Starting phenix.real_space_refine on Wed Feb 12 13:51:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tem_41191/02_2025/8tem_41191.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tem_41191/02_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_41191/02_2025/8tem_41191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tem_41191/02_2025/8tem_41191.map" model { file = "/net/cci-nas-00/data/ceres_data/8tem_41191/02_2025/8tem_41191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tem_41191/02_2025/8tem_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 7.32, per 1000 atoms: 0.92 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: 1.96 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: 0.85 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: 2.38 Time building geometry restraints manager: 2.31 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: 0.04 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: 2.220 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 23.620 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.450 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.831 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: 0.2501 time to fit residues: 36.6615 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 : 0.890 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.156967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.124842 restraints weight = 9624.840| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.14 r_work: 0.3174 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.834 Fit side-chains REVERT: A 60 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6521 (mtt-85) REVERT: A 70 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.6774 (mp10) REVERT: A 463 GLN cc_start: 0.4498 (OUTLIER) cc_final: 0.4039 (pm20) REVERT: A 469 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6991 (mt) REVERT: A 562 TRP cc_start: 0.8074 (m-10) cc_final: 0.7695 (m-10) REVERT: B 60 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6517 (mtt-85) REVERT: B 70 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.6782 (mp10) REVERT: B 463 GLN cc_start: 0.4433 (OUTLIER) cc_final: 0.3939 (pm20) REVERT: B 562 TRP cc_start: 0.8079 (m-10) cc_final: 0.7700 (m-10) outliers start: 26 outliers final: 12 residues processed: 122 average time/residue: 0.2635 time to fit residues: 41.4897 Evaluate side-chains 114 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 19 optimal weight: 0.5980 chunk 43 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.158986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126860 restraints weight = 9729.015| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.16 r_work: 0.3206 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1976 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= 0.158 Angle : 0.494 6.330 11164 Z= 0.245 Chirality : 0.040 0.153 1260 Planarity : 0.004 0.032 1380 Dihedral : 3.704 21.918 1084 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.22 % Allowed : 14.87 % Favored : 82.90 % 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: 2.52 (0.27), residues: 998 helix: 1.84 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 1.44 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 247 HIS 0.002 0.001 HIS A 531 PHE 0.011 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 121 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.870 Fit side-chains REVERT: A 70 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.6729 (mp10) REVERT: A 187 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6603 (mt0) REVERT: A 463 GLN cc_start: 0.4472 (OUTLIER) cc_final: 0.4052 (pm20) REVERT: A 469 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6863 (mt) REVERT: B 70 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.6728 (mp10) REVERT: B 187 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.6693 (mt0) REVERT: B 463 GLN cc_start: 0.4461 (OUTLIER) cc_final: 0.3984 (pm20) outliers start: 19 outliers final: 6 residues processed: 117 average time/residue: 0.2437 time to fit residues: 37.2160 Evaluate side-chains 112 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 34 optimal weight: 0.0980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.157531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.125877 restraints weight = 9756.053| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.18 r_work: 0.3181 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2362 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= 0.169 Angle : 0.508 6.292 11164 Z= 0.252 Chirality : 0.041 0.160 1260 Planarity : 0.005 0.041 1380 Dihedral : 3.675 22.051 1084 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.04 % Allowed : 13.23 % Favored : 83.72 % 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: 726 sheet: None (None), residues: 0 loop : 1.09 (0.42), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 247 HIS 0.001 0.000 HIS B 531 PHE 0.010 0.001 PHE A 267 TYR 0.009 0.001 TYR A 103 ARG 0.002 0.000 ARG A 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 to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.6680 (mp10) REVERT: A 157 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8194 (mm-30) REVERT: A 187 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6657 (mt0) REVERT: A 219 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8064 (mmm-85) REVERT: A 463 GLN cc_start: 0.4404 (OUTLIER) cc_final: 0.3993 (pm20) REVERT: B 70 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.6700 (mp10) REVERT: B 157 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8218 (mm-30) REVERT: B 187 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.6648 (mt0) REVERT: B 219 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8073 (mmm-85) REVERT: B 463 GLN cc_start: 0.4449 (OUTLIER) cc_final: 0.3983 (pm20) outliers start: 26 outliers final: 14 residues processed: 126 average time/residue: 0.2403 time to fit residues: 40.1226 Evaluate side-chains 124 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 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 28 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 68 optimal weight: 0.0980 chunk 88 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 71 optimal weight: 0.0370 chunk 8 optimal weight: 1.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.158121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.126378 restraints weight = 9645.020| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.17 r_work: 0.3191 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2566 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= 0.146 Angle : 0.482 6.250 11164 Z= 0.240 Chirality : 0.040 0.153 1260 Planarity : 0.004 0.036 1380 Dihedral : 3.581 21.068 1084 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.46 % Allowed : 15.57 % Favored : 81.97 % 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: 2.78 (0.27), residues: 998 helix: 2.14 (0.19), residues: 726 sheet: None (None), residues: 0 loop : 1.22 (0.42), residues: 272 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 0.029 0.001 PHE A 310 TYR 0.009 0.001 TYR B 22 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 129 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.857 Fit side-chains REVERT: A 70 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.6718 (mp10) REVERT: A 187 GLN cc_start: 0.6996 (OUTLIER) cc_final: 0.6603 (mt0) REVERT: A 219 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8038 (mmm-85) REVERT: B 70 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.6728 (mp10) REVERT: B 119 ASP cc_start: 0.6655 (OUTLIER) cc_final: 0.6370 (m-30) REVERT: B 187 GLN cc_start: 0.6993 (OUTLIER) cc_final: 0.6595 (mt0) REVERT: B 219 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8046 (mmm-85) REVERT: B 463 GLN cc_start: 0.4541 (OUTLIER) cc_final: 0.4102 (pm20) REVERT: B 575 MET cc_start: 0.7096 (tpp) cc_final: 0.6633 (mpp) outliers start: 21 outliers final: 11 residues processed: 123 average time/residue: 0.2207 time to fit residues: 36.1693 Evaluate side-chains 123 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 234 LEU 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 234 LEU Chi-restraints excluded: chain B residue 463 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 68 optimal weight: 0.0970 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.157378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.125800 restraints weight = 9786.819| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.16 r_work: 0.3153 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2723 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= 0.159 Angle : 0.494 6.190 11164 Z= 0.244 Chirality : 0.041 0.158 1260 Planarity : 0.004 0.039 1380 Dihedral : 3.600 22.252 1084 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.58 % Allowed : 16.63 % 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: 2.70 (0.27), residues: 998 helix: 2.08 (0.19), residues: 730 sheet: None (None), residues: 0 loop : 1.19 (0.43), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 247 HIS 0.001 0.000 HIS B 531 PHE 0.011 0.001 PHE A 570 TYR 0.008 0.001 TYR B 103 ARG 0.001 0.000 ARG A 153 *********************** 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 to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.797 Fit side-chains REVERT: A 70 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.6720 (mp10) REVERT: A 119 ASP cc_start: 0.6729 (OUTLIER) cc_final: 0.6452 (m-30) REVERT: A 157 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8171 (mm-30) REVERT: A 187 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6652 (mt0) REVERT: A 219 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8082 (mmm-85) REVERT: A 463 GLN cc_start: 0.4420 (OUTLIER) cc_final: 0.4001 (pm20) REVERT: B 70 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.6677 (mp10) REVERT: B 119 ASP cc_start: 0.6726 (OUTLIER) cc_final: 0.6451 (m-30) REVERT: B 157 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8180 (mm-30) REVERT: B 187 GLN cc_start: 0.6981 (OUTLIER) cc_final: 0.6625 (mt0) REVERT: B 219 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8095 (mmm-85) REVERT: B 308 TYR cc_start: 0.8066 (m-10) cc_final: 0.7521 (m-80) REVERT: B 463 GLN cc_start: 0.4467 (OUTLIER) cc_final: 0.4055 (pm20) REVERT: B 575 MET cc_start: 0.7131 (tpp) cc_final: 0.6634 (mpp) outliers start: 22 outliers final: 10 residues processed: 128 average time/residue: 0.2341 time to fit residues: 39.6351 Evaluate side-chains 128 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 561 