Starting phenix.real_space_refine on Wed Sep 17 06:10:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ug8_42217/09_2025/8ug8_42217.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ug8_42217/09_2025/8ug8_42217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ug8_42217/09_2025/8ug8_42217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ug8_42217/09_2025/8ug8_42217.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ug8_42217/09_2025/8ug8_42217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ug8_42217/09_2025/8ug8_42217.map" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 42 5.16 5 C 3936 2.51 5 N 956 2.21 5 O 982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5916 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2958 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 9, 'TRANS': 365} Chain breaks: 9 Restraints were copied for chains: B Time building chain proxies: 1.93, per 1000 atoms: 0.33 Number of scatterers: 5916 At special positions: 0 Unit cell: (80.51, 87.15, 68.89, 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 42 16.00 O 982 8.00 N 956 7.00 C 3936 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: 0.53 Conformation dependent library (CDL) restraints added in 210.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 84.0% alpha, 0.0% 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 27 through 48 removed outlier: 3.742A pdb=" N VAL A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 48 " --> pdb=" O CYS A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 59 through 59 No H-bonds generated for 'chain 'A' and resid 59 through 59' Processing helix chain 'A' and resid 60 through 84 removed outlier: 4.024A pdb=" N ALA A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 82 " --> pdb=" O VAL A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 128 removed outlier: 3.846A pdb=" N ARG A 104 " --> pdb=" O PRO A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 158 Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 165 through 193 Processing helix chain 'A' and resid 246 through 265 removed outlier: 3.728A pdb=" N GLU A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 311 removed outlier: 3.825A pdb=" N VAL A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 351 Processing helix chain 'A' and resid 367 through 395 removed outlier: 3.742A pdb=" N LEU A 378 " --> pdb=" O MET A 374 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLY A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLN A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 427 removed outlier: 4.117A pdb=" N ALA A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 514 removed outlier: 3.617A pdb=" N LYS A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N MET A 511 " --> pdb=" O ILE A 507 " (cutoff:3.500A) Proline residue: A 512 - end of helix Processing helix chain 'A' and resid 534 through 562 Proline residue: A 543 - end of helix removed outlier: 3.519A pdb=" N LEU A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 48 removed outlier: 3.741A pdb=" N VAL B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 48 " --> pdb=" O CYS B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 59 through 59 No H-bonds generated for 'chain 'B' and resid 59 through 59' Processing helix chain 'B' and resid 60 through 84 removed outlier: 4.025A pdb=" N ALA B 64 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 82 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 128 removed outlier: 3.846A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 158 Proline residue: B 140 - end of helix Processing helix chain 'B' and resid 165 through 193 Processing helix chain 'B' and resid 246 through 265 removed outlier: 3.728A pdb=" N GLU B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN B 265 " --> pdb=" O VAL B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 311 removed outlier: 3.825A pdb=" N VAL B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 308 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 351 Processing helix chain 'B' and resid 367 through 395 removed outlier: 3.741A pdb=" N LEU B 378 " --> pdb=" O MET B 374 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY B 379 " --> pdb=" O GLY B 375 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 427 removed outlier: 4.117A pdb=" N ALA B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 514 removed outlier: 3.617A pdb=" N LYS B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 497 " --> pdb=" O CYS B 493 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N MET B 511 " --> pdb=" O ILE B 507 " (cutoff:3.500A) Proline residue: B 512 - end of helix Processing helix chain 