Starting phenix.real_space_refine on Tue Aug 4 16:02:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8efp_28087/08_2026/8efp_28087.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efp_28087/08_2026/8efp_28087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8efp_28087/08_2026/8efp_28087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efp_28087/08_2026/8efp_28087.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8efp_28087/08_2026/8efp_28087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efp_28087/08_2026/8efp_28087.map" } resolution = 3.8 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 13 5.16 5 C 2977 2.51 5 N 808 2.21 5 O 907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4705 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1976 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 18, 'TRANS': 224} Chain: "C" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2729 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 6, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 59 Time building chain proxies: 1.21, per 1000 atoms: 0.26 Number of scatterers: 4705 At special positions: 0 Unit cell: (76.176, 74.52, 113.436, 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 13 16.00 O 907 8.00 N 808 7.00 C 2977 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 205.7 milliseconds 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1150 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 3 sheets defined 40.2% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 217 through 222 removed outlier: 3.524A pdb=" N PHE B 220 " --> pdb=" O PRO B 217 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER B 221 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 249 Processing helix chain 'C' and resid 4 through 18 removed outlier: 3.527A pdb=" N ALA C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 68 through 77 removed outlier: 4.179A pdb=" N ASP C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 136 Processing helix chain 'C' and resid 143 through 150 removed outlier: 3.660A pdb=" N ARG C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 186 removed outlier: 4.258A pdb=" N HIS C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 262 Processing helix chain 'C' and resid 264 through 279 Processing helix chain 'C' and resid 281 through 299 Processing helix chain 'C' and resid 307 through 315 Processing helix chain 'C' and resid 322 through 339 Processing helix chain 'C' and resid 342 through 353 Processing helix chain 'C' and resid 354 through 369 Processing helix chain 'C' and resid 371 through 376 Processing helix chain 'C' and resid 383 through 404 Processing sheet with id=AA1, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.594A pdb=" N LEU B 82 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B 102 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 161 through 163 removed outlier: 3.521A pdb=" N CYS B 183 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LYS B 204 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN B 230 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N TYR B 206 " --> pdb=" O ASN B 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 22 through 24 removed outlier: 3.853A pdb=" N SER C 206 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU C 160 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS C 210 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL C 158 " --> pdb=" O LYS C 210 " (cutoff:3.500A) 177 hydrogen bonds defined for protein. 522 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: 0.73 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 959 1.33 - 1.45: 1038 1.45 - 1.57: 2773 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 4790 Sorted by residual: bond pdb=" N LEU C 263 " pdb=" CA LEU C 263 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.14e-02 7.69e+03 1.42e+01 bond pdb=" N ASP C 173 " pdb=" CA ASP C 173 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.70e-03 1.06e+04 9.06e+00 bond pdb=" N LYS C 177 " pdb=" CA LYS C 177 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.26e-02 6.30e+03 8.83e+00 bond pdb=" CA LYS C 177 " pdb=" C LYS C 177 " ideal model delta sigma weight residual 1.519 1.534 -0.016 5.30e-03 3.56e+04 8.82e+00 bond pdb=" N THR C 264 " pdb=" CA THR C 264 " ideal model