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 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 = 0.3760 r_free = 0.3760 target = 0.156544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124894 restraints weight = 9836.863| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.11 r_work: 0.3175 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2879 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= 0.164 Angle : 0.496 6.222 11164 Z= 0.246 Chirality : 0.041 0.157 1260 Planarity : 0.004 0.041 1380 Dihedral : 3.613 21.921 1084 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.04 % Allowed : 16.63 % 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: 2.56 (0.27), residues: 998 helix: 1.88 (0.19), residues: 742 sheet: None (None), residues: 0 loop : 1.42 (0.44), 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 531 PHE 0.023 0.001 PHE B 310 TYR 0.008 0.001 TYR A 103 ARG 0.001 0.000 ARG A 18 *********************** 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 135 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.6718 (mp10) REVERT: A 187 GLN cc_start: 0.6993 (OUTLIER) cc_final: 0.6625 (mt0) REVERT: A 219 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8080 (mmm-85) REVERT: A 463 GLN cc_start: 0.4314 (OUTLIER) cc_final: 0.3892 (pm20) REVERT: B 70 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.6680 (mp10) REVERT: B 187 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6606 (mt0) REVERT: B 219 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8084 (mmm-85) REVERT: B 308 TYR cc_start: 0.8093 (m-10) cc_final: 0.7511 (m-80) REVERT: B 463 GLN cc_start: 0.4328 (OUTLIER) cc_final: 0.3907 (pm20) REVERT: B 575 MET cc_start: 0.7190 (tpp) cc_final: 0.6742 (mpp) outliers start: 26 outliers final: 14 residues processed: 130 average time/residue: 0.2320 time to fit residues: 40.0092 Evaluate side-chains 130 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 357 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 14 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.0770 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.156638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.124582 restraints weight = 9886.882| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.18 r_work: 0.3152 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2957 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 : 0.504 7.145 11164 Z= 0.250 Chirality : 0.041 0.155 1260 Planarity : 0.004 0.044 1380 Dihedral : 3.617 22.397 1084 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.58 % Allowed : 16.86 % 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 (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: 2.59 (0.27), residues: 998 helix: 1.90 (0.19), residues: 742 sheet: None (None), residues: 0 loop : 1.43 (0.44), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 247 HIS 0.001 0.000 HIS B 312 PHE 0.014 0.001 PHE A 570 TYR 0.008 0.001 TYR A 103 ARG 0.001 0.000 ARG A 18 *********************** 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 to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.6724 (mp10) REVERT: A 119 ASP cc_start: 0.6720 (OUTLIER) cc_final: 0.6500 (m-30) REVERT: A 157 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8190 (mm-30) REVERT: A 187 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6653 (mt0) REVERT: A 219 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8074 (mmm-85) REVERT: A 222 ARG cc_start: 0.7470 (ptp-110) cc_final: 0.7119 (mtm-85) REVERT: A 463 GLN cc_start: 0.4394 (OUTLIER) cc_final: 0.3955 (pm20) REVERT: B 70 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.6731 (mp10) REVERT: B 119 ASP cc_start: 0.6673 (OUTLIER) cc_final: 0.6441 (m-30) REVERT: B 157 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8180 (mm-30) REVERT: B 187 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.6628 (mt0) REVERT: B 219 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8084 (mmm-85) REVERT: B 222 ARG cc_start: 0.7474 (ptp-110) cc_final: 0.7121 (mtm-85) REVERT: B 308 TYR cc_start: 0.8107 (m-10) cc_final: 0.7523 (m-80) REVERT: B 463 GLN cc_start: 0.4406 (OUTLIER) cc_final: 0.3932 (pm20) REVERT: B 575 MET cc_start: 0.7244 (tpp) cc_final: 0.6953 (tpt) outliers start: 22 outliers final: 12 residues processed: 131 average time/residue: 0.2483 time to fit residues: 42.3935 Evaluate side-chains 131 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 357 VAL 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 357 VAL 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 58 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.156096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.124313 restraints weight = 9947.991| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.17 r_work: 0.3127 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 0.033 8218 Z= 0.171 Angle : 0.513 7.774 11164 Z= 0.254 Chirality : 0.041 0.158 1260 Planarity : 0.004 0.044 1380 Dihedral : 3.637 22.346 1084 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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 (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: 2.00 (0.19), residues: 730 sheet: None (None), residues: 0 loop : 1.15 (0.43), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 247 HIS 0.001 0.000 HIS A 312 