Starting phenix.real_space_refine on Wed Jul 1 22:20:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dwj_27756/07_2026/8dwj_27756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dwj_27756/07_2026/8dwj_27756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dwj_27756/07_2026/8dwj_27756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dwj_27756/07_2026/8dwj_27756.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dwj_27756/07_2026/8dwj_27756.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dwj_27756/07_2026/8dwj_27756.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dwj_27756/07_2026/8dwj_27756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dwj_27756/07_2026/8dwj_27756.cif" } resolution = 3.9 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= 0.003 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 14 5.49 5 S 13 5.16 5 C 1905 2.51 5 N 525 2.21 5 O 585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3043 Number of models: 1 Model: "" Number of chains: 4 Chain: "P" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 117 Unusual residues: {'GTP': 1} Classifications: {'RNA': 4, 'undetermined': 1} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3, None: 1} Not linked: pdbres="GTP P 1 " pdbres=" C P 2 " Chain: "T" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 144 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "A" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2781 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 24, 'TRANS': 314} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 556 SG CYS A 37 35.483 27.676 19.865 1.00234.26 S ATOM 576 SG CYS A 40 35.253 23.162 19.878 1.00251.45 S ATOM 775 SG CYS A 65 36.508 25.850 23.034 1.00220.03 S ATOM 801 SG CYS A 68 38.485 25.430 20.056 1.00211.90 S Time building chain proxies: 1.02, per 1000 atoms: 0.34 Number of scatterers: 3043 At special positions: 0 Unit cell: (67.914, 67.914, 82.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 13 16.00 P 14 15.00 O 585 8.00 N 525 7.00 C 1905 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 99.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 40 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 37 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 65 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 68 " Number of angles added : 6 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 642 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 4 sheets defined 38.9% alpha, 14.2% beta 3 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 4 through 17 Processing helix chain 'A' and resid 74 through 82 Processing helix chain 'A' and resid 82 through 97 removed outlier: 3.545A pdb=" N ARG A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 146 through 152 removed outlier: 4.212A pdb=" N LYS A 151 " --> pdb=" O ASP A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'A' and resid 274 through 287 removed outlier: 3.522A pdb=" N ALA A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 297 Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 314 through 324 removed outlier: 3.512A pdb=" N ILE A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 removed outlier: 4.306A pdb=" N LYS A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 126 Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 292 116 hydrogen bonds defined for protein. 306 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 9 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 3 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 0.35 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 801 1.34 - 1.45: 621 1.45 - 1.57: 1675 1.57 - 1.69: 25 1.69 - 1.81: 20 Bond restraints: 3142 Sorted by residual: bond pdb=" N VAL A 232 " pdb=" CA VAL A 232 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.21e-02 6.83e+03 8.34e+00 bond pdb=" N ILE A 308 " pdb=" CA ILE A 308 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.21e-02 6.83e+03 8.01e+00 bond pdb=" N LYS A 300 " pdb=" CA LYS A 300 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.14e-02 7.69e+03 7.83e+00 bond pdb=" N ILE A 103 " pdb=" CA ILE A 103 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.26e-02 6.30e+03 7.56e+00 bond pdb=" N SER A 100 " pdb=" CA SER A 100 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.21e-02 6.83e+03 7.40e+00 ... (remaining 3137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 4118 2.27 - 4.54: 144 4.54 - 6.80: 20 6.80 - 9.07: 9 9.07 - 11.34: 6 Bond angle restraints: 4297 Sorted by residual: angle pdb=" N ARG A 87 " pdb=" CA ARG A 87 " pdb=" C ARG A 87 " ideal model delta sigma weight residual 110.97 105.46 5.51 1.09e+00 8.42e-01 2.55e+01 angle pdb=" CA LYS A 161 " pdb=" CB LYS A 161 " pdb=" CG LYS A 161 " ideal model delta sigma weight residual 114.10 122.41 -8.31 2.00e+00 2.50e-01 1.73e+01 angle pdb=" N3 DT T 1 " pdb=" C4 DT T 1 " pdb=" O4 DT T 1 " ideal model delta sigma weight residual 119.90 122.24 -2.34 6.00e-01 2.78e+00 1.53e+01 angle pdb=" O4' DC T 5 " pdb=" C4' DC T 5 " pdb=" C3' DC T 5 " ideal model delta sigma weight residual 106.00 103.71 2.29 6.00e-01 2.78e+00 1.45e+01 angle pdb=" PB GTP P 1 " pdb=" O3B GTP P 1 " pdb=" PG GTP P 1 " ideal model delta sigma weight residual 120.50 131.84 -11.34 3.00e+00 1.11e-01 1.43e+01 ... (remaining 4292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 1656 17.58 - 35.16: 166 35.16 - 52.73: 40 52.73 - 70.31: 12 70.31 - 87.88: 5 Dihedral angle restraints: 1879 sinusoidal: 881 harmonic: 998 Sorted by residual: dihedral pdb=" C5' GTP P 1 " pdb=" O5' GTP P 1 " pdb=" PA GTP P 1 " pdb=" O3A GTP P 1 " ideal model delta sinusoidal sigma weight residual 69.27 143.55 -74.28 1 2.00e+01 2.50e-03 1.75e+01 dihedral pdb=" C8 GTP P 1 " pdb=" C1' GTP P 1 " pdb=" N9 GTP P 1 " pdb=" O4' GTP P 1 " ideal model delta sinusoidal sigma weight residual 104.59 42.71 61.88 1 2.00e+01 2.50e-03 1.27e+01 dihedral pdb=" CA GLU A 114 " pdb=" C GLU A 114 " pdb=" N LYS A 115 " pdb=" CA LYS A 115 " ideal model delta harmonic sigma weight residual -180.00 -162.47 -17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 1876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 267 0.040 - 0.079: 105 0.079 - 0.118: 47 0.118 - 0.158: 22 0.158 - 0.197: 10 Chirality restraints: 451 Sorted by residual: chirality pdb=" CA MET A 281 " pdb=" N MET A 281 " pdb=" C MET A 281 " pdb=" CB MET A 281 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.74e-01 chirality pdb=" CA LEU A 336 " pdb=" N LEU A 336 " pdb=" C LEU A 336 " pdb=" CB LEU A 336 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA MET A 307 " pdb=" N MET A 307 " pdb=" C MET A 307 " pdb=" CB MET A 307 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.82e-01 ... (remaining 448 not shown) Planarity restraints: 506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 145 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO A 146 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 203 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.58e+00 pdb=" N PRO A 204 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 314 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO A 315 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 315 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 315 " -0.032 5.00e-02 4.00e+02 ... (remaining 503 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 364 2.75 - 3.29: 2886 3.29 - 3.83: 5595 3.83 - 4.36: 6432 4.36 - 4.90: 10310 Nonbonded interactions: 25587 Sorted by model distance: nonbonded pdb=" OD1 ASP A 8 " pdb=" OH TYR A 89 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR A 55 " pdb=" OH TYR A 66 " model vdw 2.305 3.040 nonbonded pdb=" O LEU A 268 " pdb=" NE1 TRP A 294 " model vdw 2.370 3.120 nonbonded pdb=" NE2 GLN A 195 " pdb=" OG1 THR A 209 " model vdw 2.380 3.120 nonbonded pdb=" N ASP A 84 " pdb=" OD1 ASP A 84 " model vdw 2.384 3.120 ... (remaining 25582 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.250 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5735 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 : 0.008 0.182 3147 Z= 0.428 Angle : 1.183 22.256 4303 Z= 0.620 Chirality : 0.060 0.197 451 Planarity : 0.008 0.064 506 Dihedral : 15.494 87.883 1237 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.33 % Allowed : 14.29 % Favored : 85.38 % 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: -2.71 (0.41), residues: 337 helix: -2.26 (0.37), residues: 116 sheet: -1.88 (0.68), residues: 51 loop : -1.29 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 264 TYR 0.015 0.002 TYR A 321 PHE 0.010 0.002 PHE A 293 TRP 0.031 0.003 TRP A 266 HIS 0.002 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.37 ( 3142) covalent geometry : angle 1.05955 / 0.61 ( 4297) hydrogen bonds : bond 0.18315 / 10.76 ( 125) hydrogen bonds : angle 9.02912 / 8.59 ( 324) metal coordination : bond 0.16030 / 8.02 ( 4) metal coordination : angle 14.13845 / 4.71 ( 6) Misc. bond : bond 0.05167 / 2.58 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 TRP cc_start: 0.4145 (m100) cc_final: 0.3609 (m100) REVERT: A 54 TYR cc_start: 0.5763 (t80) cc_final: 0.5438 (t80) REVERT: A 87 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.5065 (mtt180) REVERT: A 91 PHE cc_start: 0.6079 (t80) cc_final: 0.5870 (t80) REVERT: A 95 LYS cc_start: 0.7872 (tttt) cc_final: 0.6654 (mmmt) REVERT: A 137 ILE cc_start: 0.6298 (mm) cc_final: 0.6040 (tp) REVERT: A 138 LYS cc_start: 0.7391 (mttt) cc_final: 0.7189 (tptm) REVERT: A 158 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6956 (mm-30) REVERT: A 176 SER cc_start: 0.4986 (m) cc_final: 0.4550 (p) REVERT: A 177 GLU cc_start: 0.6150 (tt0) cc_final: 0.5704 (mp0) REVERT: A 183 PRO cc_start: 0.5778 (Cg_exo) cc_final: 0.5374 (Cg_endo) REVERT: A 197 ARG cc_start: 0.5058 (tpt170) cc_final: 0.4835 (tpt170) REVERT: A 238 ASP cc_start: 0.6641 (m-30) cc_final: 0.6290 (t0) REVERT: A 264 ARG cc_start: 0.6642 (ptt180) cc_final: 0.6248 (ptt180) REVERT: A 267 VAL cc_start: 0.7865 (t) cc_final: 0.7536 (t) REVERT: A 279 LYS cc_start: 0.8306 (tttt) cc_final: 0.7955 (mtpp) REVERT: A 292 MET cc_start: 0.8457 (tmm) cc_final: 0.8070 (tpt) REVERT: A 322 MET cc_start: 0.7560 (mmt) cc_final: 0.7044 (ptp) REVERT: A 334 MET cc_start: 0.1538 (mmt) cc_final: 0.0138 (ttp) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.0788 time to fit residues: 8.9044 Evaluate side-chains 50 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.1980 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 0.0010 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.133264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.117333 restraints weight = 12127.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.117620 restraints weight = 10603.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.117996 restraints weight = 8373.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.118040 restraints weight = 7216.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.118648 restraints weight = 6752.475| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5571 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3147 Z= 0.166 Angle : 0.776 7.458 4303 Z= 0.392 Chirality : 0.049 0.173 451 Planarity : 0.007 0.055 506 Dihedral : 13.172 80.050 505 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.33 % Allowed : 19.60 % Favored : 78.07 % 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: -1.74 (0.42), residues: 337 helix: -0.71 (0.45), residues: 110 sheet: -2.44 (0.68), residues: 47 loop : -0.98 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 264 TYR 0.015 0.002 TYR A 185 PHE 0.013 0.002 PHE A 260 TRP 0.015 0.002 TRP A 294 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 ( 3142) covalent geometry : angle 0.76571 / 0.39 ( 4297) hydrogen bonds : bond 0.04908 / 2.82 ( 125) hydrogen bonds : angle 7.09401 / 7.78 ( 324) metal coordination : bond 0.00649 / 0.32 ( 4) metal coordination : angle 3.48218 / 1.16 ( 6) Misc. bond : bond 0.00488 / 0.24 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7569 (tmt-80) cc_final: 0.5018 (mtt180) REVERT: A 95 LYS cc_start: 0.6578 (tttt) cc_final: 0.6175 (mmmt) REVERT: A 127 LEU cc_start: 0.3874 (OUTLIER) cc_final: 0.3577 (mm) REVERT: A 176 SER cc_start: 0.3462 (m) cc_final: 0.3196 (p) REVERT: A 177 GLU cc_start: 0.5981 (tt0) cc_final: 0.4795 (mp0) REVERT: A 334 MET cc_start: 0.2342 (mmt) cc_final: 0.2014 (ttp) outliers start: 7 outliers final: 1 residues processed: 55 average time/residue: 0.1059 time to fit residues: 6.6486 Evaluate side-chains 38 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 162 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 0.3980 chunk 30 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 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 = 0.4392 r_free = 0.4392 target = 0.130172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.115992 restraints weight = 12027.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.115856 restraints weight = 10501.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.116041 restraints weight = 8580.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.116253 restraints weight = 7806.