 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6699 (m-30) REVERT: D 118 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7340 (mttt) REVERT: D 212 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7146 (tm-30) REVERT: D 216 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7944 (mtpt) REVERT: F 22 GLN cc_start: 0.5945 (pp30) cc_final: 0.5454 (tp-100) REVERT: B 43 TYR cc_start: 0.7077 (t80) cc_final: 0.6494 (t80) outliers start: 17 outliers final: 11 residues processed: 87 average time/residue: 0.1620 time to fit residues: 18.0933 Evaluate side-chains 79 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 23 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 34 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.0980 chunk 44 optimal weight: 0.0270 overall best weight: 2.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 271 ASN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.161109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.136254 restraints weight = 7169.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.131372 restraints weight = 14739.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.129399 restraints weight = 14652.161| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 4775 Z= 0.162 Angle : 0.719 16.069 6467 Z= 0.383 Chirality : 0.044 0.221 746 Planarity : 0.006 0.124 834 Dihedral : 5.073 33.693 633 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 1.03 % Allowed : 6.53 % Favored : 92.44 % Rotamer: Outliers : 3.07 % Allowed : 23.80 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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: -0.47 (0.36), residues: 582 helix: 0.99 (0.32), residues: 267 sheet: -0.25 (0.50), residues: 122 loop : -2.20 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 320 HIS 0.003 0.001 HIS D 307 PHE 0.017 0.001 PHE D 162 TYR 0.021 0.002 TYR D 35 ARG 0.002 0.000 ARG D 272 Details of bonding type rmsd hydrogen bonds : bond 0.06390 ( 224) hydrogen bonds : angle 4.67444 ( 654) covalent geometry : bond 0.00357 ( 4775) covalent geometry : angle 0.71888 ( 6467) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.521 Fit side-chains REVERT: D 19 ASP cc_start: 0.6880 (OUTLIER) cc_final: 0.6325 (m-30) REVERT: D 212 GLU cc_start: 0.7310 (tm-30) cc_final: 0.6974 (tm-30) REVERT: D 216 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8015 (mtpt) REVERT: F 22 GLN cc_start: 0.5899 (pp30) cc_final: 0.5128 (tp-100) REVERT: B 43 TYR cc_start: 0.7100 (t80) cc_final: 0.6516 (t80) outliers start: 16 outliers final: 10 residues processed: 85 average time/residue: 0.1724 time to fit residues: 18.6775 Evaluate side-chains 77 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain C residue 23 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 271 ASN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.159618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131560 restraints weight = 7165.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127871 restraints weight = 14893.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.129401 restraints weight = 12520.852| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4775 Z= 0.190 Angle : 0.752 15.382 6467 Z= 0.398 Chirality : 0.045 0.267 746 Planarity : 0.006 0.125 834 Dihedral : 5.163 34.019 633 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 1.03 % Allowed : 7.22 % Favored : 91.75 % Rotamer: Outliers : 3.07 % Allowed : 23.99 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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: 582 helix: 0.97 (0.32), residues: 266 sheet: -0.31 (0.50), residues: 122 loop : -2.25 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 299 HIS 0.003 0.001 HIS D 307 PHE 0.022 0.002 PHE D 162 TYR 0.021 0.002 TYR D 35 ARG 0.003 0.000 ARG F 25 Details of bonding type rmsd hydrogen bonds : bond 0.06694 ( 224) hydrogen bonds : angle 4.78467 ( 654) covalent geometry : bond 0.00435 ( 4775) covalent geometry : angle 0.75167 ( 6467) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.546 Fit side-chains REVERT: D 19 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6407 (m-30) REVERT: D 212 GLU cc_start: 0.7372 (tm-30) cc_final: 0.7000 (tm-30) REVERT: D 216 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7952 (mtpt) REVERT: F 22 GLN cc_start: 0.5964 (pp30) cc_final: 0.5545 (tp-100) REVERT: F 32 LEU cc_start: 0.6833 (mt) cc_final: 0.6594 (mt) REVERT: B 43 TYR cc_start: 0.7243 (t80) cc_final: 0.6560 (t80) outliers start: 16 outliers final: 12 residues processed: 84 average time/residue: 0.1877 time to fit residues: 20.6335 Evaluate side-chains 82 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain C residue 23 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 40.0000 chunk 19 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 271 ASN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.159256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.135176 restraints weight = 7115.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.135176 restraints weight = 17061.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.135458 restraints weight = 14681.802| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.5680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 4775 Z= 0.196 Angle : 0.757 14.984 6467 Z= 0.404 Chirality : 0.046 0.275 746 Planarity : 0.006 0.125 834 Dihedral : 5.243 34.222 633 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 1.03 % Allowed : 7.56 % Favored : 91.41 % Rotamer: Outliers : 2.69 % Allowed : 23.99 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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: -0.58 (0.36), residues: 582 helix: 0.90 (0.32), residues: 267 sheet: -0.42 (0.50), residues: 123 loop : -2.19 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 299 HIS 0.003 0.001 HIS B 50 PHE 0.021 0.002 PHE D 162 TYR 0.018 0.002 TYR D 35 ARG 0.002 0.000 ARG F 25 Details of bonding type rmsd hydrogen bonds : bond 0.06689 ( 224) hydrogen bonds : angle 4.82455 ( 654) covalent geometry : bond 0.00453 ( 4775) covalent geometry : angle 0.75699 ( 6467) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.555 Fit side-chains REVERT: D 19 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6446 (m-30) REVERT: D 212 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7049 (tm-30) REVERT: D 216 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8060 (mtpt) REVERT: D 415 LYS cc_start: 0.8307 (mmmm) cc_final: 0.7870 (mttt) REVERT: F 48 LYS cc_start: 0.6006 (mmmm) cc_final: 0.5762 (mmmm) REVERT: B 43 TYR cc_start: 0.7080 (t80) cc_final: 0.6541 (t80) outliers start: 14 outliers final: 11 residues processed: 81 average time/residue: 0.1666 time to fit residues: 17.4562 Evaluate side-chains 80 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain C residue 23 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 271 ASN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.159239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135453 restraints weight = 7235.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.132967 restraints weight = 12986.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.129675 restraints weight = 12778.560| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.5818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4775 Z= 0.191 Angle : 0.765 14.692 6467 Z= 0.406 Chirality : 0.046 0.255 746 Planarity : 0.006 0.125 834 Dihedral : 5.209 34.300 633 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 1.03 % Allowed : 7.39 % Favored : 91.58 % Rotamer: Outliers : 2.69 % Allowed : 24.57 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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: -0.54 (0.36), residues: 582 helix: 0.93 (0.32), residues: 267 sheet: -0.41 (0.50), residues: 123 loop : -2.16 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 299 HIS 0.003 0.001 HIS D 307 PHE 0.021 0.002 PHE D 162 TYR 0.019 0.002 TYR D 35 ARG 0.002 0.000 ARG D 136 Details of bonding type rmsd hydrogen bonds : bond 0.06617 ( 224) hydrogen bonds : angle 4.80770 ( 654) covalent geometry : bond 0.00439 ( 4775) covalent geometry : angle 0.76467 ( 6467) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1838.56 seconds wall clock time: 33 minutes 1.17 seconds (1981.17 seconds total)