PHE 0.025 0.001 PHE A 310 TYR 0.006 0.001 TYR B 495 ARG 0.003 0.000 ARG A 18 *********************** 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 140 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.6804 (mp10) REVERT: A 119 ASP cc_start: 0.6788 (OUTLIER) cc_final: 0.6495 (m-30) REVERT: A 187 GLN cc_start: 0.7028 (OUTLIER) cc_final: 0.6709 (mt0) REVERT: A 219 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8152 (mmm-85) REVERT: A 222 ARG cc_start: 0.7512 (ptp-110) cc_final: 0.7143 (mtm-85) REVERT: A 463 GLN cc_start: 0.4465 (OUTLIER) cc_final: 0.4046 (pm20) REVERT: A 573 MET cc_start: 0.7876 (mmm) cc_final: 0.7517 (mtp) REVERT: B 70 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.6794 (mp10) REVERT: B 119 ASP cc_start: 0.6767 (OUTLIER) cc_final: 0.6482 (m-30) REVERT: B 187 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6675 (mt0) REVERT: B 219 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8149 (mmm-85) REVERT: B 222 ARG cc_start: 0.7501 (ptp-110) cc_final: 0.7141 (mtm-85) REVERT: B 463 GLN cc_start: 0.4460 (OUTLIER) cc_final: 0.4054 (pm20) REVERT: B 569 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7828 (mmt) REVERT: B 573 MET cc_start: 0.7893 (mmm) cc_final: 0.7543 (mtp) REVERT: B 575 MET cc_start: 0.7190 (tpp) cc_final: 0.6865 (tpt) outliers start: 25 outliers final: 12 residues processed: 135 average time/residue: 0.2473 time to fit residues: 43.5068 Evaluate side-chains 136 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 357 VAL 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 357 VAL Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 569 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 68 optimal weight: 0.1980 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.0970 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.157406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.126434 restraints weight = 9751.632| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.13 r_work: 0.3136 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3156 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= 0.149 Angle : 0.500 8.391 11164 Z= 0.248 Chirality : 0.040 0.153 1260 Planarity : 0.004 0.044 1380 Dihedral : 3.591 22.277 1084 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.46 % Allowed : 16.98 % 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 (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: 2.67 (0.27), residues: 998 helix: 2.06 (0.19), residues: 730 sheet: None (None), residues: 0 loop : 1.16 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 247 HIS 0.001 0.000 HIS B 312 PHE 0.029 0.001 PHE A 310 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 139 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.6737 (OUTLIER) cc_final: 0.6515 (m-30) REVERT: A 157 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8242 (mm-30) REVERT: A 187 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6658 (mt0) REVERT: A 219 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8083 (mmm-85) REVERT: A 222 ARG cc_start: 0.7388 (ptp-110) cc_final: 0.7109 (mtm-85) REVERT: A 463 GLN cc_start: 0.4443 (OUTLIER) cc_final: 0.3979 (pm20) REVERT: A 573 MET cc_start: 0.7692 (mmm) cc_final: 0.7414 (mtp) REVERT: B 119 ASP cc_start: 0.6721 (OUTLIER) cc_final: 0.6520 (m-30) REVERT: B 157 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8244 (mm-30) REVERT: B 187 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6621 (mt0) REVERT: B 219 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8080 (mmm-85) REVERT: B 222 ARG cc_start: 0.7449 (ptp-110) cc_final: 0.7161 (mtm-85) REVERT: B 463 GLN cc_start: 0.4425 (OUTLIER) cc_final: 0.3989 (pm20) REVERT: B 573 MET cc_start: 0.7660 (mmm) cc_final: 0.7358 (mtp) REVERT: B 575 MET cc_start: 0.7285 (tpp) cc_final: 0.6995 (tpt) outliers start: 21 outliers final: 12 residues processed: 136 average time/residue: 0.2308 time to fit residues: 41.2206 Evaluate side-chains 133 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 357 VAL Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 561 THR 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 357 VAL 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 19 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 0.0980 chunk 8 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.156001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.124302 restraints weight = 9794.670| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.21 r_work: 0.3148 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3230 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= 0.176 Angle : 0.518 8.430 11164 Z= 0.257 Chirality : 0.041 0.159 1260 Planarity : 0.004 0.044 1380 Dihedral : 3.626 21.712 1084 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.34 % Allowed : 16.98 % 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 (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: 2.61 (0.27), residues: 998 helix: 2.02 (0.19), residues: 730 sheet: None (None), residues: 0 loop : 1.10 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 247 HIS 0.001 0.000 HIS A 312 PHE 0.030 0.001 PHE A 310 TYR 0.007 0.001 TYR B 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: 4102.76 seconds wall clock time: 73 minutes 25.09 seconds (4405.09 seconds total)