Starting phenix.real_space_refine on Tue Feb 3 16:23:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hjk_52217/02_2026/9hjk_52217.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hjk_52217/02_2026/9hjk_52217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hjk_52217/02_2026/9hjk_52217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hjk_52217/02_2026/9hjk_52217.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hjk_52217/02_2026/9hjk_52217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hjk_52217/02_2026/9hjk_52217.map" } resolution = 3.27 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= 0.001 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 3162 2.51 5 N 764 2.21 5 O 862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4818 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3839 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 24, 'TRANS': 492} Chain breaks: 1 Chain: "B" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 881 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.31, per 1000 atoms: 0.27 Number of scatterers: 4818 At special positions: 0 Unit cell: (97.344, 81.536, 84.032, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 862 8.00 N 764 7.00 C 3162 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 399 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 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: 0.46 Conformation dependent library (CDL) restraints added in 337.3 milliseconds 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 3 sheets defined 65.9% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 29 through 50 removed outlier: 3.798A pdb=" N ALA A 44 " --> pdb=" O THR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 58 through 87 removed outlier: 3.765A pdb=" N CYS A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 104 through 132 Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 163 through 175 removed outlier: 3.789A pdb=" N MET A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 210 Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 223 through 236 removed outlier: 3.569A pdb=" N GLY A 227 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 249 through 252 Processing helix chain 'A' and resid 254 through 281 Proline residue: A 260 - end of helix Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 304 through 328 removed outlier: 3.736A pdb=" N ALA A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 342 Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 359 through 376 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 386 through 406 removed outlier: 4.021A pdb=" N LEU A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 483 removed outlier: 3.563A pdb=" N LEU A 476 " --> pdb=" O CYS A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 513 removed outlier: 3.771A pdb=" N THR A 494 " --> pdb=" O PHE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'A' and resid 535 through 551 Processing helix chain 'A' and resid 552 through 573 removed outlier: 3.860A pdb=" N ARG A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.515A pdb=" N MET B 31 " --> pdb=" O PRO B 28 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.254A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 12 removed outlier: 4.084A pdb=" N TYR B 104 " --> pdb=" O VAL B 98 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 933 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: 0.77 Time building geometry restraints manager: 0.60 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: 730 1.31 - 1.44: 1347 1.44 - 1.56: 2816 1.56 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 4935 Sorted by residual: bond pdb=" C ILE A 177 " pdb=" O ILE A 177 " ideal model delta sigma weight residual 1.233 1.183 0.050 1.22e-02 6.72e+03 1.71e+01 bond pdb=" N VAL A 282 " pdb=" CA VAL A 282 " ideal model delta sigma weight residual 1.461 1.499 -0.037 1.17e-02 7.31e+03 1.03e+01 bond pdb=" N VAL B 5 " pdb=" CA VAL B 5 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.33e+00 bond pdb=" N ILE A 281 " pdb=" CA ILE A 281 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.30e+00 bond pdb=" N VAL A 471 " pdb=" CA VAL A 471 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.75e+00 ... (remaining 4930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 6257 1.39 - 2.78: 