Starting phenix.real_space_refine on Mon Nov 17 22:17:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5v6p_8637/11_2025/5v6p_8637.cif Found real_map, /net/cci-nas-00/data/ceres_data/5v6p_8637/11_2025/5v6p_8637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5v6p_8637/11_2025/5v6p_8637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5v6p_8637/11_2025/5v6p_8637.map" model { file = "/net/cci-nas-00/data/ceres_data/5v6p_8637/11_2025/5v6p_8637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5v6p_8637/11_2025/5v6p_8637.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 3030 2.51 5 N 698 2.21 5 O 764 1.98 5 H 4676 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9194 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 4597 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 3, 'TRANS': 266} Chain breaks: 1 Restraints were copied for chains: B Time building chain proxies: 3.92, per 1000 atoms: 0.43 Number of scatterers: 9194 At special positions: 0 Unit cell: (87.75, 90.45, 76.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 O 764 8.00 N 698 7.00 C 3030 6.00 H 4676 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 372.7 milliseconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1060 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 94.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 10 through 31 Processing helix chain 'A' and resid 34 through 45 Processing helix chain 'A' and resid 45 through 69 removed outlier: 3.702A pdb=" N MET A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 99 Proline residue: A 87 - end of helix removed outlier: 3.623A pdb=" N LEU A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 135 removed outlier: 8.314A pdb=" N PHE A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 147 through 176 removed outlier: 3.638A pdb=" N SER A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 220 removed outlier: 3.642A pdb=" N LEU A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 289 Processing helix chain 'A' and resid 295 through 324 removed outlier: 4.106A pdb=" N LYS A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASP A 302 " --> pdb=" O MET A 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 31 Processing helix chain 'B' and resid 34 through 45 Processing helix chain 'B' and resid 45 through 69 removed outlier: 3.702A pdb=" N MET B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 99 Proline residue: B 87 - end of helix removed outlier: 3.624A pdb=" N LEU B 99 " --> pdb=" O PHE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 135 removed outlier: 8.314A pdb=" N PHE B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 147 through 176 removed outlier: 3.638A pdb=" N SER B 151 " --> pdb=" O PHE B 147 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 220 removed outlier: 3.641A pdb=" N LEU B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 289 Processing helix chain 'B' and resid 295 through 324 removed outlier: 4.106A pdb=" N LYS B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASP B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) 395 hydrogen bonds defined for protein. 1185 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: 2.15 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: 0.96 - 1.13: 4670 1.13 - 1.30: 681 1.30 - 1.48: 1955 1.48 - 1.65: 1952 1.65 - 1.83: 46 Bond restraints: 9304 Sorted by residual: bond pdb=" NE2 HIS A 79 " pdb=" HE2 HIS A 79 " ideal model delta sigma weight residual 0.860 1.052 -0.192 2.00e-02 2.50e+03 9.24e+01 bond pdb=" NE2 HIS B 79 " pdb=" HE2 HIS B 79 " ideal model delta sigma weight residual 0.860 1.052 -0.192 2.00e-02 2.50e+03 9.20e+01 bond pdb=" NH1 ARG A 128 " pdb="HH12 ARG A 128 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.42e+01 bond pdb=" NH1 ARG B 128 " pdb="HH12 ARG B 128 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.39e+01 