Starting phenix.real_space_refine on Tue Aug 4 17:03:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vuh_65363/08_2026/9vuh_65363.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vuh_65363/08_2026/9vuh_65363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vuh_65363/08_2026/9vuh_65363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vuh_65363/08_2026/9vuh_65363.map" model { file = "/net/cci-nas-00/data/ceres_data/9vuh_65363/08_2026/9vuh_65363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vuh_65363/08_2026/9vuh_65363.cif" } resolution = 2.7 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 P 2 5.49 5 S 31 5.16 5 Cl 2 4.86 5 C 3341 2.51 5 N 899 2.21 5 O 926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s 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: 5201 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2413 Classifications: {'peptide': 298} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1777 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 206} Chain: "C" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 986 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'LZE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.04, per 1000 atoms: 0.20 Number of scatterers: 5201 At special positions: 0 Unit cell: (95.76, 90.63, 84.36, 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) Cl 2 17.00 S 31 16.00 P 2 15.00 O 926 8.00 N 899 7.00 C 3341 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: 0.29 Conformation dependent library (CDL) restraints added in 133.4 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1210 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 3 sheets defined 62.0% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 434 through 436 No H-bonds generated for 'chain 'A' and resid 434 through 436' Processing helix chain 'A' and resid 480 through 492 Processing helix chain 'A' and resid 522 through 530 Processing helix chain 'A' and resid 535 through 556 Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 616 through 634 removed outlier: 4.373A pdb=" N ASP A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 655 Processing helix chain 'A' and resid 668 through 674 Processing helix chain 'A' and resid 683 through 689 Processing helix chain 'A' and resid 693 through 704 Processing helix chain 'A' and resid 713 through 719 Processing helix chain 'A' and resid 720 through 724 Processing helix chain 'A' and resid 731 through 735 Processing helix chain 'B' and resid 77 through 97 Processing helix chain 'B' and resid 100 through 118 removed outlier: 3.656A pdb=" N MET B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 140 Processing helix chain 'B' and resid 145 through 161 Processing helix chain 'B' and resid 171 through 192 Processing helix chain 'B' and resid 201 through 212 removed outlier: 3.522A pdb=" N ILE B 205 " --> pdb=" O PRO B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 232 Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.589A pdb=" N ARG B 239 " --> pdb=" O ASN B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 258 Processing helix chain 'B' and resid 267 through 272 removed outlier: 3.641A pdb=" N GLY B 272 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 291 removed outlier: 3.840A pdb=" N LEU B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 113 through 117 removed outlier: 4.042A pdb=" N ILE C 117 " --> pdb=" O PRO C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 146 Processing helix chain 'C' and resid 148 through 155 Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 163 through 173 removed outlier: 4.211A pdb=" N LYS C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 216 Processing sheet with id=AA1, first strand: chain 'A' and resid 438 through 446 removed outlier: 6.627A pdb=" N ARG A 454 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ARG A 443 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL A 452 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLU A 445 " --> pdb=" O GLY A 450 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLY A 450 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE A 512 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 502 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN A 517 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL A 500 " --> pdb=" O ASN A 517 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA3, first strand: chain 'A' and resid 568 through 570 278 hydrogen bonds defined for protein. 