Starting phenix.real_space_refine on Mon Sep 23 20:07:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xly_22252/09_2024/6xly_22252.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xly_22252/09_2024/6xly_22252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xly_22252/09_2024/6xly_22252.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xly_22252/09_2024/6xly_22252.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xly_22252/09_2024/6xly_22252.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xly_22252/09_2024/6xly_22252.cif" } resolution = 3.1 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 9 5.16 5 C 3230 2.51 5 N 912 2.21 5 O 959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5111 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5110 Classifications: {'peptide': 646} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 616} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.84, per 1000 atoms: 0.75 Number of scatterers: 5111 At special positions: 0 Unit cell: (78.662, 89.292, 87.166, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 9 16.00 O 959 8.00 N 912 7.00 C 3230 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: 1.76 Conformation dependent library (CDL) restraints added in 900.6 milliseconds 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1186 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 3 sheets defined 58.4% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 23 through 29 removed outlier: 3.863A pdb=" N VAL A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 56 through 68 removed outlier: 3.689A pdb=" N ARG A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 removed outlier: 3.521A pdb=" N LEU A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 97 Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.592A pdb=" N GLU A 104 " --> pdb=" O PRO A 100 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 127 Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.929A pdb=" N TYR A 163 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 176 removed outlier: 3.605A pdb=" N LEU A 173 " --> pdb=" O HIS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 189 removed outlier: 3.631A pdb=" N ARG A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 210 removed outlier: 3.611A pdb=" N VAL A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 220 removed outlier: 3.596A pdb=" N ARG A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 238 removed outlier: 3.511A pdb=" N GLN A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 removed outlier: 3.613A pdb=" N TRP A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.554A pdb=" N VAL A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 295 Processing helix chain 'A' and resid 296 through 299 removed outlier: 3.958A pdb=" N LEU A 299 " --> pdb=" O ALA A 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 300 through 312 removed outlier: 3.662A pdb=" N GLU A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.592A pdb=" N SER A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 345 removed outlier: 3.520A pdb=" N VAL A 340 " --> pdb=" O MET A 336 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 374 removed outlier: 3.960A pdb=" N THR A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 360 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 372 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 392 removed outlier: 3.529A pdb=" N GLN A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 432 removed outlier: 3.677A pdb=" N ALA A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 486 Processing helix chain 'A' and resid 486 through 497 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.764A pdb=" N LYS A 505 " --> pdb=" O GLN A 502 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 506 " --> pdb=" O GLY A 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 502 through 506' Processing helix chain 'A' and resid 517 through 528 Processing helix chain 'A' and resid 529 through 536 removed outlier: 4.065A pdb=" N GLU A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 removed outlier: 4.158A pdb=" N ASP A 545 " --> pdb=" O ASP A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 580 removed outlier: 3.535A pdb=" N ASN A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY A 563 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A 570 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 601 removed outlier: 4.067A pdb=" N PHE A 597 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 removed outlier: 4.020A pdb=" N ILE A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 630 removed outlier: 3.792A pdb=" N CYS A 629 " --> pdb=" O PRO A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 644 removed outlier: 4.134A pdb=" N TYR A 640 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A 641 " --> pdb=" O ASP A 637 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 139 removed outlier: 8.212A pdb=" N TYR A 147 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N VAL A 261 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL A 149 " --> pdb=" O VAL A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 394 through 398 removed outlier: 3.805A pdb=" N ILE A 462 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR A 454 " --> pdb=" O VAL A 463 " (cutoff:3.500A) 205 hydrogen bonds defined for protein. 