Starting phenix.real_space_refine on Thu Jul 2 02:03:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pxj_71971/07_2026/9pxj_71971_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pxj_71971/07_2026/9pxj_71971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pxj_71971/07_2026/9pxj_71971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pxj_71971/07_2026/9pxj_71971.map" model { file = "/net/cci-nas-00/data/ceres_data/9pxj_71971/07_2026/9pxj_71971_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pxj_71971/07_2026/9pxj_71971_neut.cif" } resolution = 3.18 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= 0.026 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 11 5.16 5 C 3445 2.51 5 N 909 2.21 5 O 1068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5433 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3431 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 18, 'TRANS': 422} Chain breaks: 1 Chain: "F" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2002 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 235} Time building chain proxies: 0.91, per 1000 atoms: 0.17 Number of scatterers: 5433 At special positions: 0 Unit cell: (68.68, 84.84, 135.744, 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 11 16.00 O 1068 8.00 N 909 7.00 C 3445 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: 0.25 Conformation dependent library (CDL) restraints added in 123.6 milliseconds 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1250 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 10 sheets defined 7.5% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.941A pdb=" N LEU A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 387 Processing helix chain 'A' and resid 447 through 451 removed outlier: 3.739A pdb=" N GLY A 450 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 555 removed outlier: 3.549A pdb=" N TYR A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 747 through 751 removed outlier: 3.523A pdb=" N ASN A 750 " --> pdb=" O LYS A 747 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 348 through 354 removed outlier: 4.869A pdb=" N VAL A 348 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL A 413 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ARG A 350 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TYR A 415 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASN A 352 " --> pdb=" O TYR A 415 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL A 417 " --> pdb=" O ASN A 352 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ARG A 354 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLU A 419 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN A 414 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N VAL A 399 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER A 416 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL A 397 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.554A pdb=" N ALA A 704 " --> pdb=" O TRP A 725 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 620 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N PHE A 599 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N VAL A 507 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N THR A 493 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL A 482 " --> pdb=" O TRP A 477 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU A 484 " --> pdb=" O PRO A 475 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TYR A 486 " --> pdb=" O VAL A 473 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL A 473 " --> pdb=" O TYR A 486 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALA A 488 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLY A 471 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N TYR A 490 " --> pdb=" O ASN A 469 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ASN A 469 " --> pdb=" O TYR A 490 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS A 492 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG A 467 " --> pdb=" O LYS A 492 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 461 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL A 429 " --> pdb=" O PRO F 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 501 through 502 removed outlier: 6.047A pdb=" N