Starting phenix.real_space_refine on Tue Feb 13 10:55:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8b_22725/02_2024/7k8b_22725.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8b_22725/02_2024/7k8b_22725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8b_22725/02_2024/7k8b_22725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8b_22725/02_2024/7k8b_22725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8b_22725/02_2024/7k8b_22725.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8b_22725/02_2024/7k8b_22725.pdb" } resolution = 2.94 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 ------------------------------------------------------------------------------- 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= 0.225 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 28 5.16 5 C 3588 2.51 5 N 919 2.21 5 O 1008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 64": "OD1" <-> "OD2" Residue "A PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 145": "OD1" <-> "OD2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5543 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5543 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 37, 'TRANS': 688} Chain breaks: 1 Time building chain proxies: 3.58, per 1000 atoms: 0.65 Number of scatterers: 5543 At special positions: 0 Unit cell: (112.32, 77.76, 76.68, 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 28 16.00 O 1008 8.00 N 919 7.00 C 3588 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1328 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 2 sheets defined 71.3% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 Processing helix chain 'A' and resid 13 through 37 removed outlier: 3.715A pdb=" N VAL A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N SER A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 62 removed outlier: 3.778A pdb=" N ALA A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 101 Processing helix chain 'A' and resid 110 through 114 removed outlier: 3.628A pdb=" N LYS A 113 " --> pdb=" O GLY A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 160 Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 170 through 204 removed outlier: 3.776A pdb=" N LEU A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Proline residue: A 195 - end of helix removed outlier: 3.654A pdb=" N LEU A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 234 Proline residue: A 214 - end of helix Processing helix chain 'A' and resid 241 through 272 removed outlier: 3.532A pdb=" N VAL A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR A 247 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 302 removed outlier: 4.653A pdb=" N ARG A 288 " --> pdb=" O MET A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 309 through 342 removed outlier: 3.644A pdb=" N ILE A 328 " --> pdb=" O MET A 324 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.729A pdb=" N ALA A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 343 through 348' Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.914A pdb=" N ARG A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 418 through 422 removed outlier: 3.827A pdb=" N GLN A 421 " --> pdb=" O PRO A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 449 removed outlier: 3.811A pdb=" N ASP A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 483 Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 525 through 535 Processing helix chain 'A' and resid 549 through 581 removed outlier: 3.748A pdb=" N SER A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A 557 " --> pdb=" O GLU A 553 " (cutoff:3.500A) Proline residue: A 565 - end of helix removed outlier: 3.809A pdb=" N THR A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 612 removed outlier: 3.942A pdb=" N ILE A 590 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 594 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 599 " --> pdb=" O MET A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 628 through 659 removed outlier: 3.946A pdb=" N ILE A 632 " --> pdb=" O MET A 628 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ARG