804 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: 0.52 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 836 1.31 - 1.43: 1359 1.43 - 1.56: 3071 1.56 - 1.68: 1 1.68 - 1.81: 53 Bond restraints: 5320 Sorted by residual: bond pdb=" C7 LZE A 801 " pdb=" N6 LZE A 801 " ideal model delta sigma weight residual 1.335 1.451 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" C15 LZE A 801 " pdb=" N14 LZE A 801 " ideal model delta sigma weight residual 1.343 1.455 -0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" O3P SEP A 589 " pdb=" P SEP A 589 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" O2P SEP A 589 " pdb=" P SEP A 589 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" O1P SEP A 589 " pdb=" P SEP A 589 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.24e+01 ... (remaining 5315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 6972 1.68 - 3.36: 174 3.36 - 5.04: 30 5.04 - 6.71: 5 6.71 - 8.39: 4 Bond angle restraints: 7185 Sorted by residual: angle pdb=" N ILE C 164 " pdb=" CA ILE C 164 " pdb=" C ILE C 164 " ideal model delta sigma weight residual 112.50 107.54 4.96 1.39e+00 5.18e-01 1.27e+01 angle pdb=" CA ILE B 182 " pdb=" CB ILE B 182 " pdb=" CG1 ILE B 182 " ideal model delta sigma weight residual 110.40 115.84 -5.44 1.70e+00 3.46e-01 1.03e+01 angle pdb=" CA ILE B 204 " pdb=" C ILE B 204 " pdb=" O ILE B 204 " ideal model delta sigma weight residual 121.17 117.84 3.33 1.06e+00 8.90e-01 9.86e+00 angle pdb=" C ASN C 161 " pdb=" N PRO C 162 " pdb=" CA PRO C 162 " ideal model delta sigma weight residual 119.82 122.87 -3.05 9.80e-01 1.04e+00 9.69e+00 angle pdb=" CA MET A 734 " pdb=" CB MET A 734 " pdb=" CG MET A 734 " ideal model delta sigma weight residual 114.10 120.02 -5.92 2.00e+00 2.50e-01 8.77e+00 ... (remaining 7180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.05: 2978 22.05 - 44.10: 222 44.10 - 66.15: 45 66.15 - 88.20: 7 88.20 - 110.26: 8 Dihedral angle restraints: 3260 sinusoidal: 1396 harmonic: 1864 Sorted by residual: dihedral pdb=" CA PHE B 115 " pdb=" C PHE B 115 " pdb=" N TYR B 116 " pdb=" CA TYR B 116 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA SEP A 589 " pdb=" C SEP A 589 " pdb=" N PRO A 590 " pdb=" CA PRO A 590 " ideal model delta harmonic sigma weight residual 0.00 22.86 -22.86 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA GLY A 588 " pdb=" C GLY A 588 " pdb=" N SEP A 589 " pdb=" CA SEP A 589 " ideal model delta harmonic sigma weight residual 180.00 160.57 19.43 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 3257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.885: 788 0.885 - 1.769: 0 1.769 - 2.654: 0 2.654 - 3.538: 0 3.538 - 4.423: 1 Chirality restraints: 789 Sorted by residual: chirality pdb=" C5 LZE A 801 " pdb=" C25 LZE A 801 " pdb=" C4 LZE A 801 " pdb=" N6 LZE A 801 " both_signs ideal model delta sigma weight residual False 2.46 -1.96 4.42 2.00e-01 2.50e+01 4.89e+02 chirality pdb=" CA ILE C 164 " pdb=" N ILE C 164 " pdb=" C ILE C 164 " pdb=" CB ILE C 164 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE A 497 " pdb=" N ILE A 497 " pdb=" C ILE A 497 " pdb=" CB ILE A 497 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 786 not shown) Planarity restraints: 910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 665 " -0.008 2.00e-02 2.50e+03 1.21e-02 2.91e+00 pdb=" CG TYR A 665 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR A 665 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 665 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 665 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 665 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 665 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 665 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 494 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO A 495 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 495 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 495 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 164 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO B 165 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 165 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 165 " -0.019 5.00e-02 4.00e+02 ... (remaining 907 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 483 2.74 - 3.28: 5200 3.28 - 3.82: 9010 3.82 - 4.36: 11014 4.36 - 4.90: 18388 Nonbonded interactions: 44095 Sorted by model distance: nonbonded pdb=" OD1 ASP B 230 " pdb=" OG1 THR C 179 " model vdw 2.205 3.040 nonbonded pdb=" OD2 ASP B 230 " pdb=" OH TYR B 289 " model vdw 2.234 3.040 nonbonded pdb=" NZ LYS B 199 " pdb=" OE1 GLN C 154 " model vdw 2.248 3.120 nonbonded pdb=" O VAL B 211 " pdb=" NZ LYS C 134 " model vdw 2.269 3.120 nonbonded pdb=" NZ LYS A 467 " pdb=" OE2 GLU A 485 " model vdw 2.276 3.120 ... (remaining 44090 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 individual isotropic 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.350 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: 0.000 