'B' and resid 534 through 562 Proline residue: B 543 - end of helix removed outlier: 3.519A pdb=" N LEU B 562 " --> pdb=" O GLU B 558 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1392 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: 1.07 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1770 1.34 - 1.46: 1560 1.46 - 1.58: 2656 1.58 - 1.70: 0 1.70 - 1.81: 66 Bond restraints: 6052 Sorted by residual: bond pdb=" N SER A 157 " pdb=" CA SER A 157 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.22e-02 6.72e+03 8.02e+00 bond pdb=" N SER B 157 " pdb=" CA SER B 157 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.22e-02 6.72e+03 7.58e+00 bond pdb=" N CYS B 131 " pdb=" CA CYS B 131 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.22e-02 6.72e+03 7.23e+00 bond pdb=" N CYS A 131 " pdb=" CA CYS A 131 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.22e-02 6.72e+03 7.06e+00 bond pdb=" N ILE B 135 " pdb=" CA ILE B 135 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.24e-02 6.50e+03 6.85e+00 ... (remaining 6047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 8002 1.44 - 2.88: 184 2.88 - 4.31: 28 4.31 - 5.75: 8 5.75 - 7.19: 2 Bond angle restraints: 8224 Sorted by residual: angle pdb=" CA CYS B 131 " pdb=" C CYS B 131 " pdb=" O CYS B 131 " ideal model delta sigma weight residual 121.16 118.00 3.16 1.12e+00 7.97e-01 7.95e+00 angle pdb=" CA CYS A 131 " pdb=" C CYS A 131 " pdb=" O CYS A 131 " ideal model delta sigma weight residual 121.16 118.03 3.13 1.12e+00 7.97e-01 7.81e+00 angle pdb=" N ALA A 134 " pdb=" CA ALA A 134 " pdb=" C ALA A 134 " ideal model delta sigma weight residual 113.12 109.80 3.32 1.25e+00 6.40e-01 7.08e+00 angle pdb=" N ALA B 134 " pdb=" CA ALA B 134 " pdb=" C ALA B 134 " ideal model delta sigma weight residual 113.12 109.80 3.32 1.25e+00 6.40e-01 7.05e+00 angle pdb=" O ILE B 135 " pdb=" C ILE B 135 " pdb=" N LYS B 136 " ideal model delta sigma weight residual 121.90 124.56 -2.66 1.01e+00 9.80e-01 6.92e+00 ... (remaining 8219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 2958 17.15 - 34.30: 358 34.30 - 51.45: 108 51.45 - 68.60: 24 68.60 - 85.75: 8 Dihedral angle restraints: 3456 sinusoidal: 1286 harmonic: 2170 Sorted by residual: dihedral pdb=" CA ILE B 540 " pdb=" C ILE B 540 " pdb=" N CYS B 541 " pdb=" CA CYS B 541 " ideal model delta harmonic sigma weight residual 180.00 -164.24 -15.76 0 5.00e+00 4.00e-02 9.93e+00 dihedral pdb=" CA ILE A 540 " pdb=" C ILE A 540 " pdb=" N CYS A 541 " pdb=" CA CYS A 541 " ideal model delta harmonic sigma weight residual -180.00 -164.25 -15.75 0 5.00e+00 4.00e-02 9.92e+00 dihedral pdb=" CB GLU A 250 " pdb=" CG GLU A 250 " pdb=" CD GLU A 250 " pdb=" OE1 GLU A 250 " ideal model delta sinusoidal sigma weight residual 0.00 -84.77 84.77 1 3.00e+01 1.11e-03 9.70e+00 ... (remaining 3453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 750 0.037 - 0.073: 197 0.073 - 0.110: 33 0.110 - 0.147: 6 0.147 - 0.184: 2 Chirality restraints: 988 Sorted by residual: chirality pdb=" CA ILE B 135 " pdb=" N ILE B 135 " pdb=" C ILE B 135 " pdb=" CB ILE B 135 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA ILE A 135 " pdb=" N ILE A 135 " pdb=" C ILE A 135 " pdb=" CB ILE A 135 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.38e-01 chirality pdb=" CA PHE A 128 " pdb=" N PHE A 128 " pdb=" C PHE A 128 " pdb=" CB PHE A 128 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 985 not shown) Planarity restraints: 980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 127 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C SER A 127 " -0.030 2.00e-02 2.50e+03 pdb=" O SER A 127 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE A 128 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 127 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.01e+00 pdb=" C SER B 127 " 0.030 2.00e-02 2.50e+03 pdb=" O SER B 127 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE B 128 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 139 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.40e+00 pdb=" N PRO A 140 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 140 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 140 " -0.022 5.00e-02 4.00e+02 ... (remaining 977 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1465 2.79 - 3.31: 6363 3.31 - 3.84: 10154 3.84 - 4.37: 11961 4.37 - 4.90: 19905 Nonbonded interactions: 49848 Sorted by model distance: nonbonded pdb=" OH TYR A 330 " pdb=" OD1 ASN A 404 " model vdw 2.257 3.040 nonbonded pdb=" OH TYR B 330 " pdb=" OD1 ASN B 404 " model vdw 2.257 3.040 nonbonded pdb=" O VAL B 188 " pdb=" OG SER B 192 " model vdw 2.272 3.040 nonbonded pdb=" O VAL A 188 " pdb=" OG