delta sigma weight residual 1.454 1.494 -0.039 1.33e-02 5.65e+03 8.68e+00 ... (remaining 4785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 6360 4.02 - 8.05: 109 8.05 - 12.07: 15 12.07 - 16.09: 5 16.09 - 20.12: 6 Bond angle restraints: 6495 Sorted by residual: angle pdb=" C PHE B 98 " pdb=" CA PHE B 98 " pdb=" CB PHE B 98 " ideal model delta sigma weight residual 113.37 93.25 20.12 1.61e+00 3.86e-01 1.56e+02 angle pdb=" N SER C 180 " pdb=" CA SER C 180 " pdb=" C SER C 180 " ideal model delta sigma weight residual 112.94 95.36 17.58 1.41e+00 5.03e-01 1.56e+02 angle pdb=" N PRO C 215 " pdb=" CA PRO C 215 " pdb=" C PRO C 215 " ideal model delta sigma weight residual 111.19 94.15 17.04 1.57e+00 4.06e-01 1.18e+02 angle pdb=" N GLN C 194 " pdb=" CA GLN C 194 " pdb=" C GLN C 194 " ideal model delta sigma weight residual 108.23 89.70 18.53 1.72e+00 3.38e-01 1.16e+02 angle pdb=" N ARG C 195 " pdb=" CA ARG C 195 " pdb=" C ARG C 195 " ideal model delta sigma weight residual 108.76 93.60 15.16 1.69e+00 3.50e-01 8.05e+01 ... (remaining 6490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.18: 2474 18.18 - 36.37: 360 36.37 - 54.55: 101 54.55 - 72.73: 11 72.73 - 90.91: 8 Dihedral angle restraints: 2954 sinusoidal: 1197 harmonic: 1757 Sorted by residual: dihedral pdb=" C PHE B 98 " pdb=" N PHE B 98 " pdb=" CA PHE B 98 " pdb=" CB PHE B 98 " ideal model delta harmonic sigma weight residual -122.60 -97.68 -24.92 0 2.50e+00 1.60e-01 9.94e+01 dihedral pdb=" C VAL C 213 " pdb=" N VAL C 213 " pdb=" CA VAL C 213 " pdb=" CB VAL C 213 " ideal model delta harmonic sigma weight residual -122.00 -103.01 -18.99 0 2.50e+00 1.60e-01 5.77e+01 dihedral pdb=" C GLN C 194 " pdb=" N GLN C 194 " pdb=" CA GLN C 194 " pdb=" CB GLN C 194 " ideal model delta harmonic sigma weight residual -122.60 -104.35 -18.25 0 2.50e+00 1.60e-01 5.33e+01 ... (remaining 2951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 709 0.147 - 0.293: 30 0.293 - 0.440: 3 0.440 - 0.586: 0 0.586 - 0.733: 5 Chirality restraints: 747 Sorted by residual: chirality pdb=" CA VAL C 213 " pdb=" N VAL C 213 " pdb=" C VAL C 213 " pdb=" CB VAL C 213 " both_signs ideal model delta sigma weight residual False 2.44 3.17 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CA TYR C 176 " pdb=" N TYR C 176 " pdb=" C TYR C 176 " pdb=" CB TYR C 176 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CA TRP C 179 " pdb=" N TRP C 179 " pdb=" C TRP C 179 " pdb=" CB TRP C 179 " both_signs ideal model delta sigma weight residual False 2.51 3.13 -0.62 2.00e-01 2.50e+01 9.68e+00 ... (remaining 744 not shown) Planarity restraints: 848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 95 " -0.024 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" C LEU B 95 " 0.080 2.00e-02 2.50e+03 pdb=" O LEU B 95 " -0.029 2.00e-02 2.50e+03 pdb=" N PRO B 96 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 37 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C ASN B 37 " 0.046 2.00e-02 2.50e+03 pdb=" O ASN B 37 " -0.018 2.00e-02 2.50e+03 pdb=" N SER B 38 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 398 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C ILE C 398 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE C 398 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU C 399 " -0.013 2.00e-02 2.50e+03 ... (remaining 845 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 64 2.51 - 3.10: 3894 3.10 - 3.70: 7797 3.70 - 4.30: 10845 4.30 - 4.90: 16554 Nonbonded interactions: 39154 Sorted by model distance: nonbonded pdb=" O TRP C 179 " pdb=" CG TRP C 179 " model vdw 1.908 3.260 nonbonded pdb=" O TRP C 179 " pdb=" CD2 TRP C 179 " model vdw 2.113 3.260 nonbonded pdb=" N VAL C 213 " pdb=" O VAL C 213 " model vdw 2.191 2.496 nonbonded pdb=" OG1 THR C 151 " pdb=" NH1 ARG C 152 " model vdw 2.219 3.120 nonbonded pdb=" O LYS C 359 " pdb=" N VAL C 362 " model vdw 2.258 3.120 ... (remaining 39149 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.140 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 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 : 0.006 0.052 4790 Z= 0.370 Angle : 1.460 20.115 6495 Z= 0.886 Chirality : 0.085 0.733 747 Planarity : 0.007 0.067 848 Dihedral : 18.607 90.911 1804 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 33.