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 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 : 0.005 0.116 5320 Z= 0.275 Angle : 0.643 8.393 7185 Z= 0.350 Chirality : 0.163 4.423 789 Planarity : 0.004 0.042 910 Dihedral : 16.732 110.255 2050 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.74 % Favored : 97.10 % Rotamer: Outliers : 1.93 % Allowed : 16.49 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: 1.50 (0.35), residues: 620 helix: 1.44 (0.28), residues: 336 sheet: 0.06 (0.98), residues: 35 loop : 0.71 (0.43), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 264 TYR 0.029 0.002 TYR A 665 PHE 0.012 0.002 PHE A 703 TRP 0.008 0.001 TRP B 225 HIS 0.004 0.001 HIS B 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.27 ( 5320) covalent geometry : angle 0.64284 / 0.35 ( 7185) hydrogen bonds : bond 0.14048 / 9.11 ( 278) hydrogen bonds : angle 5.99230 / 4.23 ( 804) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 MET cc_start: 0.4368 (OUTLIER) cc_final: 0.4088 (mtp) REVERT: C 112 MET cc_start: 0.3794 (ptp) cc_final: 0.3423 (ptm) REVERT: C 209 ASP cc_start: 0.8967 (m-30) cc_final: 0.8728 (m-30) REVERT: C 211 LEU cc_start: 0.8569 (mt) cc_final: 0.8292 (mt) outliers start: 11 outliers final: 3 residues processed: 186 average time/residue: 0.5418 time to fit residues: 104.6377 Evaluate side-chains 119 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 SER Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain C residue 128 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN A 496 ASN A 567 ASN B 123 HIS B 197 HIS B 258 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.124249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.097794 restraints weight = 9117.026| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.65 r_work: 0.3394 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5320 Z= 0.148 Angle : 0.657 7.472 7185 Z= 0.333 Chirality : 0.042 0.206 789 Planarity : 0.005 0.044 910 Dihedral : 5.065 41.324 716 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.74 % Favored : 97.10 % Rotamer: Outliers : 4.21 % Allowed : 21.23 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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 (0.34), residues: 620 helix: 1.57 (0.27), residues: 354 sheet: -0.17 (0.96), residues: 37 loop : 0.51 (0.42), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 160 TYR 0.017 0.001 TYR B 251 PHE 0.024 0.002 PHE C 105 TRP 0.006 0.001 TRP B 225 HIS 0.005 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 5320) covalent geometry : angle 0.65714 / 0.33 ( 7185) hydrogen bonds : bond 0.03653 / 2.37 ( 278) hydrogen bonds : angle 4.86318 / 3.46 ( 804) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7269 (tm-30) REVERT: A 459 LYS cc_start: 0.8529 (tppp) cc_final: 0.8280 (mmmm) REVERT: A 509 MET cc_start: 0.5483 (mmt) cc_final: 0.4132 (ptm) REVERT: A 535 LEU cc_start: 0.9122 (mm) cc_final: 0.8487 (mm) REVERT: A 646 GLN cc_start: 0.8831 (tp40) cc_final: 0.8325 (tt0) REVERT: A 695 GLN cc_start: 0.8324 (mm-40) cc_final: 0.7436 (mm-40) REVERT: A 720 HIS cc_start: 0.8908 (t-90) cc_final: 0.8610 (t70) REVERT: B 173 ASN cc_start: 0.8439 (m-40) cc_final: 0.8023 (m-40) REVERT: B 207 MET cc_start: 0.8928 (mmm) cc_final: 0.8667 (mmm) REVERT: B 210 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: B 235 ASN cc_start: 0.8272 (p0) cc_final: 0.8014 (p0) REVERT: B 274 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8151 (p) REVERT: B 277 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8548 (pt0) REVERT: C 112 MET cc_start: 0.1644 (ptp) cc_final: 0.1413 (ptm) REVERT: C 133 ASP cc_start: 0.8498 (p0) cc_final: 0.8169 (p0) REVERT: C 140 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7933 (pp20) REVERT: C 141 ARG cc_start: 0.7910 (ttm-80) cc_final: 0.7602 (ttm-80) REVERT: C 171 PHE cc_start: 0.8751 (t80) cc_final: 0.8431 (t80) REVERT: C 207 GLU cc_start: 0.8686 (tp30) cc_final: 0.8027 (tp30) REVERT: C 211 LEU cc_start: 0.9183 (mt) cc_final: 0.8620 (mp) outliers start: 24 outliers final: 3 residues processed: 154 average time/residue: 0.4867 time to fit residues: 78.2573 Evaluate side-chains 124 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 143 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 46 optimal weight: 2.9990 chunk 11 optimal weight: 0.0970 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 176 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.125411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.099854 restraints weight = 8928.337| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.51 r_work: 0.3453 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5320 Z= 0.126 Angle : 0.611 8.360 7185 Z= 0.309 Chirality : 0.042 0.226 789 Planarity : 0.004 0.044 910 