354 2.78 - 4.17: 103 4.17 - 5.56: 23 5.56 - 6.95: 5 Bond angle restraints: 6742 Sorted by residual: angle pdb=" N VAL A 400 " pdb=" CA VAL A 400 " pdb=" C VAL A 400 " ideal model delta sigma weight residual 110.62 105.62 5.00 1.02e+00 9.61e-01 2.40e+01 angle pdb=" N VAL A 400 " pdb=" CA VAL A 400 " pdb=" CB VAL A 400 " ideal model delta sigma weight residual 110.54 117.19 -6.65 1.36e+00 5.41e-01 2.39e+01 angle pdb=" N VAL A 398 " pdb=" CA VAL A 398 " pdb=" C VAL A 398 " ideal model delta sigma weight residual 111.05 105.03 6.02 1.25e+00 6.40e-01 2.32e+01 angle pdb=" N VAL A 471 " pdb=" CA VAL A 471 " pdb=" CB VAL A 471 " ideal model delta sigma weight residual 110.58 117.53 -6.95 1.50e+00 4.44e-01 2.14e+01 angle pdb=" CA ILE A 177 " pdb=" C ILE A 177 " pdb=" O ILE A 177 " ideal model delta sigma weight residual 120.46 115.61 4.85 1.11e+00 8.12e-01 1.91e+01 ... (remaining 6737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.25: 2854 33.25 - 66.51: 103 66.51 - 99.76: 13 99.76 - 133.01: 10 133.01 - 166.27: 1 Dihedral angle restraints: 2981 sinusoidal: 1193 harmonic: 1788 Sorted by residual: dihedral pdb=" CCQ AV0 B 201 " pdb=" CCS AV0 B 201 " pdb=" OCB AV0 B 201 " pdb=" OBZ AV0 B 201 " ideal model delta sinusoidal sigma weight residual -109.41 56.86 -166.27 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CA VAL A 385 " pdb=" C VAL A 385 " pdb=" N SER A 386 " pdb=" CA SER A 386 " ideal model delta harmonic sigma weight residual 180.00 -157.44 -22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CCH AV0 B 201 " pdb=" CCJ AV0 B 201 " pdb=" CCL AV0 B 201 " pdb=" OBX AV0 B 201 " ideal model delta sinusoidal sigma weight residual -57.86 64.11 -121.97 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 2978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 588 0.045 - 0.089: 150 0.089 - 0.134: 52 0.134 - 0.179: 15 0.179 - 0.223: 5 Chirality restraints: 810 Sorted by residual: chirality pdb=" CA VAL A 280 " pdb=" N VAL A 280 " pdb=" C VAL A 280 " pdb=" CB VAL A 280 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE A 105 " pdb=" N ILE A 105 " pdb=" C ILE A 105 " pdb=" CB ILE A 105 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA VAL A 402 " pdb=" N VAL A 402 " pdb=" C VAL A 402 " pdb=" CB VAL A 402 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 807 not shown) Planarity restraints: 818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 108 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.36e+00 pdb=" C LEU A 108 " 0.053 2.00e-02 2.50e+03 pdb=" O LEU A 108 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL A 109 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 267 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.36e+00 pdb=" C LEU A 267 " -0.050 2.00e-02 2.50e+03 pdb=" O LEU A 267 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 268 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 266 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.59e+00 pdb=" C ALA A 266 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA A 266 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 267 " 0.014 2.00e-02 2.50e+03 ... (remaining 815 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1267 2.80 - 3.32: 5099 3.32 - 3.85: 7953 3.85 - 4.37: 9392 4.37 - 4.90: 16084 Nonbonded interactions: 39795 Sorted by model distance: nonbonded pdb=" OH TYR A 214 " pdb=" O VAL A 279 " model vdw 2.270 3.040 nonbonded pdb=" O SER A 483 " pdb=" OG SER A 483 " model vdw 2.271 3.040 nonbonded pdb=" O ASP A 243 " pdb=" OG1 THR A 246 " model vdw 2.284 3.040 nonbonded pdb=" O PRO A 358 " pdb=" OG1 THR A 362 " model vdw 2.314 3.040 nonbonded pdb=" O TYR A 274 " pdb=" OG SER A 278 " model vdw 2.351 3.040 ... (remaining 39790 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: 1.290 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.850 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 0.050 4937 Z= 0.354 Angle : 0.794 6.945 6746 Z= 0.522 Chirality : 0.050 0.223 810 Planarity : 0.005 0.053 818 Dihedral : 18.617 166.267 1845 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.81 % Allowed : 17.17 % Favored : 82.02 % 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: 0.51 (0.35), residues: 625 helix: 1.22 (0.28), residues: 348 sheet: -0.54 (0.77), residues: 51 loop : -0.76 (0.44), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 