bond pdb=" NE2 HIS B 122 " pdb=" HE2 HIS B 122 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.36e+01 ... (remaining 9299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 15244 2.91 - 5.81: 1086 5.81 - 8.72: 442 8.72 - 11.62: 34 11.62 - 14.53: 6 Bond angle restraints: 16812 Sorted by residual: angle pdb=" CA ASP B 161 " pdb=" CB ASP B 161 " pdb=" CG ASP B 161 " ideal model delta sigma weight residual 112.60 118.59 -5.99 1.00e+00 1.00e+00 3.59e+01 angle pdb=" CA ASP A 161 " pdb=" CB ASP A 161 " pdb=" CG ASP A 161 " ideal model delta sigma weight residual 112.60 118.57 -5.97 1.00e+00 1.00e+00 3.57e+01 angle pdb=" C ILE A 291 " pdb=" N PRO A 292 " pdb=" CA PRO A 292 " ideal model delta sigma weight residual 119.78 125.76 -5.98 1.03e+00 9.43e-01 3.37e+01 angle pdb=" C ILE B 291 " pdb=" N PRO B 292 " pdb=" CA PRO B 292 " ideal model delta sigma weight residual 119.78 125.73 -5.95 1.03e+00 9.43e-01 3.33e+01 angle pdb=" C ILE A 53 " pdb=" CA ILE A 53 " pdb=" CB ILE A 53 " ideal model delta sigma weight residual 111.97 105.84 6.13 1.28e+00 6.10e-01 2.30e+01 ... (remaining 16807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.41: 3978 11.41 - 22.81: 276 22.81 - 34.22: 58 34.22 - 45.62: 18 45.62 - 57.03: 14 Dihedral angle restraints: 4344 sinusoidal: 2276 harmonic: 2068 Sorted by residual: dihedral pdb=" CD2 HIS A 286 " pdb=" CG HIS A 286 " pdb=" ND1 HIS A 286 " pdb=" HD1 HIS A 286 " ideal model delta harmonic sigma weight residual -180.00 -139.78 -40.22 0 5.00e+00 4.00e-02 6.47e+01 dihedral pdb=" CD2 HIS B 286 " pdb=" CG HIS B 286 " pdb=" ND1 HIS B 286 " pdb=" HD1 HIS B 286 " ideal model delta harmonic sigma weight residual -180.00 -139.82 -40.18 0 5.00e+00 4.00e-02 6.46e+01 dihedral pdb=" CD2 HIS B 101 " pdb=" CG HIS B 101 " pdb=" ND1 HIS B 101 " pdb=" HD1 HIS B 101 " ideal model delta harmonic sigma weight residual 180.00 142.02 37.98 0 5.00e+00 4.00e-02 5.77e+01 ... (remaining 4341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 416 0.061 - 0.121: 227 0.121 - 0.182: 80 0.182 - 0.243: 19 0.243 - 0.304: 8 Chirality restraints: 750 Sorted by residual: chirality pdb=" CG LEU A 129 " pdb=" CB LEU A 129 " pdb=" CD1 LEU A 129 " pdb=" CD2 LEU A 129 " both_signs ideal model delta sigma weight residual False -2.59 -2.89 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CG LEU B 129 " pdb=" CB LEU B 129 " pdb=" CD1 LEU B 129 " pdb=" CD2 LEU B 129 " both_signs ideal model delta sigma weight residual False -2.59 -2.89 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CG LEU A 197 " pdb=" CB LEU A 197 " pdb=" CD1 LEU A 197 " pdb=" CD2 LEU A 197 " both_signs ideal model delta sigma weight residual False -2.59 -2.87 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 747 not shown) Planarity restraints: 1268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 286 " 0.157 2.00e-02 2.50e+03 1.59e-01 5.69e+02 pdb=" CG HIS A 286 " 0.091 2.00e-02 2.50e+03 pdb=" ND1 HIS A 286 " 0.141 2.00e-02 2.50e+03 pdb=" CD2 HIS A 286 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 HIS A 286 " 0.075 2.00e-02 2.50e+03 pdb=" NE2 HIS A 286 " -0.028 2.00e-02 2.50e+03 pdb=" HD1 HIS A 286 " -0.371 2.00e-02 2.50e+03 pdb=" HD2 HIS A 286 " -0.134 2.00e-02 2.50e+03 pdb=" HE1 HIS A 286 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 286 " -0.156 2.00e-02 2.50e+03 1.59e-01 5.68e+02 pdb=" CG HIS B 286 " -0.091 2.00e-02 2.50e+03 pdb=" ND1 HIS B 286 " -0.141 2.00e-02 2.50e+03 pdb=" CD2 HIS B 286 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 HIS B 286 " -0.075 2.00e-02 2.50e+03 pdb=" NE2 HIS B 286 " 0.027 2.00e-02 2.50e+03 pdb=" HD1 HIS B 286 " 0.371 2.00e-02 2.50e+03 pdb=" HD2 HIS B 286 " 0.134 2.00e-02 2.50e+03 pdb=" HE1 HIS B 286 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 101 " -0.140 2.00e-02 2.50e+03 1.43e-01 4.60e+02 pdb=" CG HIS A 101 " -0.074 2.00e-02 