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.31 % Favored : 86.69 % Rotamer: Outliers : 3.07 % Allowed : 31.03 % Favored : 65.90 % Cbeta Deviations : 1.22 % 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: -4.26 (0.29), residues: 586 helix: -2.31 (0.31), residues: 203 sheet: -3.30 (0.61), residues: 49 loop : -3.21 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 124 TYR 0.027 0.002 TYR C 129 PHE 0.021 0.003 PHE B 98 TRP 0.006 0.002 TRP B 34 HIS 0.006 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.37 ( 4790) covalent geometry : angle 1.46016 / 0.89 ( 6495) hydrogen bonds : bond 0.14811 / 10.11 ( 177) hydrogen bonds : angle 8.13377 / 5.74 ( 522) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 TYR cc_start: 0.7910 (m-10) cc_final: 0.7477 (m-10) REVERT: C 275 LEU cc_start: 0.8243 (pp) cc_final: 0.7875 (pp) outliers start: 16 outliers final: 4 residues processed: 77 average time/residue: 0.0805 time to fit residues: 7.9674 Evaluate side-chains 50 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain C residue 86 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.0170 chunk 56 optimal weight: 0.0050 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.8634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 78 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN C 186 HIS ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.083091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.065210 restraints weight = 29321.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.066587 restraints weight = 20482.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.067654 restraints weight = 15800.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.068234 restraints weight = 12984.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.068912 restraints weight = 11341.143| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4790 Z= 0.192 Angle : 0.889 11.582 6495 Z= 0.447 Chirality : 0.046 0.154 747 Planarity : 0.006 0.067 848 Dihedral : 7.611 59.549 647 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 23.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 3.26 % Allowed : 29.69 % Favored : 67.05 % 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: -3.89 (0.30), residues: 586 helix: -1.86 (0.31), residues: 212 sheet: -3.47 (0.56), residues: 54 loop : -3.02 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 33 TYR 0.018 0.001 TYR B 27 PHE 0.017 0.002 PHE C 34 TRP 0.022 0.004 TRP C 179 HIS 0.004 0.001 HIS C 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 ( 4790) covalent geometry : angle 0.88937 / 0.45 ( 6495) hydrogen bonds : bond 0.07232 / 5.03 ( 177) hydrogen bonds : angle 6.80104 / 4.73 ( 522) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 LEU cc_start: 0.8552 (pp) cc_final: 0.8050 (mt) REVERT: B 108 ARG cc_start: 0.6437 (OUTLIER) cc_final: 0.5232 (pmt-80) REVERT: C 122 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8269 (pp20) REVERT: C 275 LEU cc_start: 0.8534 (pp) cc_final: 0.8285 (pp) outliers start: 17 outliers final: 10 residues processed: 67 average time/residue: 0.0654 time to fit residues: 5.7497 Evaluate side-chains 58 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 394 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 31 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 0.0370 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 GLN B 87 ASN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.082504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.064523 restraints weight = 29466.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.065921 restraints weight = 20417.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.066976 restraints weight = 15635.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.067760 restraints weight = 12782.