Dihedral : 4.645 42.756 711 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.42 % Favored : 97.42 % Rotamer: Outliers : 3.33 % Allowed : 22.28 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: 1.63 (0.34), residues: 620 helix: 1.64 (0.28), residues: 354 sheet: -0.17 (0.92), residues: 39 loop : 0.59 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 160 TYR 0.019 0.001 TYR A 665 PHE 0.012 0.002 PHE C 171 TRP 0.006 0.001 TRP B 225 HIS 0.004 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 5320) covalent geometry : angle 0.61062 / 0.31 ( 7185) hydrogen bonds : bond 0.03202 / 2.10 ( 278) hydrogen bonds : angle 4.57724 / 3.24 ( 804) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7594 (tm-30) REVERT: A 459 LYS cc_start: 0.8654 (tppp) cc_final: 0.8429 (mmmm) REVERT: A 509 MET cc_start: 0.5366 (mmt) cc_final: 0.3296 (ptm) REVERT: A 530 MET cc_start: 0.8080 (ptm) cc_final: 0.7767 (ptp) REVERT: A 646 GLN cc_start: 0.8859 (tp40) cc_final: 0.8336 (tt0) REVERT: A 695 GLN cc_start: 0.8436 (mm-40) cc_final: 0.7902 (mm-40) REVERT: B 173 ASN cc_start: 0.8495 (m-40) cc_final: 0.8141 (m110) REVERT: B 186 ARG cc_start: 0.5441 (OUTLIER) cc_final: 0.4124 (ptt180) REVERT: B 207 MET cc_start: 0.8965 (mmm) cc_final: 0.8752 (mmm) REVERT: B 210 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7470 (tm-30) REVERT: B 235 ASN cc_start: 0.8384 (p0) cc_final: 0.8057 (p0) REVERT: B 274 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8260 (p) REVERT: C 129 ASN cc_start: 0.8929 (t0) cc_final: 0.8565 (t0) REVERT: C 133 ASP cc_start: 0.8538 (p0) cc_final: 0.8187 (p0) REVERT: C 140 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7968 (pp20) REVERT: C 141 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7535 (ttm-80) REVERT: C 145 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7916 (pm20) REVERT: C 171 PHE cc_start: 0.8841 (t80) cc_final: 0.8461 (t80) REVERT: C 207 GLU cc_start: 0.8807 (tp30) cc_final: 0.8411 (tp30) outliers start: 19 outliers final: 3 residues processed: 141 average time/residue: 0.5004 time to fit residues: 73.6373 Evaluate side-chains 123 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 206 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN B 176 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.119959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.094198 restraints weight = 9166.865| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.49 r_work: 0.3362 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 5320 Z= 0.214 Angle : 0.679 13.947 7185 Z= 0.342 Chirality : 0.044 0.269 789 Planarity : 0.005 0.044 910 Dihedral : 5.070 44.610 709 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.74 % Favored : 97.10 % Rotamer: Outliers : 4.04 % Allowed : 23.68 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: 1.36 (0.34), residues: 620 helix: 1.45 (0.28), residues: 351 sheet: 0.09 (0.96), residues: 34 loop : 0.35 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 160 TYR 0.021 0.002 TYR B 251 PHE 0.015 0.002 PHE B 268 TRP 0.006 0.001 TRP B 225 HIS 0.004 0.001 HIS B 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.21 ( 5320) covalent geometry : angle 0.67884 / 0.34 ( 7185) hydrogen bonds : bond 0.03775 / 2.46 ( 278) hydrogen bonds : angle 4.62632 / 3.26 ( 804) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7767 (tm-30) REVERT: A 459 LYS cc_start: 0.8749 (tppp) cc_final: 0.8490 (mmmm) REVERT: A 509 MET cc_start: 0.5587 (mmt) cc_final: 0.3873 (ptm) REVERT: A 660 LYS cc_start: 0.8921 (tttt) cc_final: 0.8670 (ttpp) REVERT: A 695 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8016 (mm-40) REVERT: B 104 MET cc_start: 0.7778 (mpp) cc_final: 0.7534 (mpp) REVERT: B 172 GLN cc_start: 0.8186 (pm20) cc_final: 0.7973 (pm20) REVERT: B 186 ARG cc_start: 0.5390 (OUTLIER) cc_final: 0.3938 (ptt180) REVERT: B 210 GLN cc_start: 0.8379 (tp40) cc_final: 0.7605 (tm-30) REVERT: B 218 GLN cc_start: 0.8033 (tm-30) cc_final: 0.7439 (tm-30) REVERT: B 235 ASN cc_start: 0.8503 (p0) cc_final: 0.8231 (p0) REVERT: B 274 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8736 (p) REVERT: C 133 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8238 (p0) REVERT: C 145 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8092 (pm20) outliers start: 23 outliers final: 8 residues processed: 136 average time/residue: 0.5145 time to fit residues: 73.0478 Evaluate side-chains 122 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN A 679 HIS B 176 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.125209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.100326 restraints weight = 9439.954| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 3.49 r_work: 0.3527 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5320 