38 TYR 0.012 0.001 TYR A 47 PHE 0.022 0.001 PHE A 221 TRP 0.014 0.001 TRP A 107 HIS 0.012 0.002 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 4935) covalent geometry : angle 0.79294 ( 6742) SS BOND : bond 0.00060 ( 2) SS BOND : angle 1.62981 ( 4) hydrogen bonds : bond 0.14846 ( 324) hydrogen bonds : angle 6.44389 ( 933) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.174 Fit side-chains REVERT: A 306 GLN cc_start: 0.8515 (mp-120) cc_final: 0.8126 (mp10) REVERT: A 356 GLN cc_start: 0.8664 (mt0) cc_final: 0.8377 (mt0) REVERT: A 519 ARG cc_start: 0.4622 (OUTLIER) cc_final: 0.4391 (ptt90) REVERT: A 535 TYR cc_start: 0.7165 (m-80) cc_final: 0.6812 (m-80) REVERT: A 568 MET cc_start: 0.8032 (mtp) cc_final: 0.7800 (mtm) REVERT: B 39 GLN cc_start: 0.8086 (tt0) cc_final: 0.7874 (tt0) REVERT: B 80 TYR cc_start: 0.7883 (m-80) cc_final: 0.7252 (m-80) REVERT: B 82 GLN cc_start: 0.8041 (tp-100) cc_final: 0.7830 (tp40) outliers start: 4 outliers final: 0 residues processed: 120 average time/residue: 0.0601 time to fit residues: 9.4679 Evaluate side-chains 105 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.0000 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 61 optimal weight: 0.0770 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.166360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.134356 restraints weight = 6549.973| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.41 r_work: 0.3538 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4937 Z= 0.142 Angle : 0.688 9.867 6746 Z= 0.328 Chirality : 0.044 0.333 810 Planarity : 0.004 0.032 818 Dihedral : 13.738 155.969 875 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.24 % Allowed : 13.94 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.34), residues: 625 helix: 1.54 (0.27), residues: 369 sheet: -0.74 (0.72), residues: 57 loop : -0.58 (0.45), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 67 TYR 0.009 0.001 TYR A 239 PHE 0.014 0.001 PHE A 522 TRP 0.009 0.001 TRP B 33 HIS 0.003 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4935) covalent geometry : angle 0.68730 ( 6742) SS BOND : bond 0.00233 ( 2) SS BOND : angle 1.21462 ( 4) hydrogen bonds : bond 0.04128 ( 324) hydrogen bonds : angle 4.56526 ( 933) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.186 Fit side-chains REVERT: A 269 ILE cc_start: 0.9093 (mt) cc_final: 0.8808 (mt) REVERT: A 306 GLN cc_start: 0.8350 (mp-120) cc_final: 0.8018 (mp10) REVERT: A 356 GLN cc_start: 0.8658 (mt0) cc_final: 0.8433 (mt0) REVERT: A 519 ARG cc_start: 0.4774 (OUTLIER) cc_final: 0.4545 (ptt90) REVERT: A 565 ILE cc_start: 0.7709 (mt) cc_final: 0.7492 (mp) REVERT: A 568 MET cc_start: 0.7800 (mtp) cc_final: 0.7593 (mtm) REVERT: A 579 LEU cc_start: 0.8576 (tp) cc_final: 0.8254 (mp) REVERT: B 80 TYR cc_start: 0.8021 (m-80) cc_final: 0.7409 (m-80) REVERT: B 104 TYR cc_start: 0.8521 (t80) cc_final: 0.8184 (t80) outliers start: 21 outliers final: 13 residues processed: 124 average time/residue: 0.0695 time to fit residues: 11.3890 Evaluate side-chains 117 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 519 ARG Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 564 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 59 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 0.0370 chunk 48 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN B 1 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.164576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.132097 restraints weight = 6543.989| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.42 r_work: 0.3518 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4937 Z= 0.144 Angle : 0.686 10.543 6746 Z= 0.322 Chirality : 0.043 0.362 810 Planarity : 0.004 0.035 818 Dihedral : 11.142 129.074 875 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.43 % Allowed : 16.77 % Favored : 79.80 % 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: 1.17 (0.34), residues: 625 helix: 1.74 (0.27), residues: 372 sheet: -0.90 (0.70), residues: 57 loop : -0.51 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 67 TYR 0.019 0.001 TYR A 47 PHE 0.012 0.001 PHE A 522 TRP 0.011 0.001 TRP B 33 HIS 0.003 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4935) covalent geometry : angle 0.68526 ( 6742) SS BOND : bond 0.00909 ( 2) SS BOND : angle 1.81468 ( 4) hydrogen