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.068269 restraints weight = 10935.088| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4790 Z= 0.165 Angle : 0.813 12.603 6495 Z= 0.402 Chirality : 0.044 0.159 747 Planarity : 0.005 0.064 848 Dihedral : 6.939 55.980 645 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 4.02 % Allowed : 28.35 % Favored : 67.62 % 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: -3.56 (0.31), residues: 586 helix: -1.52 (0.31), residues: 224 sheet: -3.34 (0.55), residues: 56 loop : -2.88 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 44 TYR 0.013 0.001 TYR B 27 PHE 0.012 0.002 PHE B 192 TRP 0.014 0.002 TRP B 34 HIS 0.007 0.001 HIS C 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 4790) covalent geometry : angle 0.81349 / 0.40 ( 6495) hydrogen bonds : bond 0.06279 / 4.36 ( 177) hydrogen bonds : angle 6.14888 / 4.29 ( 522) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 LEU cc_start: 0.8818 (pp) cc_final: 0.8275 (mt) REVERT: B 108 ARG cc_start: 0.6562 (OUTLIER) cc_final: 0.5320 (pmt-80) REVERT: C 15 GLU cc_start: 0.9021 (tp30) cc_final: 0.8035 (mp0) REVERT: C 62 LEU cc_start: 0.9441 (tt) cc_final: 0.9215 (mm) REVERT: C 216 ASN cc_start: 0.8746 (m-40) cc_final: 0.8084 (t0) outliers start: 21 outliers final: 8 residues processed: 67 average time/residue: 0.0709 time to fit residues: 6.2599 Evaluate side-chains 53 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 30 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** 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 = 0.4256 r_free = 0.4256 target = 0.080172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.061965 restraints weight = 27468.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.063359 restraints weight = 18996.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.064459 restraints weight = 14553.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.065259 restraints weight = 11804.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.065810 restraints weight = 10083.798| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4790 Z= 0.176 Angle : 0.812 13.888 6495 Z= 0.397 Chirality : 0.043 0.127 747 Planarity : 0.005 0.061 848 Dihedral : 6.771 54.469 645 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 2.49 % Allowed : 28.16 % Favored : 69.35 % 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: -3.34 (0.32), residues: 586 helix: -1.25 (0.32), residues: 220 sheet: -3.28 (0.50), residues: 72 loop : -2.71 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 285 TYR 0.014 0.001 TYR C 393 PHE 0.010 0.002 PHE B 192 TRP 0.011 0.002 TRP B 34 HIS 0.005 0.001 HIS C 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 ( 4790) covalent geometry : angle 0.81181 / 0.40 ( 6495) hydrogen bonds : bond 0.05818 / 4.09 ( 177) hydrogen bonds : angle 6.25701 / 4.32 ( 522) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLN cc_start: 0.8998 (pt0) cc_final: 0.8644 (pt0) REVERT: B 75 LEU cc_start: 0.8799 (pp) cc_final: 0.8422 (mt) REVERT: B 108 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.5310 (pmt-80) REVERT: C 15 GLU cc_start: 0.9059 (tp30) cc_final: 0.8079 (mp0) REVERT: C 62 LEU cc_start: 0.9371 (tt) cc_final: 0.9125 (mm) REVERT: C 147 ARG cc_start: 0.9192 (ptp-170) cc_final: 0.8940 (ptp-170) outliers start: 13 outliers final: 10 residues processed: 60 average time/residue: 0.0673 time to fit residues: 5.3798 Evaluate side-chains 58 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 379 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 51 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS ** C 85 GLN ** 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 = 0.4296 r_free = 0.4296 target = 0.082763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.064705 restraints weight = 29232.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.066177 restraints weight = 20159.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.067232 restraints weight = 15427.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.067985 restraints weight = 12598.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.068549 restraints weight = 10819.302| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4790 Z= 0.146 Angle : 0.782 15.173 6495 Z= 0.379 Chirality : 0.042 0.123 747 Planarity : 0.004 0.056 848 Dihedral : 6.090 28.889 643 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 3.07 % Allowed : 27.97 % Favored : 68.97 % 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: -3.07 (0.32), residues: 586 helix: -1.07 (0.32), residues: 224 sheet: -3.00 (0.55), residues: 66 loop : -2.59 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 125 TYR 0.013 0.001 TYR C 393 PHE 0.015 0.002 PHE C 84 TRP 0.012 0.002 TRP B 34 HIS 0.006 0.001 HIS C 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 ( 4790) covalent geometry : angle 0.78151 / 