ASP A 501 " --> pdb=" O ILE F 236 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 612 through 613 Processing sheet with id=AA5, first strand: chain 'F' and resid 4 through 5 removed outlier: 6.656A pdb=" N ILE F 102 " --> pdb=" O GLN F 221 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.667A pdb=" N ALA F 56 " --> pdb=" O ILE F 11 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 16 through 18 removed outlier: 3.596A pdb=" N LYS F 25 " --> pdb=" O TYR F 37 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU F 36 " --> pdb=" O ILE F 44 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 107 through 110 removed outlier: 3.561A pdb=" N TRP F 109 " --> pdb=" O LEU F 215 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE F 207 " --> pdb=" O LYS F 124 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS F 124 " --> pdb=" O PHE F 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 136 through 138 removed outlier: 3.971A pdb=" N THR F 136 " --> pdb=" O PHE F 147 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLN F 148 " --> pdb=" O ASN F 152 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASN F 152 " --> pdb=" O GLN F 148 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP F 165 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG F 157 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL F 163 " --> pdb=" O ARG F 157 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 176 through 177 removed outlier: 3.635A pdb=" N VAL F 176 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL F 184 " --> pdb=" O VAL F 176 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TRP F 193 " --> pdb=" O ILE F 185 " (cutoff:3.500A) 195 hydrogen bonds defined for protein. 513 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: 0.93 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 976 1.32 - 1.44: 1535 1.44 - 1.57: 3035 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 5566 Sorted by residual: bond pdb=" CA LEU F 215 " pdb=" C LEU F 215 " ideal model delta sigma weight residual 1.521 1.472 0.049 1.19e-02 7.06e+03 1.72e+01 bond pdb=" CA SER A 422 " pdb=" CB SER A 422 " ideal model delta sigma weight residual 1.537 1.479 0.058 1.67e-02 3.59e+03 1.20e+01 bond pdb=" C GLN F 217 " pdb=" O GLN F 217 " ideal model delta sigma weight residual 1.249 1.221 0.028 8.50e-03 1.38e+04 1.06e+01 bond pdb=" C LEU F 215 " pdb=" O LEU F 215 " ideal model delta sigma weight residual 1.236 1.202 0.033 1.20e-02 6.94e+03 7.73e+00 bond pdb=" CA HIS F 253 " pdb=" CB HIS F 253 " ideal model delta sigma weight residual 1.534 1.500 0.034 1.34e-02 5.57e+03 6.47e+00 ... (remaining 5561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 7280 1.73 - 3.45: 243 3.45 - 5.18: 44 5.18 - 6.90: 7 6.90 - 8.63: 3 Bond angle restraints: 7577 Sorted by residual: angle pdb=" C THR A 401 " pdb=" N PRO A 402 " pdb=" CA PRO A 402 " ideal model delta sigma weight residual 120.89 115.35 5.54 1.21e+00 6.83e-01 2.09e+01 angle pdb=" N MET F 58 " pdb=" CA MET F 58 " pdb=" C MET F 58 " ideal model delta sigma weight residual 107.62 116.25 -8.63 1.97e+00 2.58e-01 1.92e+01 angle pdb=" N VAL F 164 " pdb=" CA VAL F 164 " pdb=" C VAL F 164 " ideal model delta sigma weight residual 112.96 108.98 3.98 1.00e+00 1.00e+00 1.58e+01 angle pdb=" C HIS F 253 " pdb=" CA HIS F 253 " pdb=" CB HIS F 253 " ideal model delta sigma weight residual 113.02 105.14 7.88 2.29e+00 1.91e-01 1.18e+01 angle pdb=" O THR A 357 " pdb=" C THR A 357 " pdb=" N LYS A 358 " ideal model delta sigma weight residual 123.27 119.62 3.65 1.16e+00 7.43e-01 9.92e+00 ... (remaining 7572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 2964 17.97 - 35.93: 234 35.93 - 53.90: 36 53.90 - 71.87: 13 71.87 - 89.83: 4 Dihedral angle restraints: 3251 sinusoidal: 1272 harmonic: 1979 Sorted by residual: dihedral pdb=" CA ASP A 538 " pdb=" CB ASP A 538 " pdb=" CG ASP A 538 " pdb=" OD1 ASP A 538 " ideal model delta sinusoidal sigma weight residual -30.00 -89.27 59.27 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ALA A 610 " pdb=" C ALA A 610 " pdb=" N PRO A 611 " pdb=" CA PRO A 611 " ideal model delta harmonic sigma weight residual -180.00 -163.54 -16.46 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CB GLU A 783 " pdb=" CG GLU A 783 " pdb=" CD GLU A 783 " pdb=" OE1 GLU A 783 " ideal model delta sinusoidal sigma weight residual 0.00 89.54 -89.54 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 3248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 532 0.035 - 0.071: 188 0.071 - 0.106: 77 0.106 - 0.142: 21 0.142 - 0.177: 3 Chirality restraints: 821 Sorted by residual: chirality pdb=" CA ILE A 602 " pdb=" N ILE A 602 " pdb=" C ILE A 602 " pdb=" CB ILE A 602 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CA VAL A 727 " pdb=" N VAL A 727 " pdb=" C VAL A 727 " pdb=" CB VAL A 727 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA ILE F 236 " pdb=" N ILE F 236 " pdb=" C ILE F 236 " pdb=" CB ILE F 236 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 818 not shown) Planarity restraints: 995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP F 251 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO F 252 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO F 252 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 252 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR F 223 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.11e+00 pdb=" C THR F 223 " -0.025 2.00e-02 2.50e+03 pdb=" O THR F 223 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU F 224 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER F 19 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO F 20 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO F 20 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 20 " 0.020 5.00e-02 4.00e+02 ... (remaining 992 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 992 2.77 - 3.30: 5163 3.30 - 3.83: 8824 3.83 - 4.37: 10457 4.37 - 4.90: 18105 Nonbonded interactions: 43541 Sorted by model distance: nonbonded pdb=" OD1 ASN F 63 " pdb=" OG SER F 74 " model vdw 2.237 3.040 nonbonded pdb=" OG SER A 428 " pdb=" O THR F 246 " model vdw 2.304 3.040 nonbonded pdb=" O PHE A 448 " pdb=" OG1 THR A 451 " model vdw 2.354 3.040 nonbonded pdb=" OG SER A 598 " pdb=" O TYR A 630 " model vdw 2.363 3.040 nonbonded pdb=" OG1 THR A 493 " pdb=" OD1 ASN A 508 " model vdw 2.364 3.040 ... (remaining 43536 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: 2.700 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.330 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 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 : 0.004 0.058 5566 Z= 0.240 Angle : 0.742 8.628 7577 Z= 0.418 Chirality : 0.044 0.177 821 Planarity : 0.004 0.047 995 Dihedral : 13.899 89.833 2001 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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: -1.92 (0.30), residues: 690 helix: -0.85 (0.84), residues: 34 sheet: -0.79 (0.31), residues: 258 loop : -1.67 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 78 TYR 0.012 0.001 TYR A 495 PHE 0.024 0.001 PHE A 558 TRP 0.005 0.001 TRP F 165 HIS 0.005 0.001 HIS F 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.24 ( 5566) covalent geometry : angle 0.74219 / 0.42 ( 7577) hydrogen bonds : bond 0.16015 / 11.07 ( 195) hydrogen bonds : angle 7.93428 / 5.55 ( 513) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 383 GLN cc_start: 0.8462 (mp10) cc_final: 0.8063 (mp10) REVERT: A 505 TYR cc_start: 0.8910 (p90) cc_final: 0.8684 (p90) REVERT: A 781 ASN cc_start: 0.8081 (t0) cc_final: 0.7696 (t0) REVERT: F 115 SER cc_start: 0.9008 (m) cc_final: 0.8744 (p) REVERT: F 196 ARG cc_start: 0.9016 (mpt180) cc_final: 0.8737 (mpt180) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.0993 time to fit residues: 10.3932 Evaluate side-chains 57 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 557 ASN F 106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.083887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.067825 restraints weight = 16086.412| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 4.14 r_work: 0.3112 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5566 Z= 0.167 Angle : 0.640 5.965 7577 Z= 0.331 Chirality : 0.044 0.168 821 Planarity : 0.005 0.062 995 Dihedral : 4.982 53.864 763 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.02 % Allowed : 10.92 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.31), residues: 690 helix: -0.13 (0.90), residues: 34 sheet: -0.63 (0.32), residues: 