bonds : bond 0.03997 ( 324) hydrogen bonds : angle 4.36505 ( 933) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 269 ILE cc_start: 0.9110 (mt) cc_final: 0.8865 (mt) REVERT: A 306 GLN cc_start: 0.8340 (mp-120) cc_final: 0.8042 (mp10) REVERT: A 486 ARG cc_start: 0.5374 (OUTLIER) cc_final: 0.4370 (ptt180) REVERT: A 519 ARG cc_start: 0.4865 (OUTLIER) cc_final: 0.4620 (ptt90) REVERT: A 565 ILE cc_start: 0.7807 (mt) cc_final: 0.7606 (mp) REVERT: A 568 MET cc_start: 0.7748 (mtp) cc_final: 0.7541 (mtm) REVERT: A 579 LEU cc_start: 0.8586 (tp) cc_final: 0.8218 (mp) REVERT: B 80 TYR cc_start: 0.8021 (m-80) cc_final: 0.7368 (m-80) outliers start: 17 outliers final: 10 residues processed: 120 average time/residue: 0.0739 time to fit residues: 11.4867 Evaluate side-chains 120 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 486 ARG Chi-restraints excluded: chain A residue 519 ARG Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 113 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 0.0370 chunk 17 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 53 optimal weight: 0.0670 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 550 ASN A 577 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.167082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.136055 restraints weight = 6453.853| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.32 r_work: 0.3546 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4937 Z= 0.130 Angle : 0.660 10.270 6746 Z= 0.311 Chirality : 0.042 0.263 810 Planarity : 0.004 0.033 818 Dihedral : 9.840 122.032 875 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.23 % Allowed : 17.98 % Favored : 78.79 % 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: 1.28 (0.34), residues: 625 helix: 1.87 (0.26), residues: 373 sheet: -0.85 (0.69), residues: 56 loop : -0.55 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 67 TYR 0.006 0.001 TYR A 94 PHE 0.011 0.001 PHE A 374 TRP 0.010 0.001 TRP B 33 HIS 0.001 0.000 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 4935) covalent geometry : angle 0.65815 ( 6742) SS BOND : bond 0.00283 ( 2) SS BOND : angle 2.19054 ( 4) hydrogen bonds : bond 0.03804 ( 324) hydrogen bonds : angle 4.22359 ( 933) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 269 ILE cc_start: 0.9087 (mt) cc_final: 0.8820 (mt) REVERT: A 306 GLN cc_start: 0.8315 (mp-120) cc_final: 0.8012 (mp10) REVERT: A 356 GLN cc_start: 0.8493 (mt0) cc_final: 0.8018 (mt0) REVERT: A 486 ARG cc_start: 0.5430 (OUTLIER) cc_final: 0.4477 (ptt180) REVERT: A 519 ARG cc_start: 0.4954 (OUTLIER) cc_final: 0.4546 (ptt90) REVERT: A 579 LEU cc_start: 0.8570 (tp) cc_final: 0.8150 (mp) REVERT: B 25 SER cc_start: 0.6766 (t) cc_final: 0.6485 (p) REVERT: B 44 GLU cc_start: 0.8561 (pp20) cc_final: 0.8280 (pp20) REVERT: B 80 TYR cc_start: 0.7928 (m-80) cc_final: 0.7205 (m-80) REVERT: B 104 TYR cc_start: 0.8542 (t80) cc_final: 0.7974 (t80) outliers start: 16 outliers final: 10 residues processed: 124 average time/residue: 0.0763 time to fit residues: 12.1271 Evaluate side-chains 116 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 486 ARG Chi-restraints excluded: chain A residue 519 ARG Chi-restraints excluded: chain A residue 577 HIS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 113 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 48 optimal weight: 0.0770 chunk 60 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 34 optimal weight: 0.0970 chunk 58 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 577 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.166796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.135885 restraints weight = 6588.599| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.35 r_work: 0.3553 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 4937 Z= 0.132 Angle : 0.661 10.471 6746 Z= 0.314 Chirality : 0.042 0.261 810 Planarity : 0.004 0.033 818 Dihedral : 9.466 124.304 875 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.23 % Allowed : 19.19 % Favored : 77.58 % 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: 1.36 (0.34), residues: 625 helix: 1.95 (0.26), residues: 373 sheet: -0.85 (0.70), residues: 56 loop : -0.57 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 67 TYR 0.019 0.001 TYR A 47 PHE 0.010 0.001 PHE A 522 TRP 0.010 0.001 TRP B 33 HIS 0.005 