SER A 192 " model vdw 2.272 3.040 nonbonded pdb=" O VAL B 147 " pdb=" OG1 THR B 151 " model vdw 2.289 3.040 ... (remaining 49843 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.690 Find NCS groups from input model: 0.050 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 : 0.003 0.035 6052 Z= 0.205 Angle : 0.527 7.190 8224 Z= 0.325 Chirality : 0.035 0.184 988 Planarity : 0.003 0.039 980 Dihedral : 17.040 85.753 2052 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 24.92 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.32), residues: 710 helix: 1.64 (0.22), residues: 576 sheet: None (None), residues: 0 loop : -0.34 (0.58), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 397 TYR 0.013 0.001 TYR A 124 PHE 0.009 0.001 PHE B 153 TRP 0.012 0.001 TRP A 509 HIS 0.003 0.001 HIS B 415 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6052) covalent geometry : angle 0.52735 ( 8224) hydrogen bonds : bond 0.21364 ( 468) hydrogen bonds : angle 6.39598 ( 1392) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASN cc_start: 0.8477 (m110) cc_final: 0.8240 (m110) REVERT: A 400 GLN cc_start: 0.7448 (tp40) cc_final: 0.7111 (tp40) REVERT: A 414 GLN cc_start: 0.7631 (pp30) cc_final: 0.7378 (pp30) REVERT: A 493 CYS cc_start: 0.7494 (m) cc_final: 0.7133 (t) REVERT: A 558 GLU cc_start: 0.8262 (tm-30) cc_final: 0.8051 (tm-30) REVERT: B 399 LEU cc_start: 0.7416 (tp) cc_final: 0.7205 (tp) REVERT: B 558 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7944 (tm-30) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.0614 time to fit residues: 19.1091 Evaluate side-chains 168 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 180 ASN A 414 GLN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN B 150 GLN B 180 ASN B 414 GLN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.118206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.098330 restraints weight = 15490.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.100468 restraints weight = 9984.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.102242 restraints weight = 7688.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.103269 restraints weight = 6245.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.104379 restraints weight = 5517.461| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6052 Z= 0.166 Angle : 0.629 9.920 8224 Z= 0.326 Chirality : 0.038 0.120 988 Planarity : 0.005 0.049 980 Dihedral : 3.393 12.812 796 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.94 % Allowed : 27.29 % Favored : 68.77 % 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 aren not related in a simple way. whole: 1.93 (0.31), residues: 710 helix: 1.60 (0.20), residues: 606 sheet: None (None), residues: 0 loop : -0.39 (0.62), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 366 TYR 0.017 0.001 TYR A 548 PHE 0.023 0.002 PHE B 79 TRP 0.011 0.001 TRP B 76 HIS 0.004 0.001 HIS B 415 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6052) covalent geometry : angle 0.62886 ( 8224) hydrogen bonds : bond 0.05617 ( 468) hydrogen bonds : angle 4.14347 ( 1392) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 PRO cc_start: 0.6829 (Cg_exo) cc_final: 0.6411 (Cg_endo) REVERT: A 397 ARG cc_start: 0.5137 (mmt-90) cc_final: 0.3776 (mtt90) REVERT: A 400 GLN cc_start: 0.7421 (tp40) cc_final: 0.7063 (tp40) REVERT: A 493 CYS cc_start: 0.7380 (m) cc_final: 0.7007 (t) REVERT: A 558 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8232 (tm-30) REVERT: A 560 TYR cc_start: 0.8061 (t80) cc_final: 0.7572 (t80) REVERT: B 396 PRO cc_start: 0.6772 (Cg_exo) cc_final: 0.6388 (Cg_endo) REVERT: B 397 ARG cc_start: 0.5285 (mmt-90) cc_final: 0.3949 (mtt90) REVERT: B 400 GLN cc_start: 0.7456 (tp40) cc_final: 0.7139 (tp40) REVERT: B 493 CYS cc_start: 0.7309 (m) cc_final: 0.6926 (t) REVERT: B 558 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8141 (tm-30) REVERT: B 560 TYR cc_start: 0.8086 (t80) cc_final: 0.7684 (t80) outliers start: 25 outliers final: 14 residues processed: 215 average time/residue: 0.0583 time to fit residues: 17.7588 Evaluate side-chains 188 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 124 TYR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 414 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 31 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 6 optimal weight: 0.0770 chunk 49 optimal weight: 5.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN B 418 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.116247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.096666 restraints weight = 15589.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.098953 restraints weight = 9839.