2.50e+03 pdb=" ND1 HIS A 101 " -0.125 2.00e-02 2.50e+03 pdb=" CD2 HIS A 101 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 HIS A 101 " -0.074 2.00e-02 2.50e+03 pdb=" NE2 HIS A 101 " 0.029 2.00e-02 2.50e+03 pdb=" HD1 HIS A 101 " 0.334 2.00e-02 2.50e+03 pdb=" HD2 HIS A 101 " 0.115 2.00e-02 2.50e+03 pdb=" HE1 HIS A 101 " -0.104 2.00e-02 2.50e+03 ... (remaining 1265 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 732 2.24 - 2.83: 20114 2.83 - 3.42: 26087 3.42 - 4.01: 33152 4.01 - 4.60: 50653 Nonbonded interactions: 130738 Sorted by model distance: nonbonded pdb=" O VAL A 190 " pdb=" HG1 THR A 194 " model vdw 1.653 2.450 nonbonded pdb=" O VAL B 190 " pdb=" HG1 THR B 194 " model vdw 1.653 2.450 nonbonded pdb=" O LEU A 203 " pdb=" HG1 THR A 207 " model vdw 1.665 2.450 nonbonded pdb=" O LEU B 203 " pdb=" HG1 THR B 207 " model vdw 1.665 2.450 nonbonded pdb=" OD1 ASP B 199 " pdb=" HZ1 LYS B 282 " model vdw 1.668 2.450 ... (remaining 130733 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.090 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 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 : 0.015 0.076 4628 Z= 0.808 Angle : 1.365 7.304 6272 Z= 0.975 Chirality : 0.083 0.304 750 Planarity : 0.010 0.069 738 Dihedral : 9.648 55.820 1640 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.63 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.33), residues: 532 helix: 0.44 (0.22), residues: 456 sheet: None (None), residues: 0 loop : -1.20 (0.74), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 167 TYR 0.030 0.005 TYR B 270 PHE 0.025 0.005 PHE A 95 TRP 0.039 0.008 TRP A 212 HIS 0.009 0.004 HIS B 286 Details of bonding type rmsd covalent geometry : bond 0.01459 ( 4628) covalent geometry : angle 1.36527 ( 6272) hydrogen bonds : bond 0.16413 ( 395) hydrogen bonds : angle 7.09557 ( 1185) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.8858 (mt0) cc_final: 0.8489 (mp10) REVERT: A 68 LYS cc_start: 0.8880 (mttt) cc_final: 0.8432 (mmmt) REVERT: A 116 LEU cc_start: 0.8482 (tt) cc_final: 0.8201 (mt) REVERT: A 206 GLN cc_start: 0.8574 (mt0) cc_final: 0.8372 (tm-30) REVERT: B 58 ASN cc_start: 0.7585 (m-40) cc_final: 0.7333 (m-40) REVERT: B 64 GLN cc_start: 0.8874 (mt0) cc_final: 0.8515 (mp10) REVERT: B 68 LYS cc_start: 0.8898 (mttt) cc_final: 0.8481 (mmmt) REVERT: B 116 LEU cc_start: 0.8442 (tt) cc_final: 0.8165 (mt) REVERT: B 208 CYS cc_start: 0.7647 (m) cc_final: 0.7439 (m) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.1815 time to fit residues: 77.6767 Evaluate side-chains 263 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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 = 0.4284 r_free = 0.4284 target = 0.156178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.134581 restraints weight = 34912.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.141110 restraints weight = 15266.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.145164 restraints weight = 8582.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.147633 restraints weight = 5629.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.149291 restraints weight = 4094.813| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4628 Z= 0.215 Angle : 0.737 11.297 6272 Z= 0.425 Chirality : 0.037 0.157 750 Planarity : 0.005 0.035 738 Dihedral : 4.620 25.670 578 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.38 % Allowed : 1.88 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.32), residues: 532 helix: 1.75 (0.21), residues: 462 sheet: None (None), residues: 0 loop : -0.97 (0.73), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 75 TYR 0.019 0.002 TYR A 23 PHE 0.024 0.002 PHE B 100 TRP 0.014 0.002 TRP B 212 HIS 0.006 0.002 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 4628) covalent geometry : angle 0.73741 ( 6272) hydrogen bonds : bond 0.07968 ( 395) hydrogen