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 4935) covalent geometry : angle 0.65770 ( 6742) SS BOND : bond 0.00363 ( 2) SS BOND : angle 2.78959 ( 4) hydrogen bonds : bond 0.03737 ( 324) hydrogen bonds : angle 4.22145 ( 933) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.182 Fit side-chains REVERT: A 269 ILE cc_start: 0.9084 (mt) cc_final: 0.8799 (mt) REVERT: A 306 GLN cc_start: 0.8299 (mp-120) cc_final: 0.7996 (mp10) REVERT: A 356 GLN cc_start: 0.8457 (mt0) cc_final: 0.7968 (mt0) REVERT: A 486 ARG cc_start: 0.5457 (OUTLIER) cc_final: 0.4463 (ptt180) REVERT: A 519 ARG cc_start: 0.4945 (OUTLIER) cc_final: 0.4539 (ptt90) REVERT: A 565 ILE cc_start: 0.7824 (mp) cc_final: 0.7601 (mp) REVERT: B 20 LEU cc_start: 0.8219 (mm) cc_final: 0.8013 (mm) REVERT: B 25 SER cc_start: 0.6820 (t) cc_final: 0.6493 (p) REVERT: B 80 TYR cc_start: 0.7907 (m-80) cc_final: 0.7207 (m-80) outliers start: 16 outliers final: 10 residues processed: 116 average time/residue: 0.0728 time to fit residues: 10.8971 Evaluate side-chains 114 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 486 ARG Chi-restraints excluded: chain A residue 519 ARG Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 577 HIS Chi-restraints excluded: chain B residue 113 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 36 optimal weight: 6.9990 chunk 46 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 ASN A 577 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.164495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.131649 restraints weight = 6741.089| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.49 r_work: 0.3527 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 4937 Z= 0.140 Angle : 0.688 12.140 6746 Z= 0.325 Chirality : 0.043 0.281 810 Planarity : 0.004 0.034 818 Dihedral : 9.299 125.065 875 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.04 % Allowed : 17.98 % Favored : 77.98 % 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: 1.38 (0.34), residues: 625 helix: 1.96 (0.26), residues: 373 sheet: -0.71 (0.72), residues: 56 loop : -0.59 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 38 TYR 0.006 0.001 TYR A 546 PHE 0.010 0.001 PHE A 374 TRP 0.010 0.001 TRP B 33 HIS 0.004 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4935) covalent geometry : angle 0.68504 ( 6742) SS BOND : bond 0.00292 ( 2) SS BOND : angle 2.56745 ( 4) hydrogen bonds : bond 0.03780 ( 324) hydrogen bonds : angle 4.26532 ( 933) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.177 Fit side-chains REVERT: A 269 ILE cc_start: 0.9102 (mt) cc_final: 0.8809 (mt) REVERT: A 306 GLN cc_start: 0.8337 (mp-120) cc_final: 0.8013 (mp10) REVERT: A 356 GLN cc_start: 0.8478 (mt0) cc_final: 0.7985 (mt0) REVERT: A 486 ARG cc_start: 0.5417 (OUTLIER) cc_final: 0.4350 (ptt180) REVERT: A 519 ARG cc_start: 0.4777 (OUTLIER) cc_final: 0.4342 (ptt90) REVERT: A 565 ILE cc_start: 0.7841 (mp) cc_final: 0.7560 (mt) REVERT: B 25 SER cc_start: 0.6800 (t) cc_final: 0.6468 (p) REVERT: B 80 TYR cc_start: 0.7903 (m-80) cc_final: 0.7134 (m-80) outliers start: 20 outliers final: 13 residues processed: 120 average time/residue: 0.0651 time to fit residues: 10.1808 Evaluate side-chains 113 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 399 CYS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 486 ARG Chi-restraints excluded: chain A residue 519 ARG Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 577 HIS Chi-restraints excluded: chain B residue 113 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 577 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.163549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.131103 restraints weight = 6657.778| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.45 r_work: 0.3520 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 4937 Z= 0.152 Angle : 0.688 9.895 6746 Z= 0.329 Chirality : 0.043 0.259 810 Planarity : 0.004 0.034 818 Dihedral : 9.260 125.439 875 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.64 % Allowed : 18.18 % Favored : 78.18 % 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: 1.36 (0.34), residues: 625 helix: 1.98 (0.27), residues: 373 sheet: -0.90 (0.76), residues: 51 loop : -0.63 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 404 TYR 0.007 0.001 TYR A 546 PHE 0.010 0.001 PHE A 374 TRP 0.012 0.001 TRP B 33 HIS 0.005 