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.100124 restraints weight = 7398.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.101630 restraints weight = 6264.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.102295 restraints weight = 5386.183| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6052 Z= 0.184 Angle : 0.667 14.162 8224 Z= 0.333 Chirality : 0.039 0.113 988 Planarity : 0.004 0.039 980 Dihedral : 3.500 13.666 796 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 5.36 % Allowed : 27.29 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.31), residues: 710 helix: 1.48 (0.20), residues: 596 sheet: None (None), residues: 0 loop : -0.35 (0.62), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 366 TYR 0.015 0.002 TYR A 548 PHE 0.017 0.002 PHE A 153 TRP 0.013 0.001 TRP B 76 HIS 0.003 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 6052) covalent geometry : angle 0.66747 ( 8224) hydrogen bonds : bond 0.04966 ( 468) hydrogen bonds : angle 4.07541 ( 1392) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7465 (tt) REVERT: A 167 ASP cc_start: 0.6583 (OUTLIER) cc_final: 0.6311 (t70) REVERT: A 396 PRO cc_start: 0.6897 (Cg_exo) cc_final: 0.6503 (Cg_endo) REVERT: A 397 ARG cc_start: 0.5194 (mmt-90) cc_final: 0.3898 (mtt90) REVERT: A 493 CYS cc_start: 0.7435 (m) cc_final: 0.7065 (t) REVERT: A 558 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8187 (tm-30) REVERT: A 560 TYR cc_start: 0.8042 (t80) cc_final: 0.7712 (t80) REVERT: B 107 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7516 (tt) REVERT: B 396 PRO cc_start: 0.6779 (Cg_exo) cc_final: 0.6415 (Cg_endo) REVERT: B 397 ARG cc_start: 0.5310 (mmt-90) cc_final: 0.4076 (mtt90) REVERT: B 493 CYS cc_start: 0.7407 (m) cc_final: 0.6974 (t) REVERT: B 558 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8039 (tm-30) REVERT: B 560 TYR cc_start: 0.8068 (t80) cc_final: 0.7757 (t80) outliers start: 34 outliers final: 18 residues processed: 197 average time/residue: 0.0605 time to fit residues: 17.0081 Evaluate side-chains 186 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 TYR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 504 CYS Chi-restraints excluded: chain B residue 505 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 64 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 71 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 324 GLN A 414 GLN A 418 GLN B 180 ASN B 239 GLN B 324 GLN B 414 GLN B 418 GLN ** B 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.119238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.099241 restraints weight = 15508.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.101607 restraints weight = 9722.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.103383 restraints weight = 7321.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.104015 restraints weight = 5958.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.105187 restraints weight = 5413.097| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6052 Z= 0.131 Angle : 0.619 11.472 8224 Z= 0.306 Chirality : 0.037 0.124 988 Planarity : 0.004 0.034 980 Dihedral : 3.449 12.990 796 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.89 % Allowed : 28.86 % Favored : 66.25 % 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 aren not related in a simple way. whole: 1.86 (0.31), residues: 710 helix: 1.52 (0.20), residues: 612 sheet: None (None), residues: 0 loop : -0.29 (0.66), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 366 TYR 0.019 0.001 TYR B 152 PHE 0.018 0.002 PHE B 52 TRP 0.014 0.001 TRP B 76 HIS 0.005 0.001 HIS B 415 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6052) covalent geometry : angle 0.61940 ( 8224) hydrogen bonds : bond 0.04378 ( 468) hydrogen bonds : angle 3.88723 ( 1392) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9036 (mt) REVERT: A 72 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7839 (mt) REVERT: A 107 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7349 (tt) REVERT: A 493 CYS cc_start: 0.7406 (m) cc_final: 0.7005 (t) REVERT: A 558 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8107 (tm-30) REVERT: A 560 TYR cc_start: 0.7985 (t80) cc_final: 0.7704 (t80) REVERT: B 72 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7832 (mt) REVERT: B 107 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7404 (tt) REVERT: B 180 ASN cc_start: 0.8563 (m110) cc_final: 0.8293 (m110) REVERT: B 396 PRO cc_start: 0.6774 (Cg_exo) cc_final: 0.6411 (Cg_endo) REVERT: B 397 ARG cc_start: 0.5216 (mmt-90) cc_final: 0.4102 (mtt90) REVERT: B 493 CYS cc_start: 0.7393 (m) cc_final: 0.6927 (t) REVERT: B 558 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8038 (tm-30) REVERT: B 560 TYR cc_start: 0.8020 (t80) cc_final: 0.7748 (t80) outliers start: 31 outliers final: 16 residues processed: 206 average time/residue: 0.0531 time to fit residues: 15.8120 Evaluate side-chains 184 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 TYR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 504 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 61 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 180 ASN A 414 GLN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 ASN B 418 GLN B 522 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.119318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.099348 restraints weight = 15524.