bonds : angle 5.15274 ( 1185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.8714 (mt0) cc_final: 0.8474 (mp10) REVERT: A 68 LYS cc_start: 0.8984 (mttt) cc_final: 0.8502 (mmmt) REVERT: A 164 ILE cc_start: 0.8489 (mm) cc_final: 0.8125 (mm) REVERT: B 68 LYS cc_start: 0.9047 (mttt) cc_final: 0.8517 (mmmt) REVERT: B 164 ILE cc_start: 0.8261 (mm) cc_final: 0.8018 (tp) REVERT: B 297 MET cc_start: 0.7147 (ptp) cc_final: 0.6388 (mtp) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.1742 time to fit residues: 65.6600 Evaluate side-chains 240 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.153078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.131731 restraints weight = 34844.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.137444 restraints weight = 15451.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.141004 restraints weight = 9030.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.143305 restraints weight = 6207.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.144802 restraints weight = 4714.599| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.6423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4628 Z= 0.187 Angle : 0.666 11.316 6272 Z= 0.381 Chirality : 0.036 0.139 750 Planarity : 0.004 0.032 738 Dihedral : 4.577 26.085 578 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.07 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.33), residues: 532 helix: 2.07 (0.21), residues: 464 sheet: None (None), residues: 0 loop : -0.56 (0.75), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 128 TYR 0.014 0.002 TYR A 23 PHE 0.015 0.002 PHE A 150 TRP 0.010 0.001 TRP B 305 HIS 0.005 0.001 HIS B 286 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 4628) covalent geometry : angle 0.66591 ( 6272) hydrogen bonds : bond 0.06852 ( 395) hydrogen bonds : angle 5.15010 ( 1185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.7947 (mt) cc_final: 0.7746 (mt) REVERT: A 64 GLN cc_start: 0.8677 (mt0) cc_final: 0.8388 (mp10) REVERT: A 67 THR cc_start: 0.8686 (m) cc_final: 0.8459 (p) REVERT: A 68 LYS cc_start: 0.8806 (mttt) cc_final: 0.8264 (mmmt) REVERT: A 111 PHE cc_start: 0.7593 (m-80) cc_final: 0.7221 (m-80) REVERT: A 127 ASP cc_start: 0.8299 (m-30) cc_final: 0.8036 (m-30) REVERT: B 36 LEU cc_start: 0.7949 (mt) cc_final: 0.7723 (mt) REVERT: B 68 LYS cc_start: 0.8833 (mttt) cc_final: 0.8320 (mmmt) REVERT: B 111 PHE cc_start: 0.7373 (m-80) cc_final: 0.6954 (m-80) REVERT: B 127 ASP cc_start: 0.8138 (m-30) cc_final: 0.7887 (m-30) REVERT: B 128 ARG cc_start: 0.7915 (mmt-90) cc_final: 0.7653 (mmt-90) REVERT: B 289 MET cc_start: 0.5408 (mtp) cc_final: 0.5131 (mtp) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.1704 time to fit residues: 60.8496 Evaluate side-chains 220 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 0.2980 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.153526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.131318 restraints weight = 35756.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.136899 restraints weight = 16970.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.140400 restraints weight = 10333.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.142628 restraints weight = 7306.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.144012 restraints weight = 5699.261| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.7148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4628 Z= 0.162 Angle : 0.603 7.074 6272 Z= 0.353 Chirality : 0.035 0.132 750 Planarity : 0.004 0.031 738 Dihedral : 4.691 27.187 578 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.44 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.95 (0.34), residues: 532 helix: 2.24 (0.22), residues: 466 sheet: None (None), residues: 0 loop : -0.13 (0.90), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.012 0.001 TYR