261 loop : -1.55 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 605 TYR 0.019 0.001 TYR A 495 PHE 0.028 0.002 PHE A 609 TRP 0.007 0.001 TRP A 477 HIS 0.006 0.001 HIS F 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 ( 5566) covalent geometry : angle 0.63954 / 0.33 ( 7577) hydrogen bonds : bond 0.03715 / 2.60 ( 195) hydrogen bonds : angle 6.48684 / 4.60 ( 513) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 383 GLN cc_start: 0.8536 (mp10) cc_final: 0.8102 (mp10) REVERT: A 505 TYR cc_start: 0.9137 (p90) cc_final: 0.8871 (p90) REVERT: A 609 PHE cc_start: 0.8589 (t80) cc_final: 0.8338 (t80) REVERT: A 781 ASN cc_start: 0.8194 (t0) cc_final: 0.7800 (t0) REVERT: F 116 GLU cc_start: 0.8474 (pm20) cc_final: 0.8213 (pm20) outliers start: 6 outliers final: 5 residues processed: 64 average time/residue: 0.1046 time to fit residues: 8.3399 Evaluate side-chains 59 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 760 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 349 ASN A 352 ASN ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.084834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.068619 restraints weight = 15776.562| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 4.11 r_work: 0.3124 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5566 Z= 0.118 Angle : 0.612 7.218 7577 Z= 0.313 Chirality : 0.043 0.158 821 Planarity : 0.004 0.057 995 Dihedral : 4.775 45.915 763 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.88 % Allowed : 13.14 % Favored : 84.98 % 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: -1.46 (0.31), residues: 690 helix: -0.03 (0.90), residues: 34 sheet: -0.40 (0.32), residues: 261 loop : -1.47 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 605 TYR 0.018 0.001 TYR A 495 PHE 0.014 0.001 PHE A 609 TRP 0.004 0.001 TRP A 375 HIS 0.002 0.001 HIS F 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 5566) covalent geometry : angle 0.61175 / 0.31 ( 7577) hydrogen bonds : bond 0.03195 / 2.23 ( 195) hydrogen bonds : angle 6.14705 / 4.39 ( 513) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.205 Fit side-chains REVERT: A 383 GLN cc_start: 0.8480 (mp10) cc_final: 0.7999 (mp10) REVERT: A 505 TYR cc_start: 0.9156 (p90) cc_final: 0.8920 (p90) REVERT: A 609 PHE cc_start: 0.8426 (t80) cc_final: 0.8178 (t80) REVERT: A 781 ASN cc_start: 0.8255 (t0) cc_final: 0.7850 (t0) REVERT: F 116 GLU cc_start: 0.8471 (pm20) cc_final: 0.8219 (pm20) outliers start: 11 outliers final: 6 residues processed: 69 average time/residue: 0.0941 time to fit residues: 8.1205 Evaluate side-chains 63 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 768 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 0.0470 chunk 23 optimal weight: 0.6980 chunk 44 optimal weight: 0.0000 chunk 35 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 63 optimal weight: 0.0980 chunk 19 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.086291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.069988 restraints weight = 15793.955| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 4.17 r_work: 0.3155 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5566 Z= 0.099 Angle : 0.587 6.707 7577 Z= 0.300 Chirality : 0.043 0.155 821 Planarity : 0.004 0.052 995 Dihedral : 4.549 36.061 763 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.54 % Allowed : 13.99 % Favored : 84.47 % 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 (0.32), residues: 690 helix: -0.00 (0.90), residues: 34 sheet: -0.23 (0.33), residues: 261 loop : -1.38 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 350 TYR 0.017 0.001 TYR A 495 PHE 0.009 0.001 PHE A 609 TRP 0.005 0.001 TRP F 165 HIS 0.001 0.000 HIS F 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 5566) covalent geometry : angle 0.58674 / 0.30 ( 7577) hydrogen bonds : bond 0.02800 / 1.95 ( 195) hydrogen bonds : angle 5.86001 / 4.22 ( 513) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 383 GLN cc_start: 0.8517 (mp10) cc_final: 0.8111 (mp10) REVERT: A 484 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8442 (mt) REVERT: A 505 TYR cc_start: 0.9129 (p90) cc_final: 0.8890 (p90) REVERT: A 609 PHE cc_start: 0.8122 (t80) cc_final: 0.7845 (t80) REVERT: A 623 GLU cc_start: 0.8462 (tt0) cc_final: 0.8030 (mp0) REVERT: A 781 ASN cc_start: 0.8265 (t0) cc_final: 0.7860 (t0) REVERT: F 114 LEU cc_start: 0.7873 (tp) cc_final: 0.7586 (tp) REVERT: F 116 GLU cc_start: 0.8494 (pm20) cc_final: 0.8172 (pm20) outliers start: 9 outliers final: 6 residues processed: 67 average time/residue: 0.0806 time to fit residues: 7.0599 Evaluate side-chains 66 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 768 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 0 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.082858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.066545 restraints weight = 16284.685| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 4.21 r_work: 0.3082 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 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 : 0.004 0.037 5566 Z= 0.184 Angle : 0.612 6.346 7577 Z= 0.316 Chirality : 0.044 0.163 821 Planarity : 0.004 0.051 995 Dihedral : 4.648 26.800 763 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.05 % Allowed : 14.51 % Favored : 83.45 % 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 (0.32), residues: 690 helix: -0.18 (0.90), residues: 34 sheet: -0.30 (0.33), residues: 266 loop : -1.43 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 350 TYR 0.011 0.001 TYR A 486 PHE 0.018 0.001 PHE A 770 TRP 0.006 0.001 TRP A 375 HIS 0.002 0.001 HIS F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 5566) covalent geometry : angle 0.61201 / 0.32 ( 7577) hydrogen bonds : bond 0.03108 / 2.15 ( 195) hydrogen bonds : angle 5.83206 / 4.20 ( 513) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.203 Fit side-chains REVERT: A 383 GLN cc_start: 0.8484 (mp10) cc_final: 0.8021 (mp10) REVERT: A 505 TYR cc_start: 0.9175 (p90) cc_final: 0.8919 (p90) REVERT: A 609 PHE cc_start: 0.8333 (t80) cc_final: 0.8104 (t80) REVERT: A 781 ASN cc_start: 0.8476 (t0) cc_final: 0.8126 (t0) REVERT: F 196 ARG cc_start: 0.8983 (mpt180) cc_final: 0.8759 (mpt180) outliers start: 12 outliers final: 12 residues processed: 71 average time/residue: 0.0843 time to fit residues: 7.6384 Evaluate side-chains 72 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 768 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.084288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.068031 restraints weight = 15832.705| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 4.15 r_work: 0.3113 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5566 Z= 0.119 Angle : 0.603 7.355 7577 Z= 0.308 Chirality : 0.043 0.157 821 Planarity : 0.004 0.049 995 Dihedral : 4.570 21.480 763 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.39 % Allowed : 15.19 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.32), residues: 690 helix: -0.11 (0.92), residues: 34 sheet: -0.26 (0.33), residues: 266 loop : -1.41 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 144 TYR 0.012 0.001 TYR A 486 PHE 0.007 0.001 PHE A 472 TRP 0.004 0.001 TRP F 249 HIS 0.001 0.001 HIS F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 5566) covalent geometry : angle 0.60311 / 0.31 ( 7577) hydrogen bonds : bond 0.02841 / 1.96 ( 195) hydrogen bonds : angle 5.74395 / 4.15 ( 513) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 383 GLN cc_start: 0.8459 (mp10) cc_final: 0.8006 (mp10) REVERT: A 484 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8634 (mt) REVERT: A 505 TYR cc_start: 0.9121 (p90) cc_final: 0.8880 (p90) REVERT: A 603 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.8060 (p0) REVERT: A 609 PHE cc_start: 0.8136 (t80) cc_final: 0.7881 (t80) REVERT: A 781 ASN cc_start: 0.8416 (t0) cc_final: 0.8051 (t0) REVERT: F 196 ARG cc_start: 0.9024 (mpt180) cc_final: 0.8786 (mpt180) outliers start: 14 outliers final: 9 residues processed: 73 average time/residue: 0.0857 time to fit residues: 8.0314 Evaluate side-chains 70 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 768 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.0060 chunk 24 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.085029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.068655 restraints weight = 15938.334| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 4.17 r_work: 0.3130 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5566 Z= 0.108 Angle : 0.601 7.569 7577 Z= 0.305 