603 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.47 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1378 1.33 - 1.45: 1056 1.45 - 1.57: 2791 1.57 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 5241 Sorted by residual: bond pdb=" N VAL A 544 " pdb=" CA VAL A 544 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.83e+00 bond pdb=" N HIS A 546 " pdb=" CA HIS A 546 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.29e-02 6.01e+03 7.56e+00 bond pdb=" N LEU A 543 " pdb=" CA LEU A 543 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.32e-02 5.74e+03 7.02e+00 bond pdb=" N THR A 517 " pdb=" CA THR A 517 " ideal model delta sigma weight residual 1.452 1.485 -0.033 1.25e-02 6.40e+03 6.93e+00 bond pdb=" N TYR A 538 " pdb=" CA TYR A 538 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.80e+00 ... (remaining 5236 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 6862 2.22 - 4.44: 242 4.44 - 6.66: 23 6.66 - 8.88: 7 8.88 - 11.10: 3 Bond angle restraints: 7137 Sorted by residual: angle pdb=" N ILE A 603 " pdb=" CA ILE A 603 " pdb=" C ILE A 603 " ideal model delta sigma weight residual 112.83 109.07 3.76 9.90e-01 1.02e+00 1.44e+01 angle pdb=" CA PRO A 177 " pdb=" N PRO A 177 " pdb=" CD PRO A 177 " ideal model delta sigma weight residual 112.00 106.95 5.05 1.40e+00 5.10e-01 1.30e+01 angle pdb=" C ASP A 440 " pdb=" N ARG A 441 " pdb=" CA ARG A 441 " ideal model delta sigma weight residual 123.05 128.63 -5.58 1.57e+00 4.06e-01 1.26e+01 angle pdb=" C ASP A 140 " pdb=" N SER A 141 " pdb=" CA SER A 141 " ideal model delta sigma weight residual 123.91 129.64 -5.73 1.66e+00 3.63e-01 1.19e+01 angle pdb=" C ASP A 143 " pdb=" N SER A 144 " pdb=" CA SER A 144 " ideal model delta sigma weight residual 123.05 128.42 -5.37 1.57e+00 4.06e-01 1.17e+01 ... (remaining 7132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.36: 2609 15.36 - 30.71: 340 30.71 - 46.07: 87 46.07 - 61.42: 16 61.42 - 76.78: 11 Dihedral angle restraints: 3063 sinusoidal: 1208 harmonic: 1855 Sorted by residual: dihedral pdb=" CA SER A 623 " pdb=" C SER A 623 " pdb=" N PRO A 624 " pdb=" CA PRO A 624 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ARG A 146 " pdb=" C ARG A 146 " pdb=" N TYR A 147 " pdb=" CA TYR A 147 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA PHE A 627 " pdb=" C PHE A 627 " pdb=" N ARG A 628 " pdb=" CA ARG A 628 " ideal model delta harmonic sigma weight residual 180.00 161.03 18.97 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 3060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 573 0.059 - 0.117: 154 0.117 - 0.176: 23 0.176 - 0.235: 3 0.235 - 0.293: 1 Chirality restraints: 754 Sorted by residual: chirality pdb=" CB VAL A 619 " pdb=" CA VAL A 619 " pdb=" CG1 VAL A 619 " pdb=" CG2 VAL A 619 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB VAL A 149 " pdb=" CA VAL A 149 " pdb=" CG1 VAL A 149 " pdb=" CG2 VAL A 149 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA TYR A 176 " pdb=" N TYR A 176 " pdb=" C TYR A 176 " pdb=" CB TYR A 176 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 751 not shown) Planarity restraints: 951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 623 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO A 624 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 624 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 624 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 399 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO A 400 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 400 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 400 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 99 " -0.045 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO A 100 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 100 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 100 " -0.038 5.00e-02 4.00e+02 ... (remaining 948 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1796 2.85 - 3.36: 4284 3.36 - 3.87: 8802 3.87 - 4.39: 10549 4.39 - 4.90: 17508 Nonbonded interactions: 42939 Sorted by model distance: nonbonded pdb=" OE1 GLU A 104 " pdb=" OH TYR A 417 " model vdw 2.336 3.040 nonbonded pdb=" O SER A 154 " pdb=" OG SER A 154 " model vdw 2.359 3.040 nonbonded pdb=" O GLU A 104 " pdb=" OG1 THR A 107 " model vdw 2.364 3.040 nonbonded pdb=" O ARG A 634 " pdb=" OH TYR A 640 " model vdw 2.371 3.040 nonbonded pdb=" OG1 THR A 646 " pdb=" OD1 ASP A 648 " model vdw 2.372 3.040 ... (remaining 42934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 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: 0.000 Check model and map are aligned: 0.410 Set scattering table: 0.000 Process input model: 17.560 Find