Starting phenix.real_space_refine on Fri Aug 22 21:12:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tem_41191/08_2025/8tem_41191.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tem_41191/08_2025/8tem_41191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tem_41191/08_2025/8tem_41191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tem_41191/08_2025/8tem_41191.map" model { file = "/net/cci-nas-00/data/ceres_data/8tem_41191/08_2025/8tem_41191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tem_41191/08_2025/8tem_41191.cif" } resolution = 3.02 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 58 5.16 5 C 5302 2.51 5 N 1294 2.21 5 O 1338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7992 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3996 Classifications: {'peptide': 505} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 473} Chain breaks: 2 Restraints were copied for chains: B Time building chain proxies: 2.95, per 1000 atoms: 0.37 Number of scatterers: 7992 At special positions: 0 Unit cell: (97.11, 117.03, 81.34, 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 58 16.00 O 1338 8.00 N 1294 7.00 C 5302 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: 0.48 Conformation dependent library (CDL) restraints added in 481.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1868 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 4 sheets defined 80.4% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 8 through 19 Processing helix chain 'A' and resid 21 through 33 removed outlier: 3.973A pdb=" N GLY A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 62 removed outlier: 3.921A pdb=" N ILE A 49 " --> pdb=" O PHE A 45 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 67 through 86 Processing helix chain 'A' and resid 96 through 112 removed outlier: 3.508A pdb=" N ALA A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 142 Processing helix chain 'A' and resid 143 through 151 removed outlier: 3.548A pdb=" N ILE A 147 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 148 " --> pdb=" O CYS A 145 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASN A 149 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 178 removed outlier: 3.534A pdb=" N GLY A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 192 Processing helix chain 'A' and resid 193 through 219 Processing helix chain 'A' and resid 228 through 252 removed outlier: 6.664A pdb=" N VAL A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Proline residue: A 241 - end of helix Processing helix chain 'A' and resid 253 through 258 removed outlier: 4.505A pdb=" N GLY A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.797A pdb=" N LEU A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 297 through 320 removed outlier: 3.613A pdb=" N MET A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A 313 " --> pdb=" O TYR A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'A' and resid 359 through 368 Processing helix chain 'A' and resid 464 through 480 removed outlier: 3.533A pdb=" N LEU A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 488 through 503 removed outlier: 3.689A pdb=" N LEU A 492 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 517 Processing helix chain 'A' and resid 519 through 521 No H-bonds generated for 'chain 'A' and resid 519 through 521' Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.964A pdb=" N VAL A 526 " --> pdb=" O ARG A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 538 Processing helix chain 'A' and resid 539 through 562 removed outlier: 3.587A pdb=" N TRP A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 568 Processing helix chain 'A' and resid 569 through 589 removed outlier: 3.540A pdb=" N MET A 573 " --> pdb=" O MET A 569 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 577 " --> pdb=" O MET A 573 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) Proline residue: A 579 - end of helix removed outlier: 4.394A pdb=" N LEU A 585 " --> pdb=" O ARG A 581 " (cutoff:3.500A) Proline residue: A 586 - end of helix Processing helix chain 'A' and resid 591 through 598 Processing helix chain 'B' and resid 8 through 19 Processing helix chain 'B' and resid 21 through 33 removed outlier: 3.974A pdb=" N GLY B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 62 removed outlier: 3.921A pdb=" N ILE B 49 " --> pdb=" O PHE B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 67 through 86 Processing helix chain 'B' and resid 96 through 112 removed outlier: 3.508A pdb=" N ALA B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 142 Processing helix chain 'B' and