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.101671 restraints weight = 9893.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.103120 restraints weight = 7460.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.104107 restraints weight = 6234.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.104107 restraints weight = 5514.260| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6052 Z= 0.137 Angle : 0.673 17.288 8224 Z= 0.326 Chirality : 0.039 0.136 988 Planarity : 0.004 0.044 980 Dihedral : 3.423 13.039 796 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 5.21 % Allowed : 28.39 % Favored : 66.40 % 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 aren not related in a simple way. whole: 1.86 (0.31), residues: 710 helix: 1.53 (0.20), residues: 612 sheet: None (None), residues: 0 loop : -0.41 (0.65), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 366 TYR 0.013 0.001 TYR B 548 PHE 0.015 0.001 PHE A 308 TRP 0.013 0.001 TRP B 76 HIS 0.005 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6052) covalent geometry : angle 0.67313 ( 8224) hydrogen bonds : bond 0.04306 ( 468) hydrogen bonds : angle 3.84520 ( 1392) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.274 Fit side-chains REVERT: A 31 LEU cc_start: 0.9219 (mt) cc_final: 0.9015 (mt) REVERT: A 72 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7849 (mt) REVERT: A 107 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7446 (tt) REVERT: A 180 ASN cc_start: 0.8515 (m110) cc_final: 0.8253 (m110) REVERT: A 493 CYS cc_start: 0.7538 (m) cc_final: 0.7007 (t) REVERT: B 72 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7814 (mt) REVERT: B 107 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7452 (tt) REVERT: B 180 ASN cc_start: 0.8652 (m110) cc_final: 0.8338 (m110) REVERT: B 396 PRO cc_start: 0.6868 (Cg_exo) cc_final: 0.6498 (Cg_endo) REVERT: B 397 ARG cc_start: 0.5269 (mmt-90) cc_final: 0.4132 (mtt90) REVERT: B 493 CYS cc_start: 0.7529 (m) cc_final: 0.6949 (t) REVERT: B 558 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8177 (tm-30) outliers start: 33 outliers final: 25 residues processed: 213 average time/residue: 0.0536 time to fit residues: 16.5735 Evaluate side-chains 196 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 TYR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 522 ASN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 504 CYS Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 522 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 6 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 0.0070 chunk 50 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 418 GLN A 522 ASN A 539 ASN B 414 GLN B 418 GLN B 522 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.119797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.100022 restraints weight = 15401.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.102156 restraints weight = 9839.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.103973 restraints weight = 7476.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.104637 restraints weight = 6164.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.105689 restraints weight = 5539.078| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6052 Z= 0.137 Angle : 0.695 13.104 8224 Z= 0.340 Chirality : 0.039 0.174 988 Planarity : 0.004 0.046 980 Dihedral : 3.477 15.767 796 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.52 % Allowed : 32.18 % Favored : 62.30 % 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 aren not related in a simple way. whole: 1.65 (0.31), residues: 710 helix: 1.44 (0.20), residues: 612 sheet: None (None), residues: 0 loop : -0.85 (0.61), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 83 TYR 0.031 0.001 TYR A 560 PHE 0.024 0.002 PHE B 79 TRP 0.015 0.001 TRP A 263 HIS 0.005 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6052) covalent geometry : angle 0.69459 ( 8224) hydrogen bonds : bond 0.04237 ( 468) hydrogen bonds : angle 