Starting phenix.real_space_refine on Tue Sep 24 11:42:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tem_41191/09_2024/8tem_41191.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tem_41191/09_2024/8tem_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tem_41191/09_2024/8tem_41191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tem_41191/09_2024/8tem_41191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tem_41191/09_2024/8tem_41191.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tem_41191/09_2024/8tem_41191.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 7.48, per 1000 atoms: 0.94 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: 2.10 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.89 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: 2.52 Time building geometry restraints manager: 2.43 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: 0.00 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.540 Find NCS groups from input model: 0.220 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.420 ------------------------------------------------------------------------------- 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= 0.206 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP A 230 HIS 0.002 0.001 HIS A 312 PHE 0.014 0.001 PHE B 570 TYR 0.009 0.001 TYR A 309 ARG 0.003 0.001 ARG A 523 *********************** 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 fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.894 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: 0.2372 time to fit residues: 34.8003 Evaluate side-chains 104 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 84 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 0.0470 chunk 51 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8218 Z= 0.266 Angle : 0.592 6.443 11164 Z= 0.297 Chirality : 0.044 0.169 1260 Planarity : 0.005 0.039 1380 Dihedral : 4.365 31.075 1096 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.04 % Allowed : 14.40 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.27), residues: 998 helix: 1.51 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 1.45 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 247 HIS 0.002 0.001 HIS B 312 PHE 0.009 0.001 PHE A 534 TYR 0.012 0.002 TYR A 226 ARG 0.003 0.000 ARG A 150 *********************** 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 126 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 100 time to evaluate : 0.953 Fit side-chains REVERT: A 60 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6480 (mtt-85) REVERT: A 70 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.6722 (mp10) REVERT: A 463 GLN cc_start: 0.4505 (OUTLIER) cc_final: 0.4047 (pm20) REVERT: A 469 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7070 (mt) REVERT: A 562 TRP cc_start: 0.7979 (m-10) cc_final: 0.7583 (m-10) REVERT: B 60 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6494 (mtt-85) REVERT: B 70 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.6730 (mp10) REVERT: B 463 GLN cc_start: 0.4461 (OUTLIER) cc_final: 0.3957 (pm20) REVERT: B 562 TRP cc_start: 0.7976 (m-10) cc_final: 0.7580 (m-10) outliers start: 26 outliers final: 12 residues processed: 122 average time/residue: 0.2539 time to fit residues: 39.9235 Evaluate side-chains 114 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 345 MET 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 345 MET Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 604 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8218 Z= 0.183 Angle : 0.508 6.492 11164 Z= 0.252 Chirality : 0.041 0.158 1260 Planarity : 0.004 0.033 1380 Dihedral : 3.747 22.503 1084 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.46 % Allowed : 14.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.27), residues: 998 helix: 1.78 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 1.37 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 247 HIS 0.002 0.001 HIS A 531 PHE 0.010 0.001 PHE A 534 TYR 0.009 0.001 TYR A 103 ARG 0.002 0.000 ARG B 113 *********************** 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 123 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 0.950 Fit side-chains REVERT: A 70 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.6703 (mp10) REVERT: A 187 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6519 (mt0) REVERT: A 463 GLN cc_start: 0.4530 (OUTLIER) cc_final: 0.4051 (pm20) REVERT: A 469 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6959 (mt) REVERT: A 473 MET cc_start: 0.8240 (mtm) cc_final: 0.8023 (ptp) REVERT: B 70 