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 4935) covalent geometry : angle 0.68499 ( 6742) SS BOND : bond 0.01105 ( 2) SS BOND : angle 2.60032 ( 4) hydrogen bonds : bond 0.03809 ( 324) hydrogen bonds : angle 4.29018 ( 933) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.135 Fit side-chains REVERT: A 269 ILE cc_start: 0.9102 (mt) cc_final: 0.8839 (mt) REVERT: A 306 GLN cc_start: 0.8356 (mp-120) cc_final: 0.8034 (mp10) REVERT: A 356 GLN cc_start: 0.8491 (mt0) cc_final: 0.7995 (mt0) REVERT: A 486 ARG cc_start: 0.5315 (OUTLIER) cc_final: 0.4250 (ptt180) REVERT: A 519 ARG cc_start: 0.4691 (OUTLIER) cc_final: 0.4395 (ptt90) REVERT: A 568 MET cc_start: 0.7872 (mtp) cc_final: 0.7631 (mtm) REVERT: B 25 SER cc_start: 0.6877 (t) cc_final: 0.6556 (p) REVERT: B 80 TYR cc_start: 0.7924 (m-80) cc_final: 0.7158 (m-80) outliers start: 18 outliers final: 13 residues processed: 113 average time/residue: 0.0601 time to fit residues: 8.8858 Evaluate side-chains 113 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 399 CYS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 486 ARG Chi-restraints excluded: chain A residue 519 ARG Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 577 HIS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 113 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 3 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 59 optimal weight: 0.0270 chunk 2 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 ASN A 577 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.163841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.131161 restraints weight = 6692.824| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.48 r_work: 0.3523 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 4937 Z= 0.144 Angle : 0.693 9.294 6746 Z= 0.332 Chirality : 0.044 0.369 810 Planarity : 0.004 0.035 818 Dihedral : 9.215 125.317 875 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.64 % Allowed : 18.79 % Favored : 77.58 % 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: 1.37 (0.34), residues: 625 helix: 1.98 (0.26), residues: 373 sheet: -0.68 (0.73), residues: 56 loop : -0.67 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 404 TYR 0.006 0.001 TYR A 546 PHE 0.010 0.001 PHE A 374 TRP 0.011 0.001 TRP B 33 HIS 0.006 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4935) covalent geometry : angle 0.69012 ( 6742) SS BOND : bond 0.00335 ( 2) SS BOND : angle 2.51827 ( 4) hydrogen bonds : bond 0.03803 ( 324) hydrogen bonds : angle 4.33567 ( 933) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.172 Fit side-chains REVERT: A 269 ILE cc_start: 0.9110 (mt) cc_final: 0.8851 (mt) REVERT: A 306 GLN cc_start: 0.8363 (mp-120) cc_final: 0.8037 (mp10) REVERT: A 356 GLN cc_start: 0.8490 (mt0) cc_final: 0.8273 (mt0) REVERT: A 486 ARG cc_start: 0.5314 (OUTLIER) cc_final: 0.4255 (ptt180) REVERT: A 519 ARG cc_start: 0.4700 (OUTLIER) cc_final: 0.4405 (ptt90) REVERT: B 25 SER cc_start: 0.6905 (t) cc_final: 0.6594 (p) REVERT: B 80 TYR cc_start: 0.7873 (m-80) cc_final: 0.6989 (m-80) outliers start: 18 outliers final: 13 residues processed: 116 average time/residue: 0.0656 time to fit residues: 9.9234 Evaluate side-chains 115 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 399 CYS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 486 ARG Chi-restraints excluded: chain A residue 519 ARG Chi-restraints excluded: chain A residue 521 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 577 HIS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 113 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.0370 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.160467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.127210 restraints weight = 6691.910| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.47 r_work: 0.3468 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 4937 Z= 0.199 Angle : 0.726 9.216 6746 Z= 0.352 Chirality : 0.045 0.257 810 Planarity : 0.004 0.036 818 Dihedral : 9.313 124.973 875 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.43 % Allowed : 20.20 % Favored : 76.36 % 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: 1.18 (0.34), residues: 625 helix: 1.83 (0.26), residues: 370 sheet: -0.90 (0.77), residues: 51 loop : -0.68 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 404 TYR 0.010 0.001 TYR