0.38 ( 6495) hydrogen bonds : bond 0.05469 / 3.80 ( 177) hydrogen bonds : angle 5.81795 / 4.01 ( 522) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 LEU cc_start: 0.8816 (pp) cc_final: 0.8481 (mt) REVERT: B 108 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.5177 (pmt-80) REVERT: B 163 HIS cc_start: 0.7560 (OUTLIER) cc_final: 0.6827 (t-90) REVERT: C 15 GLU cc_start: 0.9019 (tp30) cc_final: 0.8036 (mp0) REVERT: C 16 MET cc_start: 0.8620 (tpp) cc_final: 0.7960 (tpp) REVERT: C 62 LEU cc_start: 0.9386 (tt) cc_final: 0.9152 (mm) REVERT: C 84 PHE cc_start: 0.7741 (m-80) cc_final: 0.7180 (m-80) REVERT: C 147 ARG cc_start: 0.9230 (ptp-170) cc_final: 0.9007 (ptp-170) outliers start: 16 outliers final: 9 residues processed: 62 average time/residue: 0.0699 time to fit residues: 5.7716 Evaluate side-chains 57 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 379 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 52 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 54.3563 > 50:) chunk 49 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 17 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 0.0770 chunk 9 optimal weight: 2.9990 overall best weight: 2.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** 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 = 0.4211 r_free = 0.4211 target = 0.079053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.061389 restraints weight = 30178.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.062648 restraints weight = 21293.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.063626 restraints weight = 16471.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.064314 restraints weight = 13604.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.064827 restraints weight = 11754.767| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 4790 Z= 0.187 Angle : 0.821 15.270 6495 Z= 0.394 Chirality : 0.043 0.193 747 Planarity : 0.005 0.054 848 Dihedral : 6.156 32.699 643 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 2.87 % Allowed : 29.50 % Favored : 67.62 % 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: -2.88 (0.33), residues: 586 helix: -0.88 (0.33), residues: 217 sheet: -3.04 (0.56), residues: 66 loop : -2.46 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 44 TYR 0.010 0.001 TYR B 227 PHE 0.010 0.002 PHE C 315 TRP 0.010 0.002 TRP C 179 HIS 0.007 0.001 HIS B 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 ( 4790) covalent geometry : angle 0.82129 / 0.39 ( 6495) hydrogen bonds : bond 0.05191 / 3.58 ( 177) hydrogen bonds : angle 5.74126 / 3.94 ( 522) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.5231 (pmt-80) REVERT: B 163 HIS cc_start: 0.7495 (OUTLIER) cc_final: 0.7031 (t-90) REVERT: C 15 GLU cc_start: 0.9053 (tp30) cc_final: 0.8151 (mp0) outliers start: 15 outliers final: 10 residues processed: 55 average time/residue: 0.0449 time to fit residues: 3.2920 Evaluate side-chains 55 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 379 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 39 optimal weight: 0.3980 chunk 49 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** 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 = 0.4207 r_free = 0.4207 target = 0.078879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.061227 restraints weight = 27389.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.062531 restraints weight = 19073.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.063489 restraints weight = 14673.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.064157 restraints weight = 12064.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.064688 restraints weight = 10394.258| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4790 Z= 0.153 Angle : 0.844 15.689 6495 Z= 0.388 Chirality : 0.042 0.147 747 Planarity : 0.004 0.049 848 Dihedral : 6.011 32.256 643 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 2.87 % Allowed : 29.31 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.70 (0.34), residues: 586 helix: -0.69 (0.34), residues: 217 sheet: -2.94 (0.58), residues: 66 loop : -2.38 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 174 TYR 0.010 0.001 TYR C 176 PHE 0.011 0.002 PHE C 315 TRP 0.011 0.002 TRP C 179 HIS 0.009 0.002 HIS B 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 4790) covalent