resid 143 through 151 removed outlier: 3.548A pdb=" N ILE B 147 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 148 " --> pdb=" O CYS B 145 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASN B 149 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 178 removed outlier: 3.535A pdb=" N GLY B 156 " --> pdb=" O THR B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 192 Processing helix chain 'B' and resid 193 through 219 Processing helix chain 'B' and resid 228 through 252 removed outlier: 6.662A pdb=" N VAL B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 253 through 258 removed outlier: 4.505A pdb=" N GLY B 256 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 258 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.797A pdb=" N LEU B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 297 through 320 removed outlier: 3.613A pdb=" N MET B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 313 " --> pdb=" O TYR B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 Processing helix chain 'B' and resid 331 through 350 Processing helix chain 'B' and resid 359 through 368 Processing helix chain 'B' and resid 464 through 480 removed outlier: 3.532A pdb=" N LEU B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B 478 " --> pdb=" O VAL B 474 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA B 479 " --> pdb=" O GLY B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 485 Processing helix chain 'B' and resid 488 through 503 removed outlier: 3.688A pdb=" N LEU B 492 " --> pdb=" O PRO B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 517 Processing helix chain 'B' and resid 519 through 521 No H-bonds generated for 'chain 'B' and resid 519 through 521' Processing helix chain 'B' and resid 522 through 528 removed outlier: 3.965A pdb=" N VAL B 526 " --> pdb=" O ARG B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 538 Processing helix chain 'B' and resid 539 through 562 removed outlier: 3.587A pdb=" N TRP B 562 " --> pdb=" O PHE B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 568 Processing helix chain 'B' and resid 569 through 589 removed outlier: 3.540A pdb=" N MET B 573 " --> pdb=" O MET B 569 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 577 " --> pdb=" O MET B 573 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) Proline residue: B 579 - end of helix removed outlier: 4.394A pdb=" N LEU B 585 " --> pdb=" O ARG B 581 " (cutoff:3.500A) Proline residue: B 586 - end of helix Processing helix chain 'B' and resid 591 through 598 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 532 Processing sheet with id=AA3, first strand: chain 'B' and resid 93 through 94 Processing sheet with id=AA4, first strand: chain 'B' and resid 531 through 532 530 hydrogen bonds defined for protein. 1530 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: 1.34 Time building geometry restraints manager: 0.64 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: 2420 1.34 - 1.46: 2020 1.46 - 1.58: 3678 1.58 - 1.70: 0 1.70 - 1.81: 100 Bond restraints: 8218 Sorted by residual: bond pdb=" N PHE A 5 " pdb=" CA PHE A 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N PHE B 5 " pdb=" CA PHE B 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" CB LYS B 260 " pdb=" CG LYS B 260 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.54e+00 bond pdb=" CB LYS A 260 " pdb=" CG LYS A 260 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.54e+00 bond pdb=" CA ILE B 181 " pdb=" CB ILE B 181 " ideal model delta sigma weight residual 1.537 1.525 0.012 1.29e-02 6.01e+03 8.54e-01 ... (remaining 8213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 10772 1.26 - 2.51: 292 2.51 - 3.77: 70 3.77 - 5.02: 26 5.02 - 6.28: 4 Bond angle restraints: 11164 Sorted by residual: angle pdb=" CB LYS A 260 " pdb=" CG LYS A 260 " pdb=" CD LYS A 260 " ideal model delta sigma weight residual 111.30 117.29 -5.99 2.30e+00 1.89e-01 6.78e+00 angle pdb=" CB LYS B 260 " pdb=" CG LYS B 260 " pdb=" CD LYS B 260 " ideal model delta sigma weight residual 111.30 117.29 -5.99 2.30e+00 1.89e-01 6.78e+00 angle pdb=" CA LYS B 260 " pdb=" CB LYS B 260 " pdb=" CG LYS B 260 " ideal model delta sigma weight residual 114.10 118.77 -4.67 2.00e+00 2.50e-01 5.45e+00 angle pdb=" CA LYS A 260 " pdb=" CB LYS A 260 " pdb=" CG LYS A 260 " ideal model delta sigma weight residual 114.10 118.74 -4.64 2.00e+00 2.50e-01 5.38e+00 angle pdb=" N PHE A 8 " pdb=" CA PHE A 8 " pdb=" CB PHE A 8 " ideal model delta sigma weight residual 113.65 110.38 3.27 1.47e+00 4.63e-01 4.94e+00 ... (remaining 11159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 4181 