Z= 0.143 Angle : 0.698 12.787 7185 Z= 0.346 Chirality : 0.042 0.243 789 Planarity : 0.005 0.045 910 Dihedral : 5.020 48.364 709 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.58 % Favored : 97.26 % Rotamer: Outliers : 3.33 % Allowed : 25.09 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: 1.46 (0.34), residues: 620 helix: 1.44 (0.28), residues: 352 sheet: 0.11 (0.90), residues: 36 loop : 0.57 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 141 TYR 0.017 0.001 TYR B 251 PHE 0.035 0.002 PHE A 697 TRP 0.007 0.001 TRP A 622 HIS 0.004 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 ( 5320) covalent geometry : angle 0.69795 / 0.35 ( 7185) hydrogen bonds : bond 0.03286 / 2.16 ( 278) hydrogen bonds : angle 4.53377 / 3.15 ( 804) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 437 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7757 (tm-30) REVERT: A 459 LYS cc_start: 0.8783 (tppp) cc_final: 0.8525 (mmmm) REVERT: A 509 MET cc_start: 0.6134 (mmt) cc_final: 0.5118 (ttm) REVERT: A 510 ASP cc_start: 0.8390 (m-30) cc_final: 0.8067 (p0) REVERT: A 530 MET cc_start: 0.8104 (ptm) cc_final: 0.7784 (ptp) REVERT: A 660 LYS cc_start: 0.8939 (tttt) cc_final: 0.8686 (ttpp) REVERT: A 695 GLN cc_start: 0.8358 (mm-40) cc_final: 0.7798 (mm-40) REVERT: A 697 PHE cc_start: 0.8564 (t80) cc_final: 0.8223 (t80) REVERT: B 104 MET cc_start: 0.7626 (mpp) cc_final: 0.7295 (mpp) REVERT: B 171 ASP cc_start: 0.7423 (p0) cc_final: 0.7179 (p0) REVERT: B 173 ASN cc_start: 0.8409 (m-40) cc_final: 0.8094 (m110) REVERT: B 186 ARG cc_start: 0.5293 (OUTLIER) cc_final: 0.5039 (mmt180) REVERT: B 210 GLN cc_start: 0.8276 (tp40) cc_final: 0.7540 (tm-30) REVERT: B 218 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7442 (tm-30) REVERT: B 235 ASN cc_start: 0.8384 (p0) cc_final: 0.8050 (p0) REVERT: B 264 ARG cc_start: 0.8884 (mpt90) cc_final: 0.8493 (mmp-170) REVERT: B 274 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8780 (p) REVERT: C 126 ARG cc_start: 0.8471 (ptt90) cc_final: 0.8189 (ppt170) REVERT: C 133 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8239 (p0) REVERT: C 140 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8028 (pp20) REVERT: C 141 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7645 (ttm-80) REVERT: C 145 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7977 (pm20) REVERT: C 181 TYR cc_start: 0.8223 (m-80) cc_final: 0.7825 (m-80) REVERT: C 207 GLU cc_start: 0.8760 (tp30) cc_final: 0.8113 (tp30) outliers start: 19 outliers final: 4 residues processed: 129 average time/residue: 0.4521 time to fit residues: 61.0417 Evaluate side-chains 117 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 145 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 HIS B 176 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.125286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.100624 restraints weight = 9461.570| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.52 r_work: 0.3529 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5320 Z= 0.146 Angle : 0.720 14.117 7185 Z= 0.354 Chirality : 0.042 0.273 789 Planarity : 0.004 0.045 910 Dihedral : 4.954 50.925 709 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.58 % Favored : 97.26 % Rotamer: Outliers : 3.86 % Allowed : 24.56 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: 1.54 (0.34), residues: 620 helix: 1.44 (0.28), residues: 354 sheet: 0.18 (0.90), residues: 36 loop : 0.70 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 141 TYR 0.016 0.001 TYR B 251 PHE 0.025 0.002 PHE C 171 TRP 0.007 0.001 TRP A 622 HIS 0.007 0.001 HIS B 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 5320) covalent geometry : angle 0.71994 / 0.35 ( 7185) hydrogen bonds : bond 0.03264 / 2.17 ( 278) hydrogen bonds : angle 4.48886 / 3.11 ( 804) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7787 (tm-30) REVERT: A 459 LYS cc_start: 0.8806 (tppp) cc_final: 0.8538 (mmmm) REVERT: A 509 MET cc_start: 0.5988 (mmt) cc_final: 0.5045 (ttm) REVERT: A 660 LYS cc_start: 0.8948 (tttt) cc_final: 0.8690 (ttpp) REVERT: A 695 GLN cc_start: 0.8384 (mm-40) cc_final: 0.7848 (mm-40) REVERT: A 697 PHE cc_start: 0.8462 (t80) cc_final: 0.8156 (t80) REVERT: B 104 MET cc_start: 0.7621 (mpp) cc_final: 0.7348 (mpp) REVERT: B 172 GLN cc_start: 0.8195 (pm20) cc_final: 0.7980 (pm20) REVERT: B 186 ARG cc_start: 0.5316 (OUTLIER) cc_final: 0.5066 (mmt180) REVERT: B 192 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8577 (mp) REVERT: B 210 GLN cc_start: 0.8294 (tp40) cc_final: 0.7556 (tm-30) REVERT: B 218 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7453 (tm-30) REVERT: B 235 ASN cc_start: 0.8378 (p0) cc_final: 0.7994 (p0) REVERT: B 274 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8730 (p) REVERT: C 119 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8171 (mp) REVERT: C 126 ARG cc_start: 0.8446 (ptt90) cc_final: 0.8148 (ppt170) REVERT: C 133 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8262 (p0) REVERT: C 181 TYR cc_start: 0.8164 (m-80) cc_final: 0.7611 (m-80) outliers start: 22 outliers final: 6 residues processed: 130 average time/residue: 0.4286 time to fit residues: 58.5187 Evaluate side-chains 127 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 143 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 40 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN B 176 ASN B 258 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.126048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.101087 restraints weight = 9328.684| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 3.53 r_work: 0.3541 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5320 Z= 0.144 Angle : 0.730 14.959 7185 Z= 0.356 Chirality : 0.042 0.277 789 Planarity : 0.004 0.045 910 Dihedral : 4.954 53.276 709 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.58 % Favored : 97.26 % Rotamer: Outliers : 3.86 % Allowed : 25.79 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: 1.58 (0.35), residues: 620 helix: 1.51 (0.28), residues: 349 sheet: 0.20 (0.92), residues: 36 loop : 0.67 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 141 TYR 0.016 0.001 TYR B 251 PHE 0.025 0.002 PHE C 171 TRP 0.010 0.001 TRP A 622 HIS 0.004 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 ( 5320) covalent geometry : angle 0.72975 / 0.36 ( 7185) hydrogen bonds : bond 0.03210 / 2.15 ( 278) hydrogen bonds : angle 4.47893 / 3.10 ( 804) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7537 (tm-30) REVERT: A 459 LYS cc_start: 0.8847 (tppp) cc_final: 0.8545 (mmmm) REVERT: A 509 MET cc_start: 0.6208 (mmt) cc_final: 0.4981 (ttm) REVERT: A 532 GLN cc_start: 0.8257 (pm20) cc_final: 0.7967 (pm20) REVERT: A 660 LYS cc_start: 0.8957 (tttt) cc_final: 0.8713 (ttpp) REVERT: A 686 LYS cc_start: 0.8582 (mppt) cc_final: 0.8352 (mppt) REVERT: A 695 GLN cc_start: 0.8391 (mm-40) cc_final: 0.7850 (mm-40) REVERT: A 697 PHE cc_start: 0.8264 (t80) cc_final: 0.7996 (t80) REVERT: A 710 ARG cc_start: 0.7666 (mtp180) cc_final: 0.7452 (mtp180) REVERT: B 104 MET cc_start: 0.7559 (mpp) cc_final: 0.7358 (mpp) REVERT: B 171 ASP cc_start: 0.7491 (p0) cc_final: 0.7178 (p0) REVERT: B 173 ASN cc_start: 0.8382 (m-40) cc_final: 0.8112 (m110) REVERT: B 186 ARG cc_start: 0.5330 (OUTLIER) cc_final: 0.5093 (mmt180) REVERT: B 192 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8623 (mp) REVERT: B 210 GLN cc_start: 0.8275 (tp40) cc_final: 0.7552 (tm-30) REVERT: B 218 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7453 (tm-30) REVERT: B 235 ASN cc_start: 0.8365 (p0) cc_final: 0.7986 (p0) REVERT: B 274 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8692 (p) REVERT: C 119 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8063 (mp) REVERT: C 126 ARG cc_start: 0.8465 (ptt90) cc_final: 0.8174 (ppt170) REVERT: C 133 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8258 (p0) REVERT: C 140 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8090 (pp20) REVERT: C 145 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7940 (pm20) REVERT: C 181 TYR cc_start: 0.8135 (m-80) cc_final: 0.7743 (m-80) REVERT: C 207 GLU cc_start: 0.8739 (tp30) cc_final: 0.8086 (tp30) outliers start: 22 outliers final: 7 residues processed: 134 average time/residue: 0.3936 time to fit residues: 55.2010 Evaluate side-chains 124 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 145 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN A 556 ASN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.123552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.098472 restraints weight = 9404.881| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 3.53 r_work: 0.3517 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 5320 Z= 0.194 Angle : 0.796 15.972 7185 Z= 0.392 Chirality : 0.043 0.144 789 Planarity : 0.004 0.045 910 Dihedral : 5.332 56.710 709 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.06 % Favored : 96.77 % Rotamer: Outliers : 3.86 % Allowed : 26.32 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: 1.34 (0.34), residues: 620 helix: 1.32 (0.28), residues: 349 sheet: 0.01 (0.90), residues: 36 loop : 0.58 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 141 TYR 0.022 0.002 TYR B 251 PHE 0.027 0.002 PHE C 171 TRP 0.008 0.001 TRP A 622 HIS 0.004 0.001 HIS B 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.19 ( 5320) covalent geometry : angle 0.79553 / 0.39 ( 7185) hydrogen bonds : bond 0.03594 / 2.41 ( 278) hydrogen bonds : angle 4.62987 / 3.21 ( 804) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7618 (tm-30) REVERT: A 459 LYS cc_start: 0.8860 (tppp) cc_final: 0.8552 (mmmm) REVERT: A 509 MET cc_start: 0.6330 (mmt) cc_final: 0.4448 (ptm) REVERT: A 535 LEU cc_start: 0.9089 (mm) cc_final: 0.8553 (mm) REVERT: A 660 LYS cc_start: 0.8949 (tttt) cc_final: 0.8727 (ttpp) REVERT: A 686 LYS cc_start: 0.8625 (mppt) cc_final: 0.8369 (mppt) REVERT: A 695 GLN cc_start: 0.8419 (mm-40) cc_final: 0.7985 (mm-40) REVERT: A 697 PHE cc_start: 0.8302 (t80) cc_final: 0.8015 (t80) REVERT: B 104 MET cc_start: 0.7732 (mpp) cc_final: 0.7474 (mpp) REVERT: B 186 ARG cc_start: 0.5290 (OUTLIER) cc_final: 0.3900 (ptt180) REVERT: B 192 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8595 (mp) REVERT: B 210 GLN cc_start: 0.8352 (tp40) cc_final: 0.7668 (tm-30) REVERT: B 218 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7451 (tm-30) REVERT: B 235 ASN cc_start: 0.8418 (p0) cc_final: 0.8086 (p0) REVERT: B 274 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8741 (p) REVERT: B 291 ARG cc_start: 0.8990 (mpt90) cc_final: 0.8670 (mmt90) REVERT: C 133 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8271 (p0) REVERT: C 140 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8201 (tm-30) REVERT: C 145 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7919 (pm20) REVERT: C 181 TYR cc_start: 0.8369 (m-80) cc_final: 0.7938 (m-80) REVERT: C 207 GLU cc_start: 0.8762 (tp30) cc_final: 0.8081 (tp30) outliers start: 22 outliers final: 9 residues processed: 130 average time/residue: 0.4380 time to fit residues: 59.3804 Evaluate side-chains 128 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 145 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN A 556 ASN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN B 258 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.125613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.100605 restraints weight = 9347.955| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 3.62 r_work: 0.3524 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5320 Z= 0.162 Angle : 0.816 14.601 7185 Z= 0.402 Chirality : 0.043 0.141 789 Planarity : 0.004 0.045 910 Dihedral : 5.311 57.584 709 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.74 % Favored : 97.10 % Rotamer: Outliers : 3.33 % Allowed : 27.72 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: 1.31 (0.34), residues: 620 helix: 1.30 (0.28), residues: 349 sheet: 0.17 (0.89), residues: 37 loop : 0.52 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 264 TYR 0.018 0.001 TYR B 251 PHE 0.028 0.002 PHE C 171 TRP 0.012 0.001 TRP A 622 HIS 0.003 0.001 HIS B 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 ( 5320) covalent geometry : angle 0.81591 / 0.40 ( 7185) hydrogen bonds : bond 0.03433 / 2.34 ( 278) hydrogen bonds : angle 4.58628 / 3.16 ( 804) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.194 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: A 509 MET cc_start: 0.6184 (mmt) cc_final: 0.4524 (ptm) REVERT: A 535 LEU cc_start: 0.9071 (mm) cc_final: 0.8564 (mm) REVERT: A 580 ASP cc_start: 0.8475 (t0) cc_final: 0.8188 (t0) REVERT: A 645 ASP cc_start: 0.8977 (t0) cc_final: 0.8666 (t0) REVERT: A 660 LYS cc_start: 0.9008 (tttt) cc_final: 0.8769 (ttpp) REVERT: A 685 ARG cc_start: 0.8311 (tpp-160) cc_final: 0.8095 (mmp80) REVERT: A 686 LYS cc_start: 0.8622 (mppt) cc_final: 0.8377 (mppt) REVERT: A 691 LEU cc_start: 0.7337 (tp) cc_final: 0.7116 (pt) REVERT: A 695 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8059 (mm-40) REVERT: A 697 PHE cc_start: 0.8157 (t80) cc_final: 0.7783 (t80) REVERT: A 716 ASP cc_start: 0.8451 (m-30) cc_final: 0.8247 (m-30) REVERT: B 104 MET cc_start: 0.7588 (mpp) cc_final: 0.7381 (mpp) REVERT: B 171 ASP cc_start: 0.7568 (p0) cc_final: 0.7260 (p0) REVERT: B 173 ASN cc_start: 0.8310 (m-40) cc_final: 0.7998 (m-40) REVERT: B 186 ARG cc_start: 0.5267 (OUTLIER) cc_final: 0.3919 (ppt170) REVERT: B 192 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8604 (mp) REVERT: B 210 GLN cc_start: 0.8307 (tp40) cc_final: 0.7582 (tm-30) REVERT: B 218 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7477 (tm-30) REVERT: B 235 ASN cc_start: 0.8371 (p0) cc_final: 0.7974 (p0) REVERT: B 274 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8762 (p) REVERT: B 291 ARG cc_start: 0.9039 (mpt90) cc_final: 0.8756 (mmt90) REVERT: C 119 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8162 (mp) REVERT: C 133 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8304 (p0) REVERT: C 140 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8153 (pp20) REVERT: C 145 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8044 (pm20) REVERT: C 181 TYR cc_start: 0.8238 (m-80) cc_final: 0.7814 (m-80) REVERT: C 207 GLU cc_start: 0.8746 (tp30) cc_final: 