geometry : angle 0.84357 / 0.39 ( 6495) hydrogen bonds : bond 0.05001 / 3.44 ( 177) hydrogen bonds : angle 5.68905 / 3.89 ( 522) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.6581 (OUTLIER) cc_final: 0.5240 (pmt-80) REVERT: C 15 GLU cc_start: 0.9076 (tp30) cc_final: 0.8135 (mp0) REVERT: C 51 HIS cc_start: 0.6661 (m-70) cc_final: 0.6003 (t-90) REVERT: C 147 ARG cc_start: 0.9170 (ptp-170) cc_final: 0.8945 (ptp-170) outliers start: 15 outliers final: 13 residues processed: 56 average time/residue: 0.0519 time to fit residues: 3.9258 Evaluate side-chains 59 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 332 PHE Chi-restraints excluded: chain C residue 379 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 21 optimal weight: 0.4980 chunk 57 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 0.0570 chunk 37 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 4 optimal weight: 0.0370 chunk 8 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 HIS ** 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 = 0.4253 r_free = 0.4253 target = 0.080325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.062192 restraints weight = 27408.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.063549 restraints weight = 18764.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.064636 restraints weight = 14361.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.065399 restraints weight = 11691.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.065950 restraints weight = 10001.398| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4790 Z= 0.136 Angle : 0.856 16.380 6495 Z= 0.392 Chirality : 0.042 0.129 747 Planarity : 0.004 0.047 848 Dihedral : 5.827 30.742 643 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 2.68 % Allowed : 29.12 % Favored : 68.20 % 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: -2.50 (0.35), residues: 586 helix: -0.47 (0.34), residues: 217 sheet: -3.14 (0.57), residues: 77 loop : -2.15 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 202 TYR 0.007 0.001 TYR B 227 PHE 0.013 0.001 PHE C 315 TRP 0.010 0.002 TRP B 34 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 4790) covalent geometry : angle 0.85640 / 0.39 ( 6495) hydrogen bonds : bond 0.04665 / 3.19 ( 177) hydrogen bonds : angle 5.55295 / 3.82 ( 522) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.5091 (pmt-80) REVERT: B 174 ASP cc_start: 0.7808 (p0) cc_final: 0.7340 (t70) REVERT: C 15 GLU cc_start: 0.8980 (tp30) cc_final: 0.8388 (mm-30) REVERT: C 51 HIS cc_start: 0.6387 (m-70) cc_final: 0.5803 (t-90) REVERT: C 147 ARG cc_start: 0.9125 (ptp-170) cc_final: 0.8891 (ptp-170) outliers start: 14 outliers final: 10 residues processed: 63 average time/residue: 0.0673 time to fit residues: 5.5021 Evaluate side-chains 59 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 332 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 HIS ** 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 = 0.4229 r_free = 0.4229 target = 0.079265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.061845 restraints weight = 26907.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.063119 restraints weight = 18384.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.064109 restraints weight = 14037.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.064783 restraints weight = 11451.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.065341 restraints weight = 9896.074| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4790 Z= 0.150 Angle : 0.857 14.676 6495 Z= 0.393 Chirality : 0.042 0.126 747 Planarity : 0.004 0.047 848 Dihedral : 5.860 33.255 643 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 1.92 % Allowed : 30.08 % Favored : 68.01 % 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: -2.46 (0.35), residues: 586 helix: -0.53 (0.34), residues: 219 sheet: -2.83 (0.60), residues: 67 loop : -2.21 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 174 TYR 0.009 0.001 TYR C 382 PHE 0.014 0.001 PHE C 84 TRP 0.011 0.002 TRP C 179 HIS 0.003 0.001 HIS C 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 4790) covalent geometry : angle 0.85748 / 0.39 ( 6495) hydrogen bonds : bond 0.04715 / 3.18 ( 177) hydrogen bonds : angle 5.49285 / 3.77 ( 522) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.180 