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.116400 restraints weight = 7120.186| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5616 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3147 Z= 0.166 Angle : 0.754 8.476 4303 Z= 0.388 Chirality : 0.049 0.198 451 Planarity : 0.006 0.057 506 Dihedral : 12.871 79.646 501 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.32 % Allowed : 19.93 % Favored : 76.74 % 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: -1.53 (0.42), residues: 337 helix: -0.21 (0.47), residues: 111 sheet: -2.35 (0.71), residues: 47 loop : -1.08 (0.42), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 126 TYR 0.022 0.002 TYR A 220 PHE 0.015 0.002 PHE A 260 TRP 0.013 0.002 TRP A 150 HIS 0.005 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 ( 3142) covalent geometry : angle 0.74803 / 0.39 ( 4297) hydrogen bonds : bond 0.04475 / 2.61 ( 125) hydrogen bonds : angle 6.79785 / 7.60 ( 324) metal coordination : bond 0.00793 / 0.40 ( 4) metal coordination : angle 2.61723 / 0.87 ( 6) Misc. bond : bond 0.00245 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7533 (tmt-80) cc_final: 0.5073 (mtt180) REVERT: A 95 LYS cc_start: 0.6690 (tttt) cc_final: 0.6239 (mmmt) REVERT: A 176 SER cc_start: 0.4809 (m) cc_final: 0.4342 (p) REVERT: A 177 GLU cc_start: 0.5934 (tt0) cc_final: 0.4723 (mp0) REVERT: A 238 ASP cc_start: 0.6196 (OUTLIER) cc_final: 0.5914 (t0) REVERT: A 334 MET cc_start: 0.2442 (OUTLIER) cc_final: 0.1295 (ttp) outliers start: 10 outliers final: 5 residues processed: 43 average time/residue: 0.0994 time to fit residues: 4.9945 Evaluate side-chains 40 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 25 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.0870 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 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 = 0.4388 r_free = 0.4388 target = 0.130776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.114750 restraints weight = 11844.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.115384 restraints weight = 8779.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.115325 restraints weight = 7410.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.115603 restraints weight = 7161.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.115599 restraints weight = 6638.897| |-----------------------------------------------------------------------------| r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5682 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3147 Z= 0.140 Angle : 0.715 12.313 4303 Z= 0.356 Chirality : 0.047 0.192 451 Planarity : 0.006 0.060 506 Dihedral : 12.693 79.096 501 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.33 % Allowed : 20.60 % Favored : 77.08 % 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: -1.32 (0.42), residues: 337 helix: 0.13 (0.47), residues: 110 sheet: -2.07 (0.64), residues: 57 loop : -1.04 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.023 0.002 TYR A 220 PHE 0.021 0.002 PHE A 194 TRP 0.013 0.002 TRP A 159 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 3142) covalent geometry : angle 0.71140 / 0.36 ( 4297) hydrogen bonds : bond 0.03977 / 2.33 ( 125) hydrogen bonds : angle 6.63207 / 7.56 ( 324) metal coordination : bond 0.00670 / 0.34 ( 4) metal coordination : angle 1.92605 / 0.64 ( 6) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7571 (tmt-80) cc_final: 0.5058 (mtt180) REVERT: A 95 LYS cc_start: 0.6790 (tttt) cc_final: 0.6225 (mmmt) REVERT: A 177 GLU cc_start: 0.6090 (tt0) cc_final: 0.4858 (mp0) REVERT: A 334 MET cc_start: 0.2799 (OUTLIER) cc_final: 0.1638 (ttp) outliers start: 7 outliers final: 2 residues processed: 38 average time/residue: 0.0771 time to fit residues: 3.4843 Evaluate side-chains 35 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 48 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 = 0.4384 r_free = 0.4384 target = 0.131217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.115094 restraints weight = 11801.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.115343 restraints weight = 8693.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.115746 restraints weight = 6835.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.115816 restraints weight = 5928.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.115879 restraints weight = 5876.316| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5722 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3147 Z= 0.150 Angle : 0.715 11.076 4303 Z= 0.361 Chirality : 0.049 0.184 451 Planarity : 0.006 0.061 506 Dihedral : 12.690 80.197 501 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.66 % Allowed : 20.27 % Favored : 77.08 % 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: -1.25 (0.43), residues: 337 helix: 0.23 (0.49), residues: 110 sheet: -1.88 (0.62), residues: 60 loop : -1.07 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.025 0.002 TYR A 220 PHE 0.014 0.002 PHE A 194 TRP 0.008 0.002 TRP A 154 HIS 0.004 0.002 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 