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.6699 (mp10) REVERT: B 187 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.6586 (mt0) REVERT: B 463 GLN cc_start: 0.4492 (OUTLIER) cc_final: 0.3985 (pm20) outliers start: 21 outliers final: 8 residues processed: 119 average time/residue: 0.2399 time to fit residues: 37.5998 Evaluate side-chains 113 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 187 GLN 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.0770 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 26 optimal weight: 0.0030 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.5752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8218 Z= 0.155 Angle : 0.497 6.333 11164 Z= 0.246 Chirality : 0.041 0.155 1260 Planarity : 0.005 0.051 1380 Dihedral : 3.678 21.764 1084 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.04 % Allowed : 13.58 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.27), residues: 998 helix: 2.06 (0.19), residues: 726 sheet: None (None), residues: 0 loop : 1.04 (0.42), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 247 HIS 0.001 0.000 HIS A 312 PHE 0.010 0.001 PHE B 534 TYR 0.008 0.001 TYR B 22 ARG 0.007 0.000 ARG B 60 *********************** 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 133 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.6580 (mp10) REVERT: A 187 GLN cc_start: 0.6973 (OUTLIER) cc_final: 0.6540 (mt0) REVERT: A 189 LEU cc_start: 0.7826 (mt) cc_final: 0.7617 (mt) REVERT: A 219 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7929 (mmm-85) REVERT: A 463 GLN cc_start: 0.4460 (OUTLIER) cc_final: 0.4037 (pm20) REVERT: A 469 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7088 (mt) REVERT: B 70 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.6587 (mp10) REVERT: B 187 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.6536 (mt0) REVERT: B 219 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7931 (mmm-85) REVERT: B 463 GLN cc_start: 0.4468 (OUTLIER) cc_final: 0.3997 (pm20) outliers start: 26 outliers final: 14 residues processed: 126 average time/residue: 0.2354 time to fit residues: 39.0028 Evaluate side-chains 125 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 219 ARG Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 234 LEU 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 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 219 ARG Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 604 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 0.0370 chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8218 Z= 0.184 Angle : 0.513 6.318 11164 Z= 0.255 Chirality : 0.041 0.162 1260 Planarity : 0.005 0.036 1380 Dihedral : 3.680 22.290 1084 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.93 % Allowed : 15.46 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.27), residues: 998 helix: 1.97 (0.19), residues: 728 sheet: None (None), residues: 0 loop : 1.13 (0.43), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 247 HIS 0.001 0.001 HIS A 531 PHE 0.023 0.001 PHE A 310 TYR 0.009 0.001 TYR B 103 ARG 0.002 0.000 ARG A 184 *********************** 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 135 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 0.892 Fit side-chains REVERT: A 70 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.6561 (mp10) REVERT: A 157 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8136 (mm-30) REVERT: A 187 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6520 (mt0) REVERT: A 219 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7976 (mmm-85) REVERT: A 463 GLN cc_start: 0.4463 (OUTLIER) cc_final: 0.4001 (pm20) REVERT: A 469 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7041 (mt) REVERT: B 70 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.6567 (mp10) REVERT: B 157 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8137 (mm-30) REVERT: B 187 GLN cc_start: 0.6940 (OUTLIER) cc_final: 0.6499 (mt0) REVERT: B 219 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7976 (mmm-85) REVERT: B 463 GLN cc_start: 0.4552 (OUTLIER) cc_final: 0.4008 (pm20) outliers start: 25 outliers final: 12 residues processed: 131 average time/residue: 0.2253 time to fit residues: 39.0472 Evaluate side-chains 126 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 469 LEU Chi-restraints excluded: chain A residue 561 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8218 Z= 0.193 Angle : 0.515 6.422 11164 Z= 0.256 Chirality : 0.042 0.163 1260 Planarity : 0.004 0.039 1380 Dihedral : 3.733 23.568 1084 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.04 % Allowed : 16.74 