3.87830 ( 1392) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.239 Fit side-chains REVERT: A 31 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9025 (mt) REVERT: A 72 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7783 (mt) REVERT: A 107 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7364 (tt) REVERT: A 180 ASN cc_start: 0.8596 (m110) cc_final: 0.8258 (m110) REVERT: A 400 GLN cc_start: 0.7672 (tp40) cc_final: 0.7153 (tm-30) REVERT: A 493 CYS cc_start: 0.7419 (m) cc_final: 0.6988 (t) REVERT: B 72 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7761 (mt) REVERT: B 107 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7413 (tt) REVERT: B 180 ASN cc_start: 0.8671 (m110) cc_final: 0.8264 (m110) REVERT: B 558 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8209 (tm-30) REVERT: B 560 TYR cc_start: 0.8141 (t80) cc_final: 0.7850 (t80) outliers start: 35 outliers final: 25 residues processed: 207 average time/residue: 0.0531 time to fit residues: 16.2215 Evaluate side-chains 193 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 TYR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 522 ASN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 504 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 17 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 70 optimal weight: 0.0980 chunk 47 optimal weight: 0.1980 chunk 34 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 522 ASN B 418 GLN B 522 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.120250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.100874 restraints weight = 15513.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.103257 restraints weight = 9685.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.105145 restraints weight = 7209.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.106074 restraints weight = 5830.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.106710 restraints weight = 5124.252| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6052 Z= 0.136 Angle : 0.706 13.256 8224 Z= 0.344 Chirality : 0.040 0.213 988 Planarity : 0.004 0.046 980 Dihedral : 3.467 14.900 796 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.52 % Allowed : 33.60 % Favored : 60.88 % 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 aren not related in a simple way. whole: 1.61 (0.31), residues: 710 helix: 1.41 (0.20), residues: 612 sheet: None (None), residues: 0 loop : -0.85 (0.62), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 83 TYR 0.013 0.001 TYR B 124 PHE 0.022 0.002 PHE B 79 TRP 0.017 0.001 TRP B 263 HIS 0.006 0.001 HIS B 415 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6052) covalent geometry : angle 0.70634 ( 8224) hydrogen bonds : bond 0.04190 ( 468) hydrogen bonds : angle 3.93258 ( 1392) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.251 Fit side-chains REVERT: A 31 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.9010 (mt) REVERT: A 72 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7775 (mt) REVERT: A 107 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7348 (tt) REVERT: A 400 GLN cc_start: 0.7623 (tp40) cc_final: 0.7062 (tm-30) REVERT: A 493 CYS cc_start: 0.7424 (m) cc_final: 0.6965 (t) REVERT: A 560 TYR cc_start: 0.8137 (t80) cc_final: 0.7828 (t80) REVERT: B 31 LEU cc_start: 0.9178 (mt) cc_final: 0.8961 (mt) REVERT: B 72 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7772 (mt) REVERT: B 107 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7423 (tt) REVERT: B 180 ASN cc_start: 0.8661 (m110) cc_final: 0.8305 (m110) REVERT: B 558 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8211 (tm-30) REVERT: B 560 TYR cc_start: 0.8089 (t80) cc_final: 0.7835 (t80) outliers start: 35 outliers final: 26 residues processed: 202 average time/residue: 0.0514 time to fit residues: 15.5648 Evaluate side-chains 197 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 TYR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 522 ASN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 504 CYS Chi-restraints excluded: chain B residue 522 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 32 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 ASN B 414 GLN B 522 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.120124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.100531 restraints weight = 15634.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.102622 restraints weight = 10041.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.104220 restraints weight = 7675.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 14)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.104220 restraints weight = 6368.