3142) covalent geometry : angle 0.71055 / 0.36 ( 4297) hydrogen bonds : bond 0.03904 / 2.25 ( 125) hydrogen bonds : angle 6.50008 / 7.43 ( 324) metal coordination : bond 0.00964 / 0.48 ( 4) metal coordination : angle 2.14361 / 0.71 ( 6) Misc. bond : bond 0.00107 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 VAL cc_start: 0.4852 (t) cc_final: 0.4610 (t) REVERT: A 87 ARG cc_start: 0.7647 (tmt-80) cc_final: 0.5023 (mtt180) REVERT: A 95 LYS cc_start: 0.7008 (tttt) cc_final: 0.6410 (mmmt) REVERT: A 177 GLU cc_start: 0.5824 (tt0) cc_final: 0.4759 (mp0) REVERT: A 334 MET cc_start: 0.2787 (OUTLIER) cc_final: 0.1165 (ttp) outliers start: 8 outliers final: 5 residues processed: 41 average time/residue: 0.0666 time to fit residues: 3.2098 Evaluate side-chains 37 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 154 TRP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 7 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 20 optimal weight: 0.0980 chunk 12 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 48 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 = 0.4391 r_free = 0.4391 target = 0.131125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.113736 restraints weight = 11833.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.114721 restraints weight = 7970.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.115392 restraints weight = 6403.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.115695 restraints weight = 5654.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.116060 restraints weight = 5323.301| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5688 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3147 Z= 0.117 Angle : 0.651 10.036 4303 Z= 0.325 Chirality : 0.046 0.179 451 Planarity : 0.006 0.062 506 Dihedral : 12.559 80.504 501 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.66 % Allowed : 21.59 % Favored : 76.74 % 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: -1.08 (0.44), residues: 337 helix: 0.57 (0.50), residues: 110 sheet: -1.82 (0.62), residues: 60 loop : -1.11 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 224 TYR 0.016 0.001 TYR A 220 PHE 0.010 0.001 PHE A 260 TRP 0.007 0.001 TRP A 294 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 ( 3142) covalent geometry : angle 0.64764 / 0.33 ( 4297) hydrogen bonds : bond 0.03517 / 2.04 ( 125) hydrogen bonds : angle 6.33142 / 7.35 ( 324) metal coordination : bond 0.00572 / 0.29 ( 4) metal coordination : angle 1.78436 / 0.59 ( 6) Misc. bond : bond 0.00054 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 VAL cc_start: 0.4794 (t) cc_final: 0.4550 (t) REVERT: A 87 ARG cc_start: 0.7253 (tmt-80) cc_final: 0.4801 (mtt180) REVERT: A 95 LYS cc_start: 0.7047 (tttt) cc_final: 0.6433 (mmmt) REVERT: A 177 GLU cc_start: 0.5892 (tt0) cc_final: 0.4806 (mp0) REVERT: A 334 MET cc_start: 0.2761 (OUTLIER) cc_final: 0.1367 (ttp) outliers start: 5 outliers final: 3 residues processed: 41 average time/residue: 0.0565 time to fit residues: 2.7523 Evaluate side-chains 33 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 0.2980 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 48 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 = 0.4375 r_free = 0.4375 target = 0.130634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.113582 restraints weight = 11883.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.114586 restraints weight = 8477.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.114975 restraints weight = 6845.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.115481 restraints weight = 6145.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.115619 restraints weight = 5719.522| |-----------------------------------------------------------------------------| r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5756 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3147 Z= 0.142 Angle : 0.725 14.647 4303 Z= 0.360 Chirality : 0.047 0.184 451 Planarity : 0.006 0.061 506 Dihedral : 12.645 81.894 501 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.66 % Allowed : 23.59 % Favored : 74.75 % 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: -1.23 (0.44), residues: 337 helix: 0.47 (0.50), residues: 110 sheet: -2.03 (0.60), residues: 62 loop : -1.14 (0.45), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.017 0.002 TYR A 220 PHE 0.009 0.001 PHE A 260 TRP 0.007 0.002 TRP A 266 HIS 0.004 0.002 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 3142) covalent geometry : angle 0.72106 / 0.36 ( 