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.27), residues: 998 helix: 1.91 (0.19), residues: 730 sheet: None (None), residues: 0 loop : 1.04 (0.43), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 247 HIS 0.002 0.001 HIS A 531 PHE 0.011 0.001 PHE A 298 TYR 0.009 0.001 TYR A 103 ARG 0.001 0.000 ARG B 587 *********************** 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 132 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.6601 (mp10) REVERT: A 187 GLN cc_start: 0.6971 (OUTLIER) cc_final: 0.6530 (mt0) REVERT: A 219 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8004 (mmm-85) REVERT: A 463 GLN cc_start: 0.4552 (OUTLIER) cc_final: 0.4059 (pm20) REVERT: B 70 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.6605 (mp10) REVERT: B 187 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6545 (mt0) REVERT: B 219 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7996 (mmm-85) REVERT: B 463 GLN cc_start: 0.4565 (OUTLIER) cc_final: 0.4005 (pm20) outliers start: 26 outliers final: 13 residues processed: 127 average time/residue: 0.2286 time to fit residues: 38.4251 Evaluate side-chains 125 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 535 VAL Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 96 optimal weight: 0.0870 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8218 Z= 0.148 Angle : 0.485 6.357 11164 Z= 0.242 Chirality : 0.040 0.153 1260 Planarity : 0.004 0.040 1380 Dihedral : 3.632 22.104 1084 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.58 % Allowed : 17.21 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.27), residues: 998 helix: 2.01 (0.19), residues: 730 sheet: None (None), residues: 0 loop : 1.10 (0.43), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 247 HIS 0.001 0.000 HIS A 312 PHE 0.030 0.001 PHE A 310 TYR 0.008 0.001 TYR B 103 ARG 0.001 0.000 ARG A 113 *********************** 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 131 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.6567 (mp10) REVERT: A 157 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8098 (mm-30) REVERT: A 187 GLN cc_start: 0.6968 (OUTLIER) cc_final: 0.6554 (mt0) REVERT: A 219 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7954 (mmm-85) REVERT: A 363 MET cc_start: 0.6557 (mtm) cc_final: 0.4916 (mmp) REVERT: A 463 GLN cc_start: 0.4399 (OUTLIER) cc_final: 0.3931 (pm20) REVERT: B 70 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.6570 (mp10) REVERT: B 157 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8103 (mm-30) REVERT: B 187 GLN cc_start: 0.6929 (OUTLIER) cc_final: 0.6529 (mt0) REVERT: B 219 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7952 (mmm-85) REVERT: B 363 MET cc_start: 0.6586 (mtm) cc_final: 0.4841 (mmp) REVERT: B 463 GLN cc_start: 0.4373 (OUTLIER) cc_final: 0.3910 (pm20) REVERT: B 573 MET cc_start: 0.7607 (mmm) cc_final: 0.7112 (mtp) outliers start: 22 outliers final: 10 residues processed: 127 average time/residue: 0.2259 time to fit residues: 37.8690 Evaluate side-chains 125 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 87 optimal weight: 0.0030 chunk 92 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3006 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= 0.149 Angle : 0.491 6.275 11164 Z= 0.244 Chirality : 0.040 0.153 1260 Planarity : 0.004 0.042 1380 Dihedral : 3.601 22.264 1084 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.46 % Allowed : 17.21 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.27), residues: 998 helix: 1.92 (0.19), residues: 742 sheet: None (None), residues: 0 loop : 1.32 (0.44), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 247 HIS 0.001 0.000 HIS A 312 PHE 0.013 0.001 PHE A 570 TYR 0.007 0.001 TYR B 103 ARG 0.002 0.000 ARG A 522 *********************** 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 133 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.6607 (mp10) REVERT: A 187 GLN cc_start: 0.6949 (OUTLIER) cc_final: 0.6540 (mt0) REVERT: A 219 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7950 (mmm-85) REVERT: A 363 MET cc_start: 0.6633 (mtm) cc_final: 0.5002 (mmp) REVERT: A 463 GLN cc_start: 0.4428 (OUTLIER) cc_final: 0.3978 (pm20) REVERT: B 70 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.6622 (mp10) REVERT: B 187 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6543 (mt0) REVERT: B 219 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7947 (mmm-85) REVERT: B 463 GLN cc_start: 0.4436 (OUTLIER) cc_final: 0.3980 (pm20) REVERT: B 573 MET cc_start: 0.7600 (mmm) cc_final: 0.7135 (mtp) outliers start: 21 outliers final: 12 residues processed: 130 average time/residue: 0.2316 time