17.24 - 34.47: 441 34.47 - 51.71: 144 51.71 - 68.94: 24 68.94 - 86.18: 24 Dihedral angle restraints: 4814 sinusoidal: 1910 harmonic: 2904 Sorted by residual: dihedral pdb=" CA LYS B 590 " pdb=" C LYS B 590 " pdb=" N GLY B 591 " pdb=" CA GLY B 591 " ideal model delta harmonic sigma weight residual 180.00 161.96 18.04 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LYS A 590 " pdb=" C LYS A 590 " pdb=" N GLY A 591 " pdb=" CA GLY A 591 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA SER B 521 " pdb=" C SER B 521 " pdb=" N ARG B 522 " pdb=" CA ARG B 522 " ideal model delta harmonic sigma weight residual 180.00 -163.87 -16.13 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 4811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 835 0.030 - 0.060: 270 0.060 - 0.090: 104 0.090 - 0.120: 41 0.120 - 0.150: 10 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA ILE B 358 " pdb=" N ILE B 358 " pdb=" C ILE B 358 " pdb=" CB ILE B 358 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ILE B 181 " pdb=" N ILE B 181 " pdb=" C ILE B 181 " pdb=" CB ILE B 181 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 1257 not shown) Planarity restraints: 1380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 258 " -0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO B 259 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 259 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 259 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 258 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.99e+00 pdb=" N PRO A 259 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 6 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO A 7 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 7 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 7 " -0.019 5.00e-02 4.00e+02 ... (remaining 1377 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 81 2.65 - 3.22: 7793 3.22 - 3.78: 12758 3.78 - 4.34: 17401 4.34 - 4.90: 28722 Nonbonded interactions: 66755 Sorted by model distance: nonbonded pdb=" O ALA B 144 " pdb=" OH TYR B 309 " model vdw 2.092 3.040 nonbonded pdb=" O ALA A 144 " pdb=" OH TYR A 309 " model vdw 2.092 3.040 nonbonded pdb=" O LEU A 58 " pdb=" OG1 THR A 62 " model vdw 2.105 3.040 nonbonded pdb=" O LEU B 58 " pdb=" OG1 THR B 62 " model vdw 2.106 3.040 nonbonded pdb=" OE2 GLU A 178 " pdb=" OG1 THR A 489 " model vdw 2.184 3.040 ... (remaining 66750 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: 0.02 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.160 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 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 0.037 8218 Z= 0.132 Angle : 0.557 6.276 11164 Z= 0.284 Chirality : 0.038 0.150 1260 Planarity : 0.004 0.035 1380 Dihedral : 17.161 86.177 2946 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.87 % Allowed : 18.50 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.84 (0.27), residues: 998 helix: 1.38 (0.19), residues: 726 sheet: None (None), residues: 0 loop : 1.12 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 523 TYR 0.009 0.001 TYR A 309 PHE 0.014 0.001 PHE B 570 TRP 0.007 0.001 TRP A 230 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8218) covalent geometry : angle 0.55738 (11164) hydrogen bonds : bond 0.12338 ( 530) hydrogen bonds : angle 4.94887 ( 1530) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.338 Fit side-chains REVERT: A 157 GLU cc_start: 0.8219 (mm-30) cc_final: 0.6878 (mt-10) REVERT: B 157 GLU cc_start: 0.8236 (mm-30) cc_final: 0.6869 (mt-10) outliers start: 16 outliers final: 8 residues processed: 112 average time/residue: 0.1061 time to fit residues: 15.5336 Evaluate side-chains 104 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 515 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.164038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.132635 restraints weight = 9529.801| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.03 r_work: 0.3222 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8218 Z= 0.134 Angle : 0.539 6.657 11164 Z= 0.269 Chirality : 0.042 0.159 1260 Planarity : 0.004 0.038 1380 Dihedral : 4.189 30.350 1096 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.64 % Allowed : 15.57 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.42 (0.27), residues: 998 helix: 1.72 (0.19), residues: 738 sheet: None (None), residues: 0 loop : 1.57 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.014 0.001 TYR B 22 PHE 0.012 0.001 PHE A 534 TRP 0.010 0.001 TRP A 247 HIS 0.002 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8218) covalent geometry : angle 0.53934 (11164) hydrogen