A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG A 658 " --> pdb=" O MET A 654 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU A 659 " --> pdb=" O VAL A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 695 removed outlier: 4.293A pdb=" N ARG A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR A 675 " --> pdb=" O GLY A 671 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ARG A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 680 " --> pdb=" O GLY A 676 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY A 681 " --> pdb=" O ARG A 677 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 695 " --> pdb=" O GLY A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 718 Processing helix chain 'A' and resid 718 through 723 Processing helix chain 'A' and resid 723 through 731 removed outlier: 3.599A pdb=" N LEU A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 736 removed outlier: 3.974A pdb=" N CYS A 735 " --> pdb=" O GLY A 732 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TRP A 736 " --> pdb=" O ASP A 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 732 through 736' Processing helix chain 'A' and resid 739 through 749 removed outlier: 4.526A pdb=" N VAL A 745 " --> pdb=" O TRP A 741 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 137 removed outlier: 3.631A pdb=" N ALA A 71 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 69 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 500 removed outlier: 3.602A pdb=" N LYS A 499 " --> pdb=" O GLN A 517 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 1020 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: 1.61 Time building geometry restraints manager: 2.45 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: 1018 1.33 - 1.45: 1294 1.45 - 1.57: 3288 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 5654 Sorted by residual: bond pdb=" CA SER A 617 " pdb=" C SER A 617 " ideal model delta sigma weight residual 1.523 1.385 0.139 1.30e-02 5.92e+03 1.14e+02 bond pdb=" N SER A 617 " pdb=" CA SER A 617 " ideal model delta sigma weight residual 1.459 1.369 0.090 1.21e-02 6.83e+03 5.52e+01 bond pdb=" CA SER A 617 " pdb=" CB SER A 617 " ideal model delta sigma weight residual 1.528 1.462 0.067 1.56e-02 4.11e+03 1.84e+01 bond pdb=" N PHE A 487 " pdb=" CA PHE A 487 " ideal model delta sigma weight residual 1.455 1.504 -0.049 1.32e-02 5.74e+03 1.38e+01 bond pdb=" CA HIS A 615 " pdb=" C HIS A 615 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.30e-02 5.92e+03 1.30e+01 ... (remaining 5649 not shown) Histogram of bond angle deviations from ideal: 98.84 - 105.88: 155 105.88 - 112.91: 3098 112.91 - 119.95: 2044 119.95 - 126.98: 2326 126.98 - 134.02: 70 Bond angle restraints: 7693 Sorted by residual: angle pdb=" N GLY A 519 " pdb=" CA GLY A 519 " pdb=" C GLY A 519 " ideal model delta sigma weight residual 110.95 124.03 -13.08 1.74e+00 3.30e-01 5.65e+01 angle pdb=" C SER A 617 " pdb=" CA SER A 617 " pdb=" CB SER A 617 " ideal model delta sigma weight residual 110.79 98.84 11.95 1.66e+00 3.63e-01 5.18e+01 angle pdb=" O ASN A 518 " pdb=" C ASN A 518 " pdb=" N GLY A 519 " ideal model delta sigma weight residual 123.46 117.78 5.68 9.90e-01 1.02e+00 3.30e+01 angle pdb=" C ASN A 518 " pdb=" N GLY A 519 " pdb=" CA GLY A 519 " ideal model delta sigma weight residual 122.20 116.94 5.26 9.50e-01 1.11e+00 3.06e+01 angle pdb=" N VAL A 612 " pdb=" CA VAL A 612 " pdb=" C VAL A 612 " ideal model delta sigma weight residual 113.00 106.35 6.65 1.30e+00 5.92e-01 2.62e+01 ... (remaining 7688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3063 17.97 - 35.94: 257 35.94 - 53.90: 46 53.90 - 71.87: 5 71.87 - 89.84: 7 Dihedral angle restraints: 3378 sinusoidal: 1313 harmonic: 2065 Sorted by residual: dihedral pdb=" C SER A 617 " pdb=" N SER A 617 " pdb=" CA SER A 617 " pdb=" CB SER A 617 " ideal model delta harmonic sigma weight residual -122.60 -105.94 -16.66 0 2.50e+00 1.60e-01 4.44e+01 dihedral pdb=" C ARG A 131 " pdb=" N ARG A 131 " pdb=" CA ARG A 131 " pdb=" CB ARG A 131 " ideal model delta harmonic sigma weight residual -122.60 -133.32 10.72 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" N ARG A 131 " pdb=" C ARG A 131 " pdb=" CA ARG A 131 " pdb=" CB ARG A 131 " ideal model delta harmonic sigma weight residual 122.80 132.97 -10.17 0 2.50e+00 1.60e-01 1.65e+01 ... (remaining 3375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 851 0.088 - 0.176: 66 0.176 - 0.265: 0 0.265 - 0.353: 0 0.353 - 0.441: 1 Chirality restraints: 918 Sorted by residual: chirality pdb=" CA ARG A 131 " pdb=" N ARG A 131 " pdb=" C ARG A 131 " pdb=" CB ARG A 131 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CA THR A 488 " pdb=" N THR A 488 " pdb=" C THR A 488 " pdb=" CB THR A 488 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CB VAL A 154 " pdb=" CA VAL A 154 " pdb=" CG1 VAL A 154 " pdb=" CG2 VAL A 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 915 not shown) Planarity restraints: 973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 75 " -0.053 5.00e-02 4.00e+02 8.12e-02 1.06e+01 pdb=" N PRO A 76 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 518 " 0.013 2.00e-02 2.50e+03 2.47e-02 6.10e+00 pdb=" C ASN A 518 " -0.043 2.00e-02 2.50e+03 pdb=" O ASN A 518 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY A 519 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 501 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO A 502 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 502 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 502 " 0.030 5.00e-02 4.00e+02 ... (remaining 970 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 746 2.75 - 3.29: 5879 3.29 - 3.83: 9282 3.83 - 4.36: 10424 4.36 - 4.90: 17760 Nonbonded interactions: 44091 Sorted by model distance: nonbonded pdb=" OD2 ASP A 185 " pdb=" OG SER A 696 " model vdw 2.214 2.440 nonbonded pdb=" C SER A 617 " pdb=" OG SER A 617 " model vdw 2.238 2.616 nonbonded pdb=" OD2 ASP A 45 " pdb=" OG SER A 48 " model vdw 2.268 2.440 nonbonded pdb=" OE1 GLU A 93 " pdb=" N ASN A 162 " model vdw 2.324 2.520 nonbonded pdb=" O LYS A 480 " pdb=" OG1 THR A 483 " model vdw 2.335 2.440 ... (remaining 44086 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: 0.040 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: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 19.960 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 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 : 0.005 0.139 5654 Z= 0.325 Angle : 0.827 13.080 7693 Z= 0.478 Chirality : 0.047 0.441 918 Planarity : 0.006 0.081 973 Dihedral : 14.135 89.841 2050 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.68 % Allowed : 1.18 % Favored : 98.14 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % 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: -0.97 (0.32), residues: 722 helix: -0.08 (0.24), residues: 476 sheet: -1.97 (0.80), residues: 33 loop : -1.47 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 86 HIS 0.004 0.001 HIS A 68 PHE 0.021 0.002 PHE A 241 TYR 0.023 0.002 TYR A 151 ARG 0.004 0.000 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.5061 (tpt) cc_final: 0.4859 (tpt) REVERT: A 117 THR cc_start: 0.7230 (t) cc_final: 0.6295 (m) REVERT: A 229 MET cc_start: 0.6778 (ppp) cc_final: 0.6485 (ppp) REVERT: A 284 MET cc_start: 0.6212 (mmm) cc_final: 0.4911 (mmt) outliers start: 4 outliers final: 1 residues processed: 119 average time/residue: 0.8184 time to fit residues: 103.7426 Evaluate side-chains 106 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 617 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5654 Z= 0.226 Angle : 0.717 11.241 7693 Z= 0.365 Chirality : 0.044 0.168 918 Planarity : 0.005 0.064 973 Dihedral : 5.169 24.430 772 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.38 % Allowed : 12.50 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.94 (0.32), residues: 722 helix: -0.06 (0.24), residues: 479 sheet: -1.55 (0.78), residues: 39 loop : -1.51 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 5 HIS 0.004 0.002 HIS A 68 PHE 0.028 0.002 PHE A 241 TYR 0.049 0.002 TYR A 30 ARG 0.008 0.001 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 5 TRP