to fit residues: 39.8712 Evaluate side-chains 128 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3122 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= 0.161 Angle : 0.509 8.144 11164 Z= 0.251 Chirality : 0.041 0.156 1260 Planarity : 0.004 0.043 1380 Dihedral : 3.609 22.125 1084 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.46 % Allowed : 17.33 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.27), residues: 998 helix: 1.90 (0.19), residues: 742 sheet: None (None), residues: 0 loop : 1.29 (0.43), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 247 HIS 0.001 0.000 HIS A 312 PHE 0.023 0.001 PHE A 310 TYR 0.006 0.001 TYR B 103 ARG 0.004 0.000 ARG A 522 *********************** 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 fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.6596 (mp10) REVERT: A 157 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8147 (mm-30) REVERT: A 187 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.6550 (mt0) REVERT: A 219 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7955 (mmm-85) REVERT: A 363 MET cc_start: 0.6573 (mtm) cc_final: 0.4967 (mmp) REVERT: A 463 GLN cc_start: 0.4474 (OUTLIER) cc_final: 0.4011 (pm20) REVERT: B 70 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.6595 (mp10) REVERT: B 157 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8144 (mm-30) REVERT: B 187 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6560 (mt0) REVERT: B 219 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7952 (mmm-85) REVERT: B 463 GLN cc_start: 0.4429 (OUTLIER) cc_final: 0.3974 (pm20) outliers start: 21 outliers final: 12 residues processed: 128 average time/residue: 0.2173 time to fit residues: 37.3452 Evaluate side-chains 129 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 0.0970 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 0.0040 chunk 24 optimal weight: 0.9980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8218 Z= 0.153 Angle : 0.506 8.542 11164 Z= 0.251 Chirality : 0.040 0.152 1260 Planarity : 0.004 0.043 1380 Dihedral : 3.590 22.016 1084 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.22 % Allowed : 17.45 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.27), residues: 998 helix: 2.05 (0.19), residues: 730 sheet: None (None), residues: 0 loop : 1.08 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 247 HIS 0.001 0.000 HIS A 312 PHE 0.013 0.001 PHE B 570 TYR 0.006 0.001 TYR B 22 ARG 0.002 0.000 ARG A 522 ********************** 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 133 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8133 (mm-30) REVERT: A 187 GLN cc_start: 0.6957 (OUTLIER) cc_final: 0.6546 (mt0) REVERT: A 219 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7944 (mmm-85) REVERT: A 222 ARG cc_start: 0.7406 (ptp-110) cc_final: 0.7131 (mtm-85) REVERT: A 363 MET cc_start: 0.6583 (mtm) cc_final: 0.4932 (mmp) REVERT: A 463 GLN cc_start: 0.4473 (OUTLIER) cc_final: 0.4013 (pm20) REVERT: A 573 MET cc_start: 0.7626 (mmm) cc_final: 0.7304 (mtp) REVERT: B 157 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8128 (mm-30) REVERT: B 187 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6558 (mt0) REVERT: B 219 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7941 (mmm-85) REVERT: B 222 ARG cc_start: 0.7408 (ptp-110) cc_final: 0.7132 (mtm-85) REVERT: B 308 TYR cc_start: 0.8078 (m-10) cc_final: 0.7491 (m-80) REVERT: B 463 GLN cc_start: 0.4422 (OUTLIER) cc_final: 0.3973 (pm20) REVERT: B 573 MET cc_start: 0.7614 (mmm) cc_final: 0.7192 (mtp) outliers start: 19 outliers final: 11 residues processed: 130 average time/residue: 0.2361 time to fit residues: 40.5796 Evaluate side-chains 130 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.155936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.125081 restraints weight = 9704.810| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.12 r_work: 0.3120 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8218 Z= 0.171 Angle : 0.521 8.629 11164 Z= 0.258 Chirality : 0.041 0.157 1260 Planarity : 0.004 0.043 1380 Dihedral : 3.593 21.695 1084 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.11 % Allowed : 17.10 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.27), residues: 998 helix: 2.01 (0.19), residues: 730 sheet: None (None), residues: 0 loop : 1.05 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 247 HIS 0.002 0.000 HIS B 593 PHE 0.013 0.001 PHE A 570 TYR 0.006 0.001 TYR A 495 ARG 0.002 0.000 ARG B 522 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1882.73 seconds wall clock time: 34 minutes 5.84 seconds (2045.84 seconds total)