NCS groups from input model: 0.080 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.006 0.076 5241 Z= 0.420 Angle : 0.950 11.095 7137 Z= 0.557 Chirality : 0.054 0.293 754 Planarity : 0.008 0.072 951 Dihedral : 15.473 76.777 1877 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.97 % Allowed : 7.78 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -5.77 (0.21), residues: 644 helix: -4.70 (0.11), residues: 363 sheet: -0.08 (1.80), residues: 10 loop : -2.41 (0.27), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 286 HIS 0.012 0.002 HIS A 213 PHE 0.016 0.002 PHE A 241 TYR 0.021 0.002 TYR A 399 ARG 0.004 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 75 average time/residue: 0.2558 time to fit residues: 23.6359 Evaluate side-chains 33 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.0470 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 125 GLN A 334 ASN A 421 GLN A 452 ASN A 456 ASN A 483 ASN A 602 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5241 Z= 0.193 Angle : 0.551 6.215 7137 Z= 0.298 Chirality : 0.042 0.290 754 Planarity : 0.006 0.047 951 Dihedral : 4.756 20.492 720 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.97 % Allowed : 11.48 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -3.91 (0.25), residues: 644 helix: -2.84 (0.19), residues: 381 sheet: -2.18 (0.91), residues: 24 loop : -1.85 (0.32), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 286 HIS 0.003 0.001 HIS A 428 PHE 0.019 0.002 PHE A 627 TYR 0.007 0.001 TYR A 311 ARG 0.004 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 49 average time/residue: 0.1905 time to fit residues: 12.5209 Evaluate side-chains 32 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5241 Z= 0.213 Angle : 0.498 5.243 7137 Z= 0.264 Chirality : 0.041 0.212 754 Planarity : 0.004 0.043 951 Dihedral : 4.202 19.310 720 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.72 % Allowed : 11.87 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.22 (0.29), residues: 644 helix: -1.30 (0.24), residues: 380 sheet: -2.53 (0.80), residues: 24 loop : -1.36 (0.34), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 600 HIS 0.004 0.001 HIS A 213 PHE 0.013 0.001 PHE A 652 TYR 0.008 0.001 TYR A 136 ARG 0.003 0.000 ARG A 521 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 47 average time/residue: 0.1988 time to fit residues: 12.2845 Evaluate side-chains 41 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 603 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 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 421 GLN A 576 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5241 Z= 0.168 Angle : 0.475 7.970 7137 Z= 0.246 Chirality : 0.042 0.305 754 Planarity : 0.004 0.039 951 Dihedral : 3.966 18.372 720 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.92 % Allowed : 12.26 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.24 (0.31), residues: 644 helix: -0.39 (0.26), residues: 380 sheet: -2.68 (0.80), residues: 24 loop : -1.12 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 246 HIS 0.002 0.001 HIS A 493 PHE 0.010 0.001 PHE A 597 TYR 0.006 0.001 TYR A 136 ARG 0.002 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 37 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 47 average time/residue: 0.2008 time to fit residues: 12.3778 Evaluate side-chains 43 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 661 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5241 Z= 0.197 Angle : 0.485 7.113 7137 Z= 0.250 Chirality : 0.042 0.263 754 Planarity : 0.004 0.038 951 Dihedral : 3.896 23.270 720 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.11 % Allowed : 13.81 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.78 (0.32), residues: 644 helix: -0.03 (0.27), residues: 387 sheet: -2.78 (0.80), residues: 24 loop : -0.89 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 600 HIS 0.002 0.001 HIS A 36 PHE 0.013 0.001 PHE A 597 TYR 0.006 0.001 TYR A 136 ARG 0.002 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 34 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 44 average time/residue: 0.1956 time to fit residues: 11.3130 Evaluate side-chains 45 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 33 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 661 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.7896 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5241 Z= 0.177 Angle : 0.481 6.054 7137 Z= 0.246 Chirality : 0.041 0.189 754 Planarity : 0.003 0.036 951 Dihedral : 3.783 21.687 720 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.53 % Allowed : 14.40 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.37 (0.33), residues: 644 helix: 0.35 (0.27), residues: 386 sheet: -2.97 (0.71), residues: 24 loop : -0.77 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 246 HIS 0.003 0.001 HIS A 102 PHE 0.011 0.001 PHE A 597 TYR 0.006 0.001 TYR A 136 ARG 0.001 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 36 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 44 