cc_start: 0.7831 (t-100) cc_final: 0.7599 (t-100) REVERT: A 20 MET cc_start: 0.5146 (tpt) cc_final: 0.4916 (tpt) REVERT: A 137 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8205 (mm) REVERT: A 264 ARG cc_start: 0.6905 (tpt-90) cc_final: 0.6550 (tpp80) REVERT: A 382 ARG cc_start: 0.6104 (mtp180) cc_final: 0.5871 (tpt90) REVERT: A 743 LYS cc_start: 0.6759 (tptm) cc_final: 0.6349 (tppt) outliers start: 20 outliers final: 10 residues processed: 119 average time/residue: 0.8277 time to fit residues: 104.8657 Evaluate side-chains 117 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5654 Z= 0.326 Angle : 0.795 12.526 7693 Z= 0.404 Chirality : 0.048 0.170 918 Planarity : 0.006 0.059 973 Dihedral : 5.491 20.429 771 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.89 % Allowed : 18.07 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.01 (0.32), residues: 722 helix: -0.16 (0.24), residues: 475 sheet: -1.37 (0.77), residues: 39 loop : -1.45 (0.47), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 736 HIS 0.004 0.002 HIS A 101 PHE 0.027 0.003 PHE A 241 TYR 0.015 0.002 TYR A 151 ARG 0.006 0.001 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 0.619 Fit side-chains REVERT: A 20 MET cc_start: 0.5153 (tpt) cc_final: 0.4928 (tpt) REVERT: A 137 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8247 (mm) REVERT: A 743 LYS cc_start: 0.6762 (tptm) cc_final: 0.6384 (tppt) outliers start: 23 outliers final: 16 residues processed: 120 average time/residue: 0.7424 time to fit residues: 95.3427 Evaluate side-chains 125 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 33 optimal weight: 30.0000 chunk 7 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 34 optimal weight: 0.0370 chunk 62 optimal weight: 0.3980 chunk 18 optimal weight: 5.9990 overall best weight: 3.4864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5654 Z= 0.244 Angle : 0.753 14.163 7693 Z= 0.372 Chirality : 0.044 0.152 918 Planarity : 0.005 0.055 973 Dihedral : 5.281 19.454 771 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.39 % Allowed : 19.93 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.84 (0.32), residues: 722 helix: -0.03 (0.24), residues: 475 sheet: -1.34 (0.81), residues: 33 loop : -1.37 (0.47), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 736 HIS 0.003 0.001 HIS A 558 PHE 0.037 0.002 PHE A 241 TYR 0.012 0.002 TYR A 151 ARG 0.002 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.5310 (tpt) cc_final: 0.5040 (tpt) REVERT: A 137 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8265 (mm) REVERT: A 229 MET cc_start: 0.6765 (ppp) cc_final: 0.6464 (pp-130) REVERT: A 271 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6639 (mm-30) REVERT: A 476 ASP cc_start: 0.5295 (OUTLIER) cc_final: 0.4786 (p0) REVERT: A 516 ILE cc_start: 0.6373 (pt) cc_final: 0.6015 (tt) REVERT: A 557 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.6890 (mp) REVERT: A 743 LYS cc_start: 0.6674 (tptm) cc_final: 0.6398 (tppt) outliers start: 26 outliers final: 15 residues processed: 116 average time/residue: 0.7871 time to fit residues: 97.5817 Evaluate side-chains 123 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 722 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 0.1980 chunk 62 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5654 Z= 0.186 Angle : 0.721 12.426 7693 Z= 0.349 Chirality : 0.043 0.211 918 Planarity : 0.005 0.050 973 Dihedral : 4.938 18.892 771 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.73 % Allowed : 21.28 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.75 (0.32), residues: 722 helix: 0.08 (0.24), residues: 480 sheet: -0.72 (0.83), residues: 34 loop : -1.61 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 5 HIS 0.002 0.001 HIS A 239 PHE 0.021 0.001 PHE A 241 TYR 0.010 0.001 TYR A 151 ARG 0.002 0.000 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.5312 (tpt) cc_final: 0.5052 (tpt) REVERT: A 39 THR cc_start: 0.5028 (t) cc_final: 0.4741 (t) REVERT: A 137 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8226 (mm) REVERT: A 476 ASP cc_start: 0.5162 (OUTLIER) cc_final: 