bonds : bond 0.04295 ( 530) hydrogen bonds : angle 4.19354 ( 1530) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.295 Fit side-chains REVERT: A 469 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6984 (mt) REVERT: B 469 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.7060 (mt) outliers start: 14 outliers final: 8 residues processed: 106 average time/residue: 0.1011 time to fit residues: 14.0224 Evaluate side-chains 100 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS B 531 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.156366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.124183 restraints weight = 9692.764| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.15 r_work: 0.3162 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8218 Z= 0.144 Angle : 0.540 6.324 11164 Z= 0.267 Chirality : 0.042 0.166 1260 Planarity : 0.005 0.035 1380 Dihedral : 3.798 23.169 1084 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.81 % Allowed : 14.52 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.37 (0.27), residues: 998 helix: 1.72 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 1.42 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.012 0.001 TYR B 103 PHE 0.009 0.001 PHE B 298 TRP 0.010 0.001 TRP A 247 HIS 0.003 0.001 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8218) covalent geometry : angle 0.54050 (11164) hydrogen bonds : bond 0.04643 ( 530) hydrogen bonds : angle 4.13602 ( 1530) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.303 Fit side-chains REVERT: A 60 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6500 (mtt-85) REVERT: A 70 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.6786 (mp10) REVERT: A 463 GLN cc_start: 0.4485 (OUTLIER) cc_final: 0.3982 (pm20) REVERT: A 469 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6970 (mt) REVERT: B 60 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6509 (mtt-85) REVERT: B 70 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.6794 (mp10) REVERT: B 463 GLN cc_start: 0.4525 (OUTLIER) cc_final: 0.4000 (pm20) REVERT: B 469 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6889 (mt) outliers start: 24 outliers final: 10 residues processed: 121 average time/residue: 0.1002 time to fit residues: 16.1372 Evaluate side-chains 112 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 604 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 85 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.157239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.125177 restraints weight = 9825.302| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.17 r_work: 0.3155 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8218 Z= 0.118 Angle : 0.508 6.404 11164 Z= 0.251 Chirality : 0.041 0.154 1260 Planarity : 0.004 0.035 1380 Dihedral : 3.717 22.420 1084 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.58 % Allowed : 14.64 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.52 (0.27), residues: 998 helix: 1.84 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 1.43 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 113 TYR 0.009 0.001 TYR A 103 PHE 0.020 0.001 PHE B 310 TRP 0.012 0.001 TRP A 247 HIS 0.001 0.000 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8218) covalent geometry : angle 0.50763 (11164) hydrogen bonds : bond 0.04057 ( 530) hydrogen bonds : angle 4.04331 ( 1530) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.6720 (mp10) REVERT: A 187 GLN cc_start: 0.7033 (OUTLIER) cc_final: 0.6680 (mt0) REVERT: A 463 GLN cc_start: 0.4388 (OUTLIER) cc_final: 0.3907 (pm20) REVERT: B 70 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.6717 (mp10) REVERT: B 187 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6669 (mt0) REVERT: B 463 GLN cc_start: 0.4435 (OUTLIER) cc_final: 0.3928 (pm20) outliers start: 22 outliers final: 12 residues processed: 123 average time/residue: 0.1002 time to fit residues: 16.3971 Evaluate side-chains 117 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 576 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 12 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 57 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.156583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.124580 restraints weight = 9728.167| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.17 r_work: 0.3141 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8218 Z= 0.117 Angle : 0.503 6.324 11164 Z= 0.250 Chirality : 0.041 0.157 1260 Planarity : 0.004 0.036 1380 Dihedral : 3.646 21.986 1084 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.28 % Allowed : 14.40 