4297) hydrogen bonds : bond 0.03641 / 2.12 ( 125) hydrogen bonds : angle 6.32643 / 7.27 ( 324) metal coordination : bond 0.00921 / 0.46 ( 4) metal coordination : angle 2.12447 / 0.71 ( 6) Misc. bond : bond 0.00095 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.070 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7308 (tmt-80) cc_final: 0.4806 (mtt180) REVERT: A 95 LYS cc_start: 0.7175 (tttt) cc_final: 0.6525 (mmmt) REVERT: A 177 GLU cc_start: 0.5956 (tt0) cc_final: 0.4811 (mp0) REVERT: A 292 MET cc_start: 0.7745 (tmm) cc_final: 0.7080 (tmm) REVERT: A 334 MET cc_start: 0.2851 (OUTLIER) cc_final: 0.1206 (ttp) outliers start: 5 outliers final: 3 residues processed: 35 average time/residue: 0.0534 time to fit residues: 2.2879 Evaluate side-chains 32 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 12 optimal weight: 0.0040 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 3 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.130821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.113833 restraints weight = 12294.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.114853 restraints weight = 8651.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.115447 restraints weight = 6945.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.115687 restraints weight = 6156.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.116174 restraints weight = 5752.907| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5714 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3147 Z= 0.116 Angle : 0.660 9.136 4303 Z= 0.332 Chirality : 0.045 0.170 451 Planarity : 0.006 0.060 506 Dihedral : 12.513 82.057 501 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.33 % Allowed : 23.92 % Favored : 74.75 % 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: -1.16 (0.44), residues: 337 helix: 0.68 (0.50), residues: 110 sheet: -2.04 (0.60), residues: 63 loop : -1.19 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 224 TYR 0.017 0.001 TYR A 220 PHE 0.009 0.001 PHE A 260 TRP 0.008 0.001 TRP A 154 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 ( 3142) covalent geometry : angle 0.65699 / 0.33 ( 4297) hydrogen bonds : bond 0.03379 / 1.96 ( 125) hydrogen bonds : angle 6.18732 / 7.21 ( 324) metal coordination : bond 0.00566 / 0.28 ( 4) metal coordination : angle 1.78547 / 0.60 ( 6) Misc. bond : bond 0.00071 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.4794 (mtt180) REVERT: A 95 LYS cc_start: 0.7084 (tttt) cc_final: 0.6454 (mmmt) REVERT: A 176 SER cc_start: 0.5324 (m) cc_final: 0.4872 (p) REVERT: A 177 GLU cc_start: 0.5696 (tt0) cc_final: 0.4606 (mp0) REVERT: A 225 VAL cc_start: 0.7293 (m) cc_final: 0.7047 (p) REVERT: A 334 MET cc_start: 0.2709 (OUTLIER) cc_final: 0.1218 (ttp) outliers start: 4 outliers final: 1 residues processed: 35 average time/residue: 0.0806 time to fit residues: 3.4320 Evaluate side-chains 32 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 17 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 2 optimal weight: 0.0040 chunk 5 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 48 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 = 0.4371 r_free = 0.4371 target = 0.130802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.114535 restraints weight = 12428.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.114461 restraints weight = 9928.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.114922 restraints weight = 8124.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.115113 restraints weight = 6700.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.115236 restraints weight = 6740.138| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5711 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3147 Z= 0.116 Angle : 0.688 13.071 4303 Z= 0.341 Chirality : 0.046 0.194 451 Planarity : 0.006 0.060 506 Dihedral : 12.460 82.588 501 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.66 % Allowed : 23.92 % Favored : 74.42 % 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: -1.08 (0.44), residues: 337 helix: 0.65 (0.50), residues: 110 sheet: -1.96 (0.61), residues: 63 loop : -1.08 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 126 TYR 0.016 0.001 TYR A 220 PHE 0.009 0.001 PHE A 241 TRP 0.007 0.001 TRP A 53 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 3142) covalent geometry : angle 0.68523 / 0.34 ( 4297) hydrogen bonds : bond 0.03385 / 1.98 ( 125) hydrogen bonds : angle 6.18953 / 7.11 ( 324) metal coordination : bond 0.00495 / 0.25 ( 4) metal coordination : angle 1.71156 / 0.57 ( 