Chirality : 0.043 0.160 821 Planarity : 0.004 0.046 995 Dihedral : 4.424 16.784 763 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.05 % Allowed : 15.87 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.32), residues: 690 helix: -0.11 (0.91), residues: 34 sheet: -0.25 (0.33), residues: 266 loop : -1.41 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 78 TYR 0.013 0.001 TYR A 495 PHE 0.021 0.001 PHE A 789 TRP 0.004 0.001 TRP F 249 HIS 0.001 0.000 HIS F 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 5566) covalent geometry : angle 0.60103 / 0.31 ( 7577) hydrogen bonds : bond 0.02708 / 1.86 ( 195) hydrogen bonds : angle 5.62431 / 4.07 ( 513) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.226 Fit side-chains REVERT: A 383 GLN cc_start: 0.8478 (mp10) cc_final: 0.8036 (mp10) REVERT: A 505 TYR cc_start: 0.9092 (p90) cc_final: 0.8845 (p90) REVERT: A 603 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.8018 (p0) REVERT: A 609 PHE cc_start: 0.8067 (t80) cc_final: 0.7860 (t80) REVERT: A 623 GLU cc_start: 0.8462 (tt0) cc_final: 0.8009 (mp0) REVERT: A 781 ASN cc_start: 0.8443 (t0) cc_final: 0.8098 (t0) REVERT: F 114 LEU cc_start: 0.7811 (tp) cc_final: 0.7507 (tp) REVERT: F 116 GLU cc_start: 0.8391 (pm20) cc_final: 0.8158 (pm20) REVERT: F 196 ARG cc_start: 0.9028 (mpt180) cc_final: 0.8796 (mpt180) outliers start: 12 outliers final: 9 residues processed: 73 average time/residue: 0.0841 time to fit residues: 8.0548 Evaluate side-chains 71 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 768 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN F 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.082287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.066069 restraints weight = 16084.811| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 4.13 r_work: 0.3070 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5566 Z= 0.206 Angle : 0.641 7.388 7577 Z= 0.330 Chirality : 0.044 0.160 821 Planarity : 0.004 0.047 995 Dihedral : 4.684 17.306 763 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.22 % Allowed : 16.72 % Favored : 81.06 % 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: -1.43 (0.31), residues: 690 helix: -0.22 (0.92), residues: 35 sheet: -0.37 (0.32), residues: 266 loop : -1.46 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 78 TYR 0.018 0.001 TYR A 486 PHE 0.009 0.001 PHE F 60 TRP 0.006 0.001 TRP A 375 HIS 0.002 0.001 HIS F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 ( 5566) covalent geometry : angle 0.64115 / 0.33 ( 7577) hydrogen bonds : bond 0.03021 / 2.06 ( 195) hydrogen bonds : angle 5.76588 / 4.17 ( 513) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 358 LYS cc_start: 0.8410 (tptp) cc_final: 0.7973 (tptp) REVERT: A 383 GLN cc_start: 0.8410 (mp10) cc_final: 0.7941 (mp10) REVERT: A 505 TYR cc_start: 0.9193 (p90) cc_final: 0.8930 (p90) REVERT: A 609 PHE cc_start: 0.8290 (t80) cc_final: 0.7957 (t80) REVERT: A 760 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8111 (p) REVERT: A 781 ASN cc_start: 0.8550 (t0) cc_final: 0.8208 (t0) REVERT: A 789 PHE cc_start: 0.8483 (p90) cc_final: 0.8270 (p90) REVERT: F 196 ARG cc_start: 0.9020 (mpt180) cc_final: 0.8757 (mpt180) outliers start: 13 outliers final: 10 residues processed: 69 average time/residue: 0.0869 time to fit residues: 7.7240 Evaluate side-chains 68 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 688 ASP Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 768 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 10 optimal weight: 0.0000 chunk 67 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN F 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.084313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.067973 restraints weight = 15790.617| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 4.17 r_work: 0.3107 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5566 Z= 0.121 Angle : 0.625 7.742 7577 Z= 0.319 Chirality : 0.043 0.158 821 Planarity : 0.004 0.047 995 Dihedral : 4.541 16.907 763 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.71 % Allowed : 17.92 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.32), residues: 690 helix: -0.28 (0.90), residues: 35 sheet: -0.32 (0.32), residues: 266 loop : -1.40 