average time/residue: 0.1934 time to fit residues: 11.2916 Evaluate side-chains 44 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 661 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 0.0370 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 chunk 38 optimal weight: 0.0020 chunk 37 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.3866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5241 Z= 0.151 Angle : 0.492 9.567 7137 Z= 0.246 Chirality : 0.042 0.311 754 Planarity : 0.003 0.036 951 Dihedral : 3.702 18.949 720 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.36 % Allowed : 15.37 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.15 (0.33), residues: 644 helix: 0.52 (0.27), residues: 386 sheet: -2.92 (0.66), residues: 24 loop : -0.66 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 377 HIS 0.003 0.001 HIS A 493 PHE 0.009 0.001 PHE A 597 TYR 0.008 0.001 TYR A 538 ARG 0.001 0.000 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 40 average time/residue: 0.2040 time to fit residues: 10.7523 Evaluate side-chains 36 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 409 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 48 optimal weight: 0.0870 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS A 456 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5241 Z= 0.162 Angle : 0.484 7.588 7137 Z= 0.246 Chirality : 0.041 0.266 754 Planarity : 0.003 0.034 951 Dihedral : 3.579 15.301 720 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.56 % Allowed : 15.56 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.00 (0.33), residues: 644 helix: 0.63 (0.27), residues: 386 sheet: -2.94 (0.68), residues: 22 loop : -0.60 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 246 HIS 0.003 0.001 HIS A 493 PHE 0.009 0.001 PHE A 597 TYR 0.010 0.001 TYR A 538 ARG 0.002 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 38 average time/residue: 0.2517 time to fit residues: 12.9547 Evaluate side-chains 39 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 31 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 661 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 60 optimal weight: 0.0030 chunk 28 optimal weight: 0.6980 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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: 0.7879 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5241 Z= 0.158 Angle : 0.471 7.397 7137 Z= 0.240 Chirality : 0.041 0.262 754 Planarity : 0.003 0.034 951 Dihedral : 3.571 15.037 720 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.56 % Allowed : 15.56 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.11 (0.33), residues: 644 helix: 0.71 (0.27), residues: 389 sheet: -2.83 (0.67), residues: 22 loop : -0.56 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 246 HIS 0.003 0.001 HIS A 179 PHE 0.009 0.001 PHE A 597 TYR 0.007 0.001 TYR A 538 ARG 0.001 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 39 average time/residue: 0.2689 time to fit residues: 14.2502 Evaluate side-chains 40 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 409 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5241 Z= 0.218 Angle : 0.520 10.707 7137 Z= 0.263 Chirality : 0.044 0.383 754 Planarity : 0.003 0.033 951 Dihedral : 3.609 16.948 720 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.56 % Allowed : 15.37 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.20 (0.33), residues: 644 helix: 0.76 (0.27), residues: 389 sheet: -2.73 (0.67), residues: 24 loop : -0.47 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 600 HIS 0.004 0.001 HIS A 179 PHE 0.009 0.001 PHE A 597 TYR 0.009 0.001 TYR A 368 ARG 0.002 0.000 ARG A 201 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 31 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 38 average time/residue: 0.2248 time to fit residues: 11.3101 Evaluate side-chains 38 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 30 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 661 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 0.0170 chunk 52 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.3194 r_free = 0.3194 target = 0.065321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.054014 restraints weight = 15601.030| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 4.21 r_work: 0.2782 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5241 Z= 0.158 Angle : 0.495 11.065 7137 Z= 0.249 Chirality : 0.043 0.351 754 Planarity : 0.003 0.034 951 Dihedral : 3.629 18.927 720 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.56 % Allowed : 15.56 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.29 (0.33), residues: 644 helix: 0.83 (0.27), residues: 389 sheet: -2.55 (1.04), residues: 12 loop : -0.58 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 377 HIS 0.004 0.001 HIS A 493 PHE 0.010 0.001 PHE A 597 TYR 0.011 0.001 TYR A 368 ARG 0.002 0.000 ARG A 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1474.28 seconds wall clock time: 27 minutes 17.14 seconds (1637.14 seconds total)