6) Misc. bond : bond 0.00066 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.4807 (mtt180) REVERT: A 95 LYS cc_start: 0.6888 (tttt) cc_final: 0.6430 (mmmt) REVERT: A 176 SER cc_start: 0.5120 (m) cc_final: 0.4737 (p) REVERT: A 177 GLU cc_start: 0.5456 (tt0) cc_final: 0.4493 (mp0) REVERT: A 225 VAL cc_start: 0.7290 (m) cc_final: 0.7046 (p) REVERT: A 292 MET cc_start: 0.7643 (tmm) cc_final: 0.7039 (tmm) REVERT: A 334 MET cc_start: 0.2487 (OUTLIER) cc_final: 0.1025 (ttp) outliers start: 5 outliers final: 2 residues processed: 33 average time/residue: 0.1019 time to fit residues: 4.0285 Evaluate side-chains 34 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 2 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.0670 chunk 7 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 11 optimal weight: 0.0060 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.132053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.115906 restraints weight = 11937.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.115884 restraints weight = 9542.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.116427 restraints weight = 7644.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.116611 restraints weight = 6150.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.116699 restraints weight = 6273.828| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5662 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3147 Z= 0.115 Angle : 0.676 11.638 4303 Z= 0.336 Chirality : 0.045 0.170 451 Planarity : 0.006 0.059 506 Dihedral : 12.329 82.823 501 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.66 % Allowed : 23.59 % Favored : 74.75 % 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: -0.94 (0.45), residues: 337 helix: 0.83 (0.50), residues: 110 sheet: -1.84 (0.62), residues: 63 loop : -1.07 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.019 0.001 TYR A 220 PHE 0.009 0.001 PHE A 260 TRP 0.008 0.001 TRP A 294 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 ( 3142) covalent geometry : angle 0.67271 / 0.34 ( 4297) hydrogen bonds : bond 0.03207 / 1.86 ( 125) hydrogen bonds : angle 6.03873 / 6.91 ( 324) metal coordination : bond 0.00309 / 0.15 ( 4) metal coordination : angle 1.90797 / 0.64 ( 6) Misc. bond : bond 0.00056 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.4854 (mtt180) REVERT: A 95 LYS cc_start: 0.6706 (tttt) cc_final: 0.6397 (mmmt) REVERT: A 176 SER cc_start: 0.5067 (m) cc_final: 0.4707 (p) REVERT: A 177 GLU cc_start: 0.5326 (tt0) cc_final: 0.4436 (mp0) REVERT: A 225 VAL cc_start: 0.7268 (m) cc_final: 0.6905 (p) REVERT: A 292 MET cc_start: 0.7673 (tmm) cc_final: 0.7031 (tmm) REVERT: A 334 MET cc_start: 0.2326 (OUTLIER) cc_final: 0.0814 (ttp) outliers start: 5 outliers final: 2 residues processed: 36 average time/residue: 0.0984 time to fit residues: 4.1901 Evaluate side-chains 36 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 48 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 = 0.4386 r_free = 0.4386 target = 0.130975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.116205 restraints weight = 11774.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.116854 restraints weight = 9339.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.116990 restraints weight = 6739.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.117127 restraints weight = 6865.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.117199 restraints weight = 6066.050| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5633 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3147 Z= 0.118 Angle : 0.675 11.184 4303 Z= 0.335 Chirality : 0.046 0.251 451 Planarity : 0.006 0.062 506 Dihedral : 12.388 83.183 501 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.66 % Allowed : 23.26 % Favored : 75.08 % 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: -1.00 (0.44), residues: 337 helix: 0.82 (0.50), residues: 110 sheet: -1.85 (0.62), residues: 63 loop : -1.15 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 197 TYR 0.017 0.001 TYR A 220 PHE 0.008 0.001 PHE A 293 TRP 0.012 0.002 TRP A 150 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 3142) covalent geometry : angle 0.67267 / 0.33 ( 4297) hydrogen bonds : bond 0.03255 / 1.89 ( 125) hydrogen bonds : angle 6.02963 / 6.82 ( 324) metal coordination : bond 0.00466 / 0.23 ( 4) metal coordination : angle 1.61656 / 0.54 ( 6) Misc. bond : bond 0.00070 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 774.18 seconds wall clock time: 14 minutes 3.29 seconds (843.29 seconds total)