B 23 PHE 0.022 0.002 PHE B 214 TRP 0.008 0.001 TRP B 305 HIS 0.005 0.002 HIS B 286 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4628) covalent geometry : angle 0.60298 ( 6272) hydrogen bonds : bond 0.06172 ( 395) hydrogen bonds : angle 4.93083 ( 1185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8498 (mttt) cc_final: 0.8261 (tptp) REVERT: A 64 GLN cc_start: 0.8651 (mt0) cc_final: 0.8424 (mp10) REVERT: A 68 LYS cc_start: 0.8878 (mttt) cc_final: 0.8265 (mmmt) REVERT: A 127 ASP cc_start: 0.7957 (m-30) cc_final: 0.7755 (m-30) REVERT: B 41 LYS cc_start: 0.8486 (mttt) cc_final: 0.8280 (tptp) REVERT: B 64 GLN cc_start: 0.8776 (mp10) cc_final: 0.8332 (mp10) REVERT: B 68 LYS cc_start: 0.8782 (mttt) cc_final: 0.8320 (mmmt) REVERT: B 111 PHE cc_start: 0.7444 (m-80) cc_final: 0.7132 (m-80) REVERT: B 127 ASP cc_start: 0.7869 (m-30) cc_final: 0.7513 (m-30) REVERT: B 203 LEU cc_start: 0.8606 (mt) cc_final: 0.8403 (mt) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.1629 time to fit residues: 56.9089 Evaluate side-chains 240 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.0030 chunk 37 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.150536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.129402 restraints weight = 34323.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.134990 restraints weight = 15581.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.138489 restraints weight = 9229.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.140725 restraints weight = 6339.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.142162 restraints weight = 4807.970| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.7597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4628 Z= 0.152 Angle : 0.566 7.445 6272 Z= 0.331 Chirality : 0.033 0.133 750 Planarity : 0.003 0.023 738 Dihedral : 4.561 27.065 578 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.01 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.34), residues: 532 helix: 2.19 (0.22), residues: 474 sheet: None (None), residues: 0 loop : -0.10 (0.93), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 128 TYR 0.009 0.001 TYR B 23 PHE 0.019 0.002 PHE A 214 TRP 0.007 0.001 TRP A 305 HIS 0.007 0.002 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4628) covalent geometry : angle 0.56595 ( 6272) hydrogen bonds : bond 0.05727 ( 395) hydrogen bonds : angle 4.81337 ( 1185) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8724 (mttt) cc_final: 0.8258 (mmmt) REVERT: A 128 ARG cc_start: 0.7871 (mmt-90) cc_final: 0.7633 (mmt-90) REVERT: A 152 PHE cc_start: 0.6126 (m-80) cc_final: 0.5608 (m-80) REVERT: A 154 LEU cc_start: 0.8086 (tt) cc_final: 0.7753 (tt) REVERT: A 191 MET cc_start: 0.6804 (tmm) cc_final: 0.6213 (tmm) REVERT: A 289 MET cc_start: 0.5140 (mtp) cc_final: 0.4874 (mtp) REVERT: A 316 SER cc_start: 0.8806 (m) cc_final: 0.8496 (p) REVERT: B 64 GLN cc_start: 0.8813 (mp10) cc_final: 0.8576 (mp10) REVERT: B 68 LYS cc_start: 0.8722 (mttt) cc_final: 0.8284 (mmmt) REVERT: B 96 MET cc_start: 0.5444 (mmt) cc_final: 0.5224 (mmt) REVERT: B 128 ARG cc_start: 0.7874 (mmt-90) cc_final: 0.7630 (mmt-90) REVERT: B 200 LEU cc_start: 0.8734 (tp) cc_final: 0.8486 (tp) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.1552 time to fit residues: 53.5288 Evaluate side-chains 227 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 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 = 0.4232 r_free = 0.4232 target = 0.151676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.129873 restraints weight = 35066.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.135793 restraints weight = 16015.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.139341 restraints weight = 9416.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.141573 restraints weight = 6506.