0.8083 (tp30) outliers start: 19 outliers final: 6 residues processed: 141 average time/residue: 0.4466 time to fit residues: 65.8394 Evaluate side-chains 127 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 145 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 7 optimal weight: 0.1980 chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN A 556 ASN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.126171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.101119 restraints weight = 9441.191| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.67 r_work: 0.3516 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5320 Z= 0.164 Angle : 0.865 16.183 7185 Z= 0.425 Chirality : 0.044 0.162 789 Planarity : 0.005 0.061 910 Dihedral : 5.329 53.974 709 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.90 % Favored : 96.94 % Rotamer: Outliers : 2.46 % Allowed : 28.77 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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 (0.34), residues: 620 helix: 1.32 (0.28), residues: 349 sheet: -0.15 (0.91), residues: 36 loop : 0.44 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 141 TYR 0.017 0.001 TYR B 251 PHE 0.027 0.002 PHE C 171 TRP 0.013 0.002 TRP C 191 HIS 0.004 0.001 HIS B 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 ( 5320) covalent geometry : angle 0.86527 / 0.43 ( 7185) hydrogen bonds : bond 0.03491 / 2.38 ( 278) hydrogen bonds : angle 4.62740 / 3.22 ( 804) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 MET cc_start: 0.6208 (mmt) cc_final: 0.4754 (ptm) REVERT: A 510 ASP cc_start: 0.8404 (p0) cc_final: 0.8177 (p0) REVERT: A 535 LEU cc_start: 0.9050 (mm) cc_final: 0.8513 (mm) REVERT: A 660 LYS cc_start: 0.9024 (tttt) cc_final: 0.8782 (ttpp) REVERT: A 685 ARG cc_start: 0.8284 (tpp-160) cc_final: 0.8067 (mmp80) REVERT: A 686 LYS cc_start: 0.8657 (mppt) cc_final: 0.8406 (mppt) REVERT: A 695 GLN cc_start: 0.8388 (mm-40) cc_final: 0.7986 (mm-40) REVERT: B 104 MET cc_start: 0.7544 (mpp) cc_final: 0.7316 (mpp) REVERT: B 171 ASP cc_start: 0.7468 (p0) cc_final: 0.7192 (p0) REVERT: B 173 ASN cc_start: 0.8296 (m-40) cc_final: 0.8031 (m-40) REVERT: B 186 ARG cc_start: 0.5339 (OUTLIER) cc_final: 0.4450 (tpt170) REVERT: B 192 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8633 (mp) REVERT: B 210 GLN cc_start: 0.8283 (tp40) cc_final: 0.7563 (tm-30) REVERT: B 218 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7458 (tm-30) REVERT: B 235 ASN cc_start: 0.8343 (p0) cc_final: 0.7927 (p0) REVERT: B 264 ARG cc_start: 0.8690 (mmt-90) cc_final: 0.8380 (mmp-170) REVERT: B 274 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8757 (p) REVERT: B 291 ARG cc_start: 0.9074 (mpt90) cc_final: 0.8794 (mmt90) REVERT: C 119 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8087 (mp) REVERT: C 133 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8299 (p0) REVERT: C 140 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8057 (pp20) REVERT: C 145 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8287 (pm20) REVERT: C 181 TYR cc_start: 0.8189 (m-80) cc_final: 0.7883 (m-80) REVERT: C 207 GLU cc_start: 0.8718 (tp30) cc_final: 0.8080 (tp30) outliers start: 14 outliers final: 4 residues processed: 126 average time/residue: 0.4496 time to fit residues: 59.1837 Evaluate side-chains 126 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 145 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 45 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN A 556 ASN B 176 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.126363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.100933 restraints weight = 9444.602| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 3.69 r_work: 0.3534 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 5320 Z= 0.168 Angle : 0.882 15.834 7185 Z= 0.428 Chirality : 0.044 0.184 789 Planarity : 0.005 0.054 910 Dihedral : 5.181 49.279 709 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.39 % Favored : 96.45 % Rotamer: Outliers : 2.28 % Allowed : 29.12 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % 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: 1.31 (0.34), residues: 620 helix: 1.31 (0.28), residues: 349 sheet: -0.08 (0.91), residues: 36 loop : 0.55 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 141 TYR 0.017 0.001 TYR B 251 PHE 0.025 0.002 PHE C 171 TRP 0.010 0.001 TRP A 622 HIS 0.004 0.001 HIS B 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 ( 5320) covalent geometry : angle 0.88183 / 0.43 ( 7185) hydrogen bonds : bond 0.03524 / 2.35 ( 278) hydrogen bonds : angle 4.65383 / 3.22 ( 804) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2277.63 seconds wall clock time: 39 minutes 27.16 seconds (2367.16 seconds total)