A 287 PHE 0.011 0.001 PHE A 374 TRP 0.015 0.001 TRP B 33 HIS 0.002 0.000 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 4935) covalent geometry : angle 0.72292 ( 6742) SS BOND : bond 0.00251 ( 2) SS BOND : angle 2.87821 ( 4) hydrogen bonds : bond 0.04088 ( 324) hydrogen bonds : angle 4.50990 ( 933) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.106 Fit side-chains REVERT: A 306 GLN cc_start: 0.8389 (mp-120) cc_final: 0.8067 (mp10) REVERT: A 356 GLN cc_start: 0.8555 (mt0) cc_final: 0.8044 (mt0) REVERT: A 486 ARG cc_start: 0.5325 (OUTLIER) cc_final: 0.4155 (ptt180) REVERT: A 519 ARG cc_start: 0.4645 (OUTLIER) cc_final: 0.4380 (ptt90) REVERT: B 25 SER cc_start: 0.6983 (t) cc_final: 0.6641 (p) REVERT: B 80 TYR cc_start: 0.7949 (m-80) cc_final: 0.7245 (m-80) outliers start: 17 outliers final: 12 residues processed: 109 average time/residue: 0.0604 time to fit residues: 8.6438 Evaluate side-chains 113 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 486 ARG Chi-restraints excluded: chain A residue 519 ARG Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 577 HIS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 ASN A 577 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.162467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.129429 restraints weight = 6628.139| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.48 r_work: 0.3497 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 4937 Z= 0.155 Angle : 0.726 12.701 6746 Z= 0.347 Chirality : 0.046 0.398 810 Planarity : 0.004 0.036 818 Dihedral : 9.235 124.617 875 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.63 % Allowed : 21.01 % Favored : 76.36 % 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 (0.34), residues: 625 helix: 1.91 (0.27), residues: 370 sheet: -0.91 (0.78), residues: 51 loop : -0.69 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 404 TYR 0.010 0.001 TYR A 96 PHE 0.010 0.001 PHE A 374 TRP 0.012 0.001 TRP B 33 HIS 0.007 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 4935) covalent geometry : angle 0.71988 ( 6742) SS BOND : bond 0.00452 ( 2) SS BOND : angle 3.79698 ( 4) hydrogen bonds : bond 0.03931 ( 324) hydrogen bonds : angle 4.46002 ( 933) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1250 Ramachandran restraints generated. 625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.184 Fit side-chains REVERT: A 269 ILE cc_start: 0.9131 (mt) cc_final: 0.8921 (mt) REVERT: A 306 GLN cc_start: 0.8383 (mp-120) cc_final: 0.8052 (mp10) REVERT: A 486 ARG cc_start: 0.5341 (OUTLIER) cc_final: 0.4271 (ptt180) REVERT: A 568 MET cc_start: 0.7989 (mtp) cc_final: 0.7726 (mtm) REVERT: B 25 SER cc_start: 0.6927 (t) cc_final: 0.6590 (p) REVERT: B 80 TYR cc_start: 0.7926 (m-80) cc_final: 0.7222 (m-80) outliers start: 13 outliers final: 11 residues processed: 113 average time/residue: 0.0644 time to fit residues: 9.5720 Evaluate side-chains 113 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 486 ARG Chi-restraints excluded: chain A residue 521 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 577 HIS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 41 optimal weight: 0.0010 chunk 50 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.162954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.130057 restraints weight = 6584.818| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.46 r_work: 0.3518 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 4937 Z= 0.153 Angle : 0.727 12.656 6746 Z= 0.349 Chirality : 0.045 0.353 810 Planarity : 0.004 0.037 818 Dihedral : 9.096 124.177 871 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.42 % Allowed : 21.21 % Favored : 76.36 % 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 (0.34), residues: 625 helix: 1.91 (0.27), residues: 370 sheet: -1.02 (0.77), residues: 51 loop : -0.69 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 404 TYR 0.007 0.001 TYR A 546 PHE 0.010 0.001 PHE A 374 TRP 0.011 0.001 TRP B 33 HIS 0.005 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 4935) covalent geometry : angle 0.72187 ( 6742) SS BOND : bond 0.00318 ( 2) SS BOND : angle 3.53645 ( 4) hydrogen bonds : bond 0.03841 ( 324) hydrogen bonds : angle 4.43545 ( 933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1211.60 seconds wall clock time: 21 minutes 30.15 seconds (1290.15 seconds total)