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.143019 restraints weight = 4974.929| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.8169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4628 Z= 0.141 Angle : 0.551 7.262 6272 Z= 0.323 Chirality : 0.033 0.125 750 Planarity : 0.003 0.020 738 Dihedral : 4.614 27.566 578 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.26 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.34), residues: 532 helix: 2.23 (0.21), residues: 474 sheet: None (None), residues: 0 loop : 0.19 (0.98), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 103 TYR 0.007 0.001 TYR B 23 PHE 0.021 0.002 PHE B 214 TRP 0.006 0.001 TRP A 305 HIS 0.006 0.002 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 4628) covalent geometry : angle 0.55083 ( 6272) hydrogen bonds : bond 0.05366 ( 395) hydrogen bonds : angle 4.72401 ( 1185) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8647 (mttt) cc_final: 0.8184 (mmmt) REVERT: A 152 PHE cc_start: 0.5902 (m-80) cc_final: 0.5442 (m-80) REVERT: A 154 LEU cc_start: 0.8122 (tt) cc_final: 0.7795 (tt) REVERT: A 316 SER cc_start: 0.8759 (m) cc_final: 0.8464 (p) REVERT: B 68 LYS cc_start: 0.8674 (mttt) cc_final: 0.8253 (mmmt) REVERT: B 96 MET cc_start: 0.5618 (mmt) cc_final: 0.5401 (mmt) REVERT: B 128 ARG cc_start: 0.7712 (mmt-90) cc_final: 0.7455 (mmt-90) REVERT: B 152 PHE cc_start: 0.6056 (m-80) cc_final: 0.5435 (m-80) REVERT: B 316 SER cc_start: 0.8698 (m) cc_final: 0.8393 (p) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1592 time to fit residues: 53.7249 Evaluate side-chains 218 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** 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 = 0.4221 r_free = 0.4221 target = 0.150861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.130444 restraints weight = 33205.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.136033 restraints weight = 14394.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.139415 restraints weight = 8172.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.141560 restraints weight = 5528.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.142992 restraints weight = 4141.748| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.8492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4628 Z= 0.140 Angle : 0.573 7.109 6272 Z= 0.329 Chirality : 0.033 0.140 750 Planarity : 0.004 0.032 738 Dihedral : 4.530 27.758 578 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.26 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.13 (0.34), residues: 532 helix: 2.30 (0.21), residues: 474 sheet: None (None), residues: 0 loop : 0.12 (1.01), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.006 0.001 TYR A 186 PHE 0.017 0.001 PHE A 54 TRP 0.006 0.001 TRP A 305 HIS 0.006 0.002 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4628) covalent geometry : angle 0.57326 ( 6272) hydrogen bonds : bond 0.05197 ( 395) hydrogen bonds : angle 4.68108 ( 1185) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8927 (mt) cc_final: 0.8661 (mt) REVERT: A 68 LYS cc_start: 0.8864 (mttt) cc_final: 0.8311 (mmmt) REVERT: A 152 PHE cc_start: 0.6242 (m-80) cc_final: 0.6017 (m-80) REVERT: A 154 LEU cc_start: 0.8670 (tt) cc_final: 0.8317 (tt) REVERT: A 316 SER cc_start: 0.8782 (m) cc_final: 0.8407 (p) REVERT: B 68 LYS cc_start: 0.8840 (mttt) cc_final: 0.8347 (mmmt) REVERT: B 96 MET cc_start: 0.5822 (mmt) cc_final: 0.5604 (mmt) REVERT: B 103 ARG cc_start: 0.7372 (mtt90) cc_final: 0.5710 (tpp-160) REVERT: B 152 PHE cc_start: 0.6407 (m-80) cc_final: 0.5970 (m-80) REVERT: B 203 LEU cc_start: 0.8804 (mt) cc_final: 0.8594 (mt) REVERT: B 316 SER cc_start: 0.8769 (m) cc_final: 0.8399 (p) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.1551 time to fit residues: 51.9321 Evaluate side-chains 203 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 0.0040 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** 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 = 0.4238 r_free = 0.4238 target = 0.152456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.131000 restraints weight = 33181.