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.61 (0.27), residues: 998 helix: 2.02 (0.19), residues: 726 sheet: None (None), residues: 0 loop : 1.15 (0.42), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 153 TYR 0.010 0.001 TYR A 103 PHE 0.008 0.001 PHE A 570 TRP 0.011 0.001 TRP B 247 HIS 0.001 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8218) covalent geometry : angle 0.50335 (11164) hydrogen bonds : bond 0.04033 ( 530) hydrogen bonds : angle 3.98168 ( 1530) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.266 Fit side-chains REVERT: A 60 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6569 (mtt-85) REVERT: A 70 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.6705 (mp10) REVERT: A 157 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8205 (mm-30) REVERT: A 187 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6662 (mt0) REVERT: A 219 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8106 (mmm-85) REVERT: A 463 GLN cc_start: 0.4529 (OUTLIER) cc_final: 0.4010 (pm20) REVERT: B 60 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6569 (mtt-85) REVERT: B 70 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.6706 (mp10) REVERT: B 157 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8211 (mm-30) REVERT: B 187 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6648 (mt0) REVERT: B 219 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8104 (mmm-85) REVERT: B 463 GLN cc_start: 0.4586 (OUTLIER) cc_final: 0.4033 (pm20) outliers start: 28 outliers final: 14 residues processed: 126 average time/residue: 0.1071 time to fit residues: 17.9037 Evaluate side-chains 122 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 576 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 76 optimal weight: 0.0570 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 92 optimal weight: 0.0470 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.157040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.125562 restraints weight = 9732.712| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.16 r_work: 0.3129 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8218 Z= 0.109 Angle : 0.494 6.696 11164 Z= 0.244 Chirality : 0.040 0.153 1260 Planarity : 0.004 0.039 1380 Dihedral : 3.636 22.220 1084 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.51 % Allowed : 15.81 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.61 (0.27), residues: 998 helix: 2.02 (0.19), residues: 730 sheet: None (None), residues: 0 loop : 1.12 (0.43), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 18 TYR 0.008 0.001 TYR A 103 PHE 0.030 0.001 PHE A 310 TRP 0.011 0.001 TRP A 247 HIS 0.001 0.000 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8218) covalent geometry : angle 0.49395 (11164) hydrogen bonds : bond 0.03793 ( 530) hydrogen bonds : angle 3.92779 ( 1530) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6498 (mtt-85) REVERT: A 70 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.6641 (mp10) REVERT: A 187 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6650 (mt0) REVERT: A 219 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8085 (mmm-85) REVERT: A 463 GLN cc_start: 0.4516 (OUTLIER) cc_final: 0.4016 (pm20) REVERT: B 20 MET cc_start: 0.5504 (mtm) cc_final: 0.5215 (mtm) REVERT: B 60 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6450 (mtt-85) REVERT: B 70 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.6637 (mp10) REVERT: B 187 GLN cc_start: 0.6996 (OUTLIER) cc_final: 0.6631 (mt0) REVERT: B 219 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8084 (mmm-85) REVERT: B 463 GLN cc_start: 0.4545 (OUTLIER) cc_final: 0.4030 (pm20) outliers start: 30 outliers final: 16 residues processed: 128 average time/residue: 0.0994 time to fit residues: 16.9939 Evaluate side-chains 128 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 604 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.155022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.123187 restraints weight = 9776.801| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.12 r_work: 0.3122 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8218 Z= 0.138 Angle : 0.534 6.352 11164 Z= 0.265 Chirality : 0.042 0.166 1260 Planarity : 0.005 0.041 1380 Dihedral : 3.745 23.138 1084 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.04 % Allowed : 16.28 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.35 (0.27), residues: 998 helix: 1.74 (0.19), residues: 742 sheet: None (None), residues: 0 loop : 1.31 (0.44), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 587 TYR 0.009 0.001 TYR A 495 PHE 0.013 0.001 PHE B 298 TRP 0.007 