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.104220 restraints weight = 6367.729| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6052 Z= 0.142 Angle : 0.738 15.556 8224 Z= 0.356 Chirality : 0.042 0.277 988 Planarity : 0.004 0.045 980 Dihedral : 3.484 14.241 796 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.05 % Allowed : 34.38 % Favored : 60.57 % 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 aren not related in a simple way. whole: 1.55 (0.31), residues: 710 helix: 1.36 (0.20), residues: 612 sheet: None (None), residues: 0 loop : -0.82 (0.63), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 83 TYR 0.012 0.001 TYR B 124 PHE 0.021 0.002 PHE B 308 TRP 0.019 0.001 TRP A 263 HIS 0.006 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6052) covalent geometry : angle 0.73768 ( 8224) hydrogen bonds : bond 0.04203 ( 468) hydrogen bonds : angle 4.04306 ( 1392) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.228 Fit side-chains REVERT: A 31 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8992 (mt) REVERT: A 61 ASP cc_start: 0.7134 (m-30) cc_final: 0.6922 (m-30) REVERT: A 72 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7813 (mt) REVERT: A 107 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7378 (tt) REVERT: A 324 GLN cc_start: 0.7119 (tp-100) cc_final: 0.6679 (tt0) REVERT: A 493 CYS cc_start: 0.7550 (m) cc_final: 0.7057 (t) REVERT: A 560 TYR cc_start: 0.8062 (t80) cc_final: 0.7760 (t80) REVERT: B 31 LEU cc_start: 0.9179 (mt) cc_final: 0.8976 (mt) REVERT: B 72 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7800 (mt) REVERT: B 107 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7444 (tt) REVERT: B 180 ASN cc_start: 0.8633 (m110) cc_final: 0.8283 (m110) REVERT: B 558 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8202 (tm-30) REVERT: B 560 TYR cc_start: 0.8116 (t80) cc_final: 0.7833 (t80) outliers start: 32 outliers final: 22 residues processed: 197 average time/residue: 0.0458 time to fit residues: 13.4697 Evaluate side-chains 192 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 TYR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 504 CYS Chi-restraints excluded: chain B residue 522 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 522 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.119738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.099549 restraints weight = 15957.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.101675 restraints weight = 10290.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.103460 restraints weight = 7897.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.104145 restraints weight = 6582.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.104152 restraints weight = 5950.926| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6052 Z= 0.155 Angle : 0.766 16.198 8224 Z= 0.368 Chirality : 0.042 0.218 988 Planarity : 0.004 0.039 980 Dihedral : 3.501 13.820 796 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.57 % Allowed : 35.33 % Favored : 60.09 % 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 aren not related in a simple way. whole: 1.51 (0.31), residues: 710 helix: 1.32 (0.20), residues: 604 sheet: None (None), residues: 0 loop : -0.51 (0.64), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 83 TYR 0.016 0.001 TYR A 548 PHE 0.022 0.002 PHE B 308 TRP 0.020 0.002 TRP B 263 HIS 0.011 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 6052) covalent geometry : angle 0.76598 ( 8224) hydrogen bonds : bond 0.04223 ( 468) hydrogen bonds : angle 4.12037 ( 1392) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.236 Fit side-chains REVERT: A 61 ASP cc_start: 0.7150 (m-30) cc_final: 0.6941 (m-30) REVERT: A 72 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7843 (mt) REVERT: A 107 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7439 (tt) REVERT: A 180 ASN cc_start: 0.8594 (m110) cc_final: 0.8224 (m110) REVERT: A 324 GLN cc_start: 0.7204 (tp-100) cc_final: 0.6794 (tt0) REVERT: A 493 CYS cc_start: 0.7608 (m) cc_final: 0.7104 (t) REVERT: A 560 TYR cc_start: 0.8050 (t80) cc_final: 0.7775 (t80) REVERT: B 31 LEU cc_start: 0.9171 (mt) cc_final: 0.8968 (mt) REVERT: B 72 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7830 (mt) REVERT: B 107 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7462 (tt) REVERT: B 155 TRP cc_start: 0.6577 (t60) cc_final: 0.6371 (t60) REVERT: B 180 ASN cc_start: 0.8681 (m110) cc_final: 0.8325 (m110) REVERT: B 558 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8208 (tm-30) REVERT: B 560 TYR cc_start: 0.8118 (t80) cc_final: 0.7887 (t80) outliers start: 29 outliers final: 23 residues processed: 195 average time/residue: 0.0457 time to fit residues: 13.3960 Evaluate side-chains 193 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 TYR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 522 ASN Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 504 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 73 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 ASN B 150 GLN B 180 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.120085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.101190 restraints weight = 16002.