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.136776 restraints weight = 14346.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.140211 restraints weight = 8232.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.142414 restraints weight = 5623.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.143818 restraints weight = 4242.683| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.8579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4628 Z= 0.141 Angle : 0.569 7.573 6272 Z= 0.321 Chirality : 0.033 0.130 750 Planarity : 0.003 0.029 738 Dihedral : 4.492 28.579 578 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.07 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.32 (0.35), residues: 532 helix: 2.41 (0.22), residues: 476 sheet: None (None), residues: 0 loop : 0.34 (1.10), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.006 0.001 TYR A 104 PHE 0.020 0.002 PHE B 214 TRP 0.005 0.001 TRP B 305 HIS 0.012 0.002 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4628) covalent geometry : angle 0.56855 ( 6272) hydrogen bonds : bond 0.05052 ( 395) hydrogen bonds : angle 4.57935 ( 1185) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8836 (mt) cc_final: 0.8623 (mt) REVERT: A 68 LYS cc_start: 0.8890 (mttt) cc_final: 0.8304 (mmmt) REVERT: A 154 LEU cc_start: 0.8633 (tt) cc_final: 0.8387 (tt) REVERT: A 316 SER cc_start: 0.8756 (m) cc_final: 0.8375 (p) REVERT: B 61 LEU cc_start: 0.8780 (mt) cc_final: 0.8506 (mt) REVERT: B 68 LYS cc_start: 0.8892 (mttt) cc_final: 0.8348 (mmmt) REVERT: B 96 MET cc_start: 0.5863 (mmt) cc_final: 0.5627 (mmt) REVERT: B 103 ARG cc_start: 0.7440 (mtt90) cc_final: 0.5799 (tpp-160) REVERT: B 152 PHE cc_start: 0.6458 (m-80) cc_final: 0.6002 (m-80) REVERT: B 316 SER cc_start: 0.8748 (m) cc_final: 0.8375 (p) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1483 time to fit residues: 50.5194 Evaluate side-chains 215 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** 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 = 0.4216 r_free = 0.4216 target = 0.150760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.129807 restraints weight = 33283.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.135382 restraints weight = 14432.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.138827 restraints weight = 8271.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.140961 restraints weight = 5631.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.142516 restraints weight = 4274.551| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.8869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4628 Z= 0.144 Angle : 0.580 6.758 6272 Z= 0.331 Chirality : 0.034 0.139 750 Planarity : 0.003 0.022 738 Dihedral : 4.427 27.757 578 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.26 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.40 (0.35), residues: 532 helix: 2.44 (0.22), residues: 476 sheet: None (None), residues: 0 loop : 0.53 (1.14), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 128 TYR 0.006 0.001 TYR A 186 PHE 0.022 0.002 PHE B 46 TRP 0.006 0.001 TRP B 305 HIS 0.007 0.002 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 4628) covalent geometry : angle 0.58044 ( 6272) hydrogen bonds : bond 0.04943 ( 395) hydrogen bonds : angle 4.67229 ( 1185) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8878 (mt) cc_final: 0.8586 (mt) REVERT: A 68 LYS cc_start: 0.8737 (mttt) cc_final: 0.8279 (mmmt) REVERT: A 128 ARG cc_start: 0.7481 (mmt-90) cc_final: 0.7162 (mmt-90) REVERT: A 316 SER cc_start: 0.8700 (m) cc_final: 0.8326 (p) REVERT: B 68 LYS cc_start: 0.8712 (mttt) cc_final: 0.8359 (mmmt) REVERT: B 96 MET cc_start: 0.5731 (mmt) cc_final: 0.5464 (mmt) REVERT: B 103 ARG cc_start: 0.7473 (mtt90) cc_final: 0.5957 (tpp-160) REVERT: B 316 SER cc_start: 0.8676 (m) cc_final: 0.8309 (p) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.1621 time to fit residues: 52.8407 Evaluate side-chains 198 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 210 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.149508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.129124 restraints weight = 33506.