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 78 TYR 0.016 0.001 TYR A 486 PHE 0.007 0.001 PHE A 472 TRP 0.005 0.001 TRP A 477 HIS 0.001 0.001 HIS F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 5566) covalent geometry : angle 0.62490 / 0.32 ( 7577) hydrogen bonds : bond 0.02779 / 1.91 ( 195) hydrogen bonds : angle 5.67552 / 4.08 ( 513) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 358 LYS cc_start: 0.8386 (tptp) cc_final: 0.7859 (tptp) REVERT: A 383 GLN cc_start: 0.8441 (mp10) cc_final: 0.7985 (mp10) REVERT: A 484 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.7502 (pp) REVERT: A 505 TYR cc_start: 0.9148 (p90) cc_final: 0.8908 (p90) REVERT: A 603 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.8066 (p0) REVERT: A 605 ARG cc_start: 0.8671 (mtp85) cc_final: 0.8364 (mtp85) REVERT: A 609 PHE cc_start: 0.8045 (t80) cc_final: 0.7807 (t80) REVERT: A 781 ASN cc_start: 0.8465 (t0) cc_final: 0.8117 (t0) outliers start: 10 outliers final: 8 residues processed: 68 average time/residue: 0.0881 time to fit residues: 7.6088 Evaluate side-chains 69 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 768 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.5980 chunk 1 optimal weight: 0.1980 chunk 63 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.084675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.068326 restraints weight = 15850.503| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 4.19 r_work: 0.3123 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5566 Z= 0.115 Angle : 0.621 8.050 7577 Z= 0.315 Chirality : 0.043 0.156 821 Planarity : 0.004 0.047 995 Dihedral : 4.484 18.312 763 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.71 % Allowed : 17.75 % Favored : 80.55 % 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: -1.30 (0.32), residues: 690 helix: -0.27 (0.90), residues: 35 sheet: -0.26 (0.32), residues: 266 loop : -1.37 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 78 TYR 0.015 0.001 TYR A 486 PHE 0.020 0.001 PHE A 789 TRP 0.005 0.001 TRP F 249 HIS 0.001 0.000 HIS F 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 5566) covalent geometry : angle 0.62063 / 0.32 ( 7577) hydrogen bonds : bond 0.02725 / 1.88 ( 195) hydrogen bonds : angle 5.53119 / 3.98 ( 513) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 358 LYS cc_start: 0.8378 (tptp) cc_final: 0.7905 (tptp) REVERT: A 383 GLN cc_start: 0.8471 (mp10) cc_final: 0.8026 (mp10) REVERT: A 484 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.7449 (pp) REVERT: A 505 TYR cc_start: 0.9107 (p90) cc_final: 0.8852 (p90) REVERT: A 580 ARG cc_start: 0.8644 (mmm-85) cc_final: 0.8432 (mmm-85) REVERT: A 609 PHE cc_start: 0.8041 (t80) cc_final: 0.7808 (t80) REVERT: A 781 ASN cc_start: 0.8464 (t0) cc_final: 0.8119 (t0) outliers start: 10 outliers final: 8 residues processed: 69 average time/residue: 0.0907 time to fit residues: 8.2087 Evaluate side-chains 69 residues out of total 586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 768 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 1 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 0.0870 chunk 36 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.083545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.067291 restraints weight = 15997.217| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 4.14 r_work: 0.3097 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5566 Z= 0.150 Angle : 0.635 7.776 7577 Z= 0.324 Chirality : 0.043 0.157 821 Planarity : 0.004 0.046 995 Dihedral : 4.556 16.861 763 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.88 % Allowed : 18.09 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.32), residues: 690 helix: -0.21 (0.91), residues: 35 sheet: -0.45 (0.31), residues: 278 loop : -1.40 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 78 TYR 0.017 0.001 TYR A 486 PHE 0.007 0.001 PHE A 472 TRP 0.005 0.001 TRP A 477 HIS 0.001 0.001 HIS F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 5566) covalent geometry : angle 0.63489 / 0.32 ( 7577) hydrogen bonds : bond 0.02826 / 1.94 ( 195) hydrogen bonds : angle 5.58304 / 4.02 ( 513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1306.85 seconds wall clock time: 23 minutes 17.58 seconds (1397.58 seconds total)