0.001 TRP B 230 HIS 0.001 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8218) covalent geometry : angle 0.53436 (11164) hydrogen bonds : bond 0.04466 ( 530) hydrogen bonds : angle 4.05691 ( 1530) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 60 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6482 (mtt-85) REVERT: A 70 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.6740 (mp10) REVERT: A 187 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6632 (mt0) REVERT: A 219 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8101 (mmm-85) REVERT: A 463 GLN cc_start: 0.4552 (OUTLIER) cc_final: 0.3992 (pm20) REVERT: B 20 MET cc_start: 0.5599 (mtm) cc_final: 0.5299 (mtm) REVERT: B 60 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6476 (mtt-85) REVERT: B 70 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.6752 (mp10) REVERT: B 187 GLN cc_start: 0.7043 (OUTLIER) cc_final: 0.6675 (mt0) REVERT: B 219 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8095 (mmm-85) REVERT: B 463 GLN cc_start: 0.4571 (OUTLIER) cc_final: 0.4009 (pm20) outliers start: 26 outliers final: 12 residues processed: 122 average time/residue: 0.0889 time to fit residues: 14.4466 Evaluate side-chains 123 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 91 optimal weight: 0.0970 chunk 74 optimal weight: 0.9980 chunk 98 optimal weight: 0.0570 chunk 29 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.160657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129263 restraints weight = 9647.644| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.99 r_work: 0.3149 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8218 Z= 0.108 Angle : 0.506 6.823 11164 Z= 0.250 Chirality : 0.041 0.153 1260 Planarity : 0.004 0.043 1380 Dihedral : 3.669 22.460 1084 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.93 % Allowed : 16.63 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.53 (0.27), residues: 998 helix: 1.88 (0.19), residues: 742 sheet: None (None), residues: 0 loop : 1.33 (0.44), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 113 TYR 0.007 0.001 TYR A 103 PHE 0.030 0.001 PHE B 310 TRP 0.013 0.001 TRP A 247 HIS 0.001 0.000 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8218) covalent geometry : angle 0.50592 (11164) hydrogen bonds : bond 0.03830 ( 530) hydrogen bonds : angle 3.97723 ( 1530) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6542 (mtt-85) REVERT: A 70 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.6670 (mp10) REVERT: A 157 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8273 (mm-30) REVERT: A 187 GLN cc_start: 0.6971 (OUTLIER) cc_final: 0.6582 (mt0) REVERT: A 219 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8108 (mmm-85) REVERT: A 463 GLN cc_start: 0.4445 (OUTLIER) cc_final: 0.3972 (pm20) REVERT: B 60 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6530 (mtt-85) REVERT: B 70 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.6671 (mp10) REVERT: B 157 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8282 (mm-30) REVERT: B 187 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6695 (mt0) REVERT: B 219 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8095 (mmm-85) REVERT: B 463 GLN cc_start: 0.4444 (OUTLIER) cc_final: 0.3968 (pm20) outliers start: 25 outliers final: 12 residues processed: 126 average time/residue: 0.0896 time to fit residues: 15.0799 Evaluate side-chains 129 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 576 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 56 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.158462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127659 restraints weight = 9652.423| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.93 r_work: 0.3174 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8218 Z= 0.141 Angle : 0.551 8.010 11164 Z= 0.272 Chirality : 0.042 0.168 1260 Planarity : 0.005 0.044 1380 Dihedral : 3.758 22.730 1084 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.28 % Allowed : 16.16 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.34 (0.27), residues: 998 helix: 1.74 (0.19), residues: 742 sheet: None (None), residues: 0 loop : 1.26 (0.43), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 18 TYR 0.009 0.001 TYR A 495 PHE 0.014 0.001 PHE B 570 TRP 0.008 0.001 TRP A 247 HIS 0.001 0.000 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8218) covalent geometry : angle 0.55124 (11164) hydrogen bonds : bond 0.04455 ( 530) hydrogen bonds : angle 4.08864 ( 1530) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6684 (mtt-85) REVERT: A 70 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.6838 (mp10) REVERT: A 187 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6656 (mt0) REVERT: A 219 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8183 (mmm-85) REVERT: A 463 GLN cc_start: 0.4678 (OUTLIER) cc_final: 0.4077 (pm20) REVERT: A 573 MET cc_start: 0.7956 (mmm) cc_final: 0.7458 (mtp) REVERT: B 60 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6676 (mtt-85) REVERT: B 70 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.6836 (mp10) REVERT: B 187 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6750 (mt0) REVERT: B 219 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8174 (mmm-85) REVERT: B 463 GLN cc_start: 0.4573 (OUTLIER) cc_final: 0.4037 (pm20) REVERT: B 573 MET cc_start: 0.7957 (mmm) cc_final: 0.7453 (mtp) outliers start: 28 outliers final: 14 residues processed: 124 average time/residue: 0.0914 time to fit residues: 15.1259 Evaluate side-chains 127 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 576 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 68 optimal weight: 0.0980 chunk 98 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.158690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.125645 restraints weight = 9669.863| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.94 r_work: 0.3132 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8218 Z= 0.110 Angle : 0.521 8.571 11164 Z= 0.258 Chirality : 0.041 0.153 1260 Planarity : 0.004 0.044 1380 Dihedral : 3.650 21.052 1084 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.81 % Allowed : 16.51 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.57 (0.27), residues: 998 helix: 2.00 (0.19), residues: 730 sheet: None (None), residues: 0 loop : 1.08 (0.43), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 113 TYR 0.007 0.001 TYR B 22 PHE 0.013 0.001 PHE A 570 TRP 0.013 0.001 TRP A 247 HIS 0.001 0.000 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8218) covalent geometry : angle 0.52070 (11164) hydrogen bonds : bond 0.03816 ( 530) hydrogen bonds : angle 4.01541 ( 1530) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6527 (mtt-85) REVERT: A 70 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.6685 (mp10) REVERT: A 157 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8300 (mm-30) REVERT: A 187 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.6512 (mt0) REVERT: A 202 MET cc_start: 0.9035 (mmm) cc_final: 0.8828 (mmt) REVERT: A 219 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8082 (mmm-85) REVERT: A 463 GLN cc_start: 0.4434 (OUTLIER) cc_final: 0.3988 (pm20) REVERT: A 573 MET cc_start: 0.7895 (mmm) cc_final: 0.7515 (mtp) REVERT: B 60 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6498 (mtt-85) REVERT: B 70 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.6671 (mp10) REVERT: B 157 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8301 (mm-30) REVERT: B 187 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6705 (mt0) REVERT: B 219 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8078 (mmm-85) REVERT: B 463 GLN cc_start: 0.4453 (OUTLIER) cc_final: 0.4043 (pm20) REVERT: B 573 MET cc_start: 0.7902 (mmm) cc_final: 0.7525 (mtp) outliers start: 24 outliers final: 14 residues processed: 135 average time/residue: 0.0893 time to fit residues: 16.2419 Evaluate side-chains 135 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 576 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 53 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 70 optimal weight: 0.0970 chunk 66 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.158727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.127140 restraints weight = 9669.345| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.12 r_work: 0.3128 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8218 Z= 0.114 Angle : 0.533 8.537 11164 Z= 0.265 Chirality : 0.041 0.154 1260 Planarity : 0.004 0.045 1380 Dihedral : 3.614 20.882 1084 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.81 % Allowed : 16.74 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 2.59 (0.27), residues: 998 helix: 2.01 (0.19), residues: 728 sheet: None (None), residues: 0 loop : 1.11 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 522 TYR 0.006 0.001 TYR A 103 PHE 0.030 0.001 PHE B 310 TRP 0.011 0.001 TRP B 247 HIS 0.002 0.001 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8218) covalent geometry : angle 0.53346 (11164) hydrogen bonds : bond 0.03859 ( 530) hydrogen bonds : angle 4.03433 ( 1530) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2106.21 seconds wall clock time: 36 minutes 38.18 seconds (2198.18 seconds total)