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.134649 restraints weight = 14402.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.137958 restraints weight = 8256.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.139892 restraints weight = 5647.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.141365 restraints weight = 4368.334| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.9070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 4628 Z= 0.183 Angle : 0.619 6.815 6272 Z= 0.359 Chirality : 0.034 0.127 750 Planarity : 0.004 0.022 738 Dihedral : 4.474 28.689 578 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.07 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.19 (0.35), residues: 532 helix: 2.32 (0.21), residues: 474 sheet: None (None), residues: 0 loop : 0.38 (1.09), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 128 TYR 0.007 0.001 TYR A 186 PHE 0.035 0.002 PHE A 152 TRP 0.010 0.001 TRP A 305 HIS 0.005 0.002 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 4628) covalent geometry : angle 0.61880 ( 6272) hydrogen bonds : bond 0.04961 ( 395) hydrogen bonds : angle 4.90672 ( 1185) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8908 (mttt) cc_final: 0.8338 (mmmt) REVERT: A 86 LEU cc_start: 0.8887 (tt) cc_final: 0.8486 (tp) REVERT: A 128 ARG cc_start: 0.7610 (mmt-90) cc_final: 0.7372 (mmt-90) REVERT: A 316 SER cc_start: 0.8752 (m) cc_final: 0.8385 (p) REVERT: B 68 LYS cc_start: 0.8886 (mttt) cc_final: 0.8442 (mmmt) REVERT: B 96 MET cc_start: 0.5617 (mmt) cc_final: 0.4987 (mmt) REVERT: B 316 SER cc_start: 0.8717 (m) cc_final: 0.8346 (p) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.1561 time to fit residues: 49.9309 Evaluate side-chains 196 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 chunk 50 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** 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 = 0.4225 r_free = 0.4225 target = 0.151731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.131130 restraints weight = 32875.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.136618 restraints weight = 14415.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.139998 restraints weight = 8326.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.142040 restraints weight = 5699.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.143618 restraints weight = 4390.469| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.9444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4628 Z= 0.151 Angle : 0.608 7.715 6272 Z= 0.341 Chirality : 0.035 0.167 750 Planarity : 0.003 0.025 738 Dihedral : 4.495 30.792 578 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.63 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.35), residues: 532 helix: 2.30 (0.22), residues: 476 sheet: None (None), residues: 0 loop : 0.59 (1.11), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 128 TYR 0.006 0.001 TYR A 186 PHE 0.018 0.001 PHE A 54 TRP 0.009 0.001 TRP A 305 HIS 0.011 0.002 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4628) covalent geometry : angle 0.60847 ( 6272) hydrogen bonds : bond 0.04858 ( 395) hydrogen bonds : angle 4.76941 ( 1185) =============================================================================== Job complete usr+sys time: 2181.55 seconds wall clock time: 37 minutes 47.34 seconds (2267.34 seconds total)