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: B 108 ARG cc_start: 0.6633 (OUTLIER) cc_final: 0.5159 (pmt-80) REVERT: C 15 GLU cc_start: 0.8983 (tp30) cc_final: 0.8417 (mm-30) REVERT: C 51 HIS cc_start: 0.6514 (m-70) cc_final: 0.5983 (t-90) REVERT: C 147 ARG cc_start: 0.9125 (ptp-170) cc_final: 0.8917 (ptp-170) outliers start: 10 outliers final: 9 residues processed: 57 average time/residue: 0.0845 time to fit residues: 6.1541 Evaluate side-chains 57 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 332 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 47 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 40.0000 chunk 6 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** 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 = 0.4179 r_free = 0.4179 target = 0.076977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.059013 restraints weight = 28376.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.060271 restraints weight = 19974.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.061174 restraints weight = 15560.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.061851 restraints weight = 12892.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.062341 restraints weight = 11200.755| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 4790 Z= 0.196 Angle : 0.847 14.250 6495 Z= 0.406 Chirality : 0.043 0.182 747 Planarity : 0.005 0.048 848 Dihedral : 6.197 37.947 643 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 25.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer: Outliers : 2.49 % Allowed : 30.46 % Favored : 67.05 % 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: -2.65 (0.34), residues: 586 helix: -0.60 (0.34), residues: 219 sheet: -3.21 (0.55), residues: 64 loop : -2.33 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 268 TYR 0.013 0.001 TYR C 393 PHE 0.016 0.002 PHE B 195 TRP 0.008 0.002 TRP B 34 HIS 0.006 0.002 HIS C 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 ( 4790) covalent geometry : angle 0.84734 / 0.41 ( 6495) hydrogen bonds : bond 0.04574 / 3.13 ( 177) hydrogen bonds : angle 5.56224 / 3.81 ( 522) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.183 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: B 75 LEU cc_start: 0.8950 (mm) cc_final: 0.8642 (pp) REVERT: B 108 ARG cc_start: 0.6412 (OUTLIER) cc_final: 0.5129 (pmt-80) REVERT: B 258 ILE cc_start: 0.9461 (pt) cc_final: 0.9139 (mt) REVERT: C 15 GLU cc_start: 0.9032 (tp30) cc_final: 0.8519 (mp0) REVERT: C 51 HIS cc_start: 0.7038 (m-70) cc_final: 0.6420 (t-90) REVERT: C 84 PHE cc_start: 0.8066 (m-80) cc_final: 0.7826 (m-80) outliers start: 13 outliers final: 9 residues processed: 58 average time/residue: 0.0588 time to fit residues: 4.4751 Evaluate side-chains 55 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 332 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 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 = 0.4199 r_free = 0.4199 target = 0.077954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.060241 restraints weight = 26969.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.061473 restraints weight = 18637.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.062444 restraints weight = 14335.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.063099 restraints weight = 11759.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.063669 restraints weight = 10163.475| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4790 Z= 0.152 Angle : 0.855 17.110 6495 Z= 0.397 Chirality : 0.043 0.149 747 Planarity : 0.004 0.045 848 Dihedral : 6.016 35.950 643 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 1.92 % Allowed : 31.03 % Favored : 67.05 % 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: -2.57 (0.34), residues: 586 helix: -0.51 (0.34), residues: 219 sheet: -3.20 (0.55), residues: 64 loop : -2.30 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 125 TYR 0.009 0.001 TYR C 393 PHE 0.010 0.001 PHE C 84 TRP 0.010 0.002 TRP C 179 HIS 0.006 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 4790) covalent geometry : angle 0.85536 / 0.40 ( 6495) hydrogen bonds : bond 0.04438 / 3.02 ( 177) hydrogen bonds : angle 5.49517 / 3.74 ( 522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1186.43 seconds wall clock time: 21 minutes 7.27 seconds (1267.27 seconds total)