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.103668 restraints weight = 10058.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.104986 restraints weight = 7445.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.106291 restraints weight = 6220.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.107190 restraints weight = 5406.959| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6052 Z= 0.147 Angle : 0.809 16.486 8224 Z= 0.386 Chirality : 0.044 0.275 988 Planarity : 0.004 0.038 980 Dihedral : 3.537 13.866 796 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.10 % Allowed : 35.65 % Favored : 60.25 % 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 aren not related in a simple way. whole: 1.39 (0.30), residues: 710 helix: 1.23 (0.20), residues: 604 sheet: None (None), residues: 0 loop : -0.53 (0.64), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 83 TYR 0.014 0.001 TYR A 152 PHE 0.023 0.002 PHE A 308 TRP 0.021 0.002 TRP B 263 HIS 0.011 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6052) covalent geometry : angle 0.80917 ( 8224) hydrogen bonds : bond 0.04198 ( 468) hydrogen bonds : angle 4.19991 ( 1392) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.219 Fit side-chains REVERT: A 61 ASP cc_start: 0.7102 (m-30) cc_final: 0.6899 (m-30) REVERT: A 72 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7816 (mt) REVERT: A 107 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7397 (tt) REVERT: A 180 ASN cc_start: 0.8569 (m110) cc_final: 0.8215 (m110) REVERT: A 324 GLN cc_start: 0.7193 (tp-100) cc_final: 0.6784 (tt0) REVERT: A 493 CYS cc_start: 0.7491 (m) cc_final: 0.7007 (t) REVERT: A 560 TYR cc_start: 0.7912 (t80) cc_final: 0.7677 (t80) REVERT: B 72 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7794 (mt) REVERT: B 107 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7405 (tt) REVERT: B 174 MET cc_start: 0.8344 (mmt) cc_final: 0.7691 (mmm) REVERT: B 558 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8156 (tm-30) REVERT: B 560 TYR cc_start: 0.8059 (t80) cc_final: 0.7831 (t80) outliers start: 26 outliers final: 21 residues processed: 189 average time/residue: 0.0498 time to fit residues: 14.1561 Evaluate side-chains 192 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 124 TYR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 504 CYS Chi-restraints excluded: chain A residue 522 ASN Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 TYR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 504 CYS Chi-restraints excluded: chain B residue 522 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 0.3980 chunk 12 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 414 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 = 0.4000 r_free = 0.4000 target = 0.121219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.101481 restraints weight = 15991.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.103605 restraints weight = 10412.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.105379 restraints weight = 7973.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.106295 restraints weight = 6598.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.106803 restraints weight = 5860.603| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.245 6052 Z= 0.320 Angle : 1.402 59.199 8224 Z= 0.848 Chirality : 0.054 0.998 988 Planarity : 0.005 0.068 980 Dihedral : 3.867 36.322 796 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.26 % Allowed : 35.65 % Favored : 60.09 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 aren not related in a simple way. whole: 1.39 (0.31), residues: 710 helix: 1.24 (0.20), residues: 604 sheet: None (None), residues: 0 loop : -0.58 (0.64), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 104 TYR 0.012 0.001 TYR B 548 PHE 0.022 0.002 PHE A 308 TRP 0.019 0.002 TRP B 263 HIS 0.010 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00594 ( 6052) covalent geometry : angle 1.40233 ( 8224) hydrogen bonds : bond 0.04209 ( 468) hydrogen bonds : angle 4.20429 ( 1392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1070.46 seconds wall clock time: 19 minutes 26.54 seconds (1166.54 seconds total)