0.4711 (p0) REVERT: A 516 ILE cc_start: 0.6342 (pt) cc_final: 0.6018 (tt) REVERT: A 557 ILE cc_start: 0.7251 (OUTLIER) cc_final: 0.6890 (mt) REVERT: A 743 LYS cc_start: 0.6613 (tptm) cc_final: 0.6339 (tppt) REVERT: A 751 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7686 (pp) outliers start: 28 outliers final: 14 residues processed: 119 average time/residue: 0.7599 time to fit residues: 96.5976 Evaluate side-chains 120 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 751 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5654 Z= 0.233 Angle : 0.737 12.373 7693 Z= 0.362 Chirality : 0.044 0.149 918 Planarity : 0.005 0.048 973 Dihedral : 5.015 19.592 771 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 5.57 % Allowed : 21.79 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.59 (0.32), residues: 722 helix: 0.18 (0.24), residues: 468 sheet: -1.19 (0.78), residues: 39 loop : -1.28 (0.47), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 736 HIS 0.003 0.001 HIS A 558 PHE 0.023 0.002 PHE A 445 TYR 0.011 0.001 TYR A 151 ARG 0.002 0.000 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 110 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.5370 (tpt) cc_final: 0.5106 (tpt) REVERT: A 137 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8279 (mm) REVERT: A 226 LEU cc_start: 0.7468 (mp) cc_final: 0.7212 (mm) REVERT: A 229 MET cc_start: 0.6645 (ppp) cc_final: 0.6161 (ppp) REVERT: A 264 ARG cc_start: 0.6918 (tpt-90) cc_final: 0.6407 (tpp80) REVERT: A 284 MET cc_start: 0.6259 (mmm) cc_final: 0.5460 (mmt) REVERT: A 476 ASP cc_start: 0.5282 (OUTLIER) cc_final: 0.4801 (p0) REVERT: A 516 ILE cc_start: 0.6332 (pt) cc_final: 0.5974 (tt) REVERT: A 570 ILE cc_start: 0.7819 (tt) cc_final: 0.7595 (tt) REVERT: A 751 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7735 (pp) outliers start: 33 outliers final: 20 residues processed: 127 average time/residue: 0.8152 time to fit residues: 110.8105 Evaluate side-chains 130 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 751 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 38 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 27 optimal weight: 0.0770 chunk 41 optimal weight: 8.9990 overall best weight: 3.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5654 Z= 0.230 Angle : 0.740 11.687 7693 Z= 0.363 Chirality : 0.044 0.210 918 Planarity : 0.005 0.045 973 Dihedral : 4.992 19.924 771 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.07 % Allowed : 23.48 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.57 (0.32), residues: 722 helix: 0.21 (0.25), residues: 465 sheet: -0.71 (0.82), residues: 34 loop : -1.41 (0.45), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 736 HIS 0.016 0.002 HIS A 239 PHE 0.017 0.002 PHE A 134 TYR 0.012 0.001 TYR A 151 ARG 0.002 0.000 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 107 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.5409 (tpt) cc_final: 0.5114 (tpt) REVERT: A 132 HIS cc_start: 0.5852 (OUTLIER) cc_final: 0.5636 (m90) REVERT: A 137 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8253 (mm) REVERT: A 226 LEU cc_start: 0.7500 (mp) cc_final: 0.7201 (mm) REVERT: A 229 MET cc_start: 0.6561 (ppp) cc_final: 0.6003 (ppp) REVERT: A 264 ARG cc_start: 0.6906 (tpt-90) cc_final: 0.6413 (tpp80) REVERT: A 284 MET cc_start: 0.6326 (mmm) cc_final: 0.5595 (mmt) REVERT: A 476 ASP cc_start: 0.5244 (OUTLIER) cc_final: 0.4770 (p0) REVERT: A 516 ILE cc_start: 0.6413 (pt) cc_final: 0.6034 (tt) REVERT: A 751 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7720 (pp) outliers start: 30 outliers final: 22 residues processed: 119 average time/residue: 0.7631 time to fit residues: 97.1425 Evaluate side-chains 131 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 751 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 66 optimal weight: 0.0980 chunk 60 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5654 Z= 0.271 Angle : 0.779 11.763 7693 Z= 0.383 Chirality : 0.046 0.154 918 Planarity : 0.005 0.050 973 Dihedral : 5.211 21.054 771 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 6.08 % Allowed : 23.31 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.67 (0.32), residues: 722 helix: 0.14 (0.24), residues: 465 sheet: -0.93 (0.84), residues: 31 loop : -1.43 (0.44), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 736 HIS 0.008 0.002 HIS A 239 PHE 0.021 0.002 PHE A 445 TYR 0.013 0.002 TYR A 151 ARG 0.003 0.000 ARG A 677 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 108 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8329 (mm) REVERT: A 160 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.6852 (tm-30) REVERT: A 226 LEU cc_start: 0.7524 (mp) cc_final: 0.7249 (mm) REVERT: A 229 MET cc_start: 0.6618 (ppp) cc_final: 0.6024 (ppp) REVERT: A 264 ARG cc_start: 0.6959 (tpt-90) cc_final: 0.6432 (tpp80) REVERT: A 284 MET cc_start: 0.6364 (mmm) cc_final: 0.5652 (mmt) REVERT: A 476 ASP cc_start: 0.5330 (OUTLIER) cc_final: 0.4824 (p0) REVERT: A 656 GLU cc_start: 0.6784 (pt0) cc_final: 0.6549 (pt0) REVERT: A 751 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7780 (pp) outliers start: 36 outliers final: 29 residues processed: 124 average time/residue: 0.7822 time to fit residues: 103.6235 Evaluate side-chains 139 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 106 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 TRP Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 751 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 28 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5654 Z= 0.229 Angle : 0.767 11.467 7693 Z= 0.372 Chirality : 0.045 0.222 918 Planarity : 0.005 0.049 973 Dihedral : 5.055 19.899 771 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 5.74 % Allowed : 24.49 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.68 (0.32), residues: 722 helix: 0.13 (0.24), residues: 472 sheet: -0.48 (0.86), residues: 33 loop : -1.54 (0.44), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 736 HIS 0.008 0.002 HIS A 239 PHE 0.015 0.001 PHE A 134 TYR 0.012 0.001 TYR A 151 ARG 0.002 0.000 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 106 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8317 (mm) REVERT: A 160 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.6774 (tm-30) REVERT: A 229 MET cc_start: 0.6608 (ppp) cc_final: 0.5998 (ppp) REVERT: A 264 ARG cc_start: 0.6937 (tpt-90) cc_final: 0.6427 (tpp80) REVERT: A 284 MET cc_start: 0.6430 (mmm) cc_final: 0.5734 (mmt) REVERT: A 476 ASP cc_start: 0.5177 (OUTLIER) cc_final: 0.4692 (p0) REVERT: A 516 ILE cc_start: 0.6457 (pt) cc_final: 0.6060 (tt) REVERT: A 557 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.6354 (pp) REVERT: A 656 GLU cc_start: 0.6720 (pt0) cc_final: 0.6489 (pt0) REVERT: A 751 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7734 (pp) outliers start: 34 outliers final: 26 residues processed: 120 average time/residue: 0.7962 time to fit residues: 101.9196 Evaluate side-chains 134 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 103 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 TRP Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 751 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 7.9990 chunk 47 optimal weight: 0.2980 chunk 71 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 5 optimal weight: 0.0070 chunk 44 optimal weight: 0.0970 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5654 Z= 0.190 Angle : 0.753 10.952 7693 Z= 0.362 Chirality : 0.043 0.185 918 Planarity : 0.005 0.045 973 Dihedral : 4.726 18.633 771 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.72 % Allowed : 27.20 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.46 (0.32), residues: 722 helix: 0.31 (0.25), residues: 468 sheet: -0.25 (0.90), residues: 34 loop : -1.50 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 5 HIS 0.006 0.001 HIS A 239 PHE 0.011 0.001 PHE A 240 TYR 0.010 0.001 TYR A 151 ARG 0.002 0.000 ARG A 744 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8269 (mm) REVERT: A 229 MET cc_start: 0.6579 (ppp) cc_final: 0.5915 (ppp) REVERT: A 264 ARG cc_start: 0.6781 (tpt-90) cc_final: 0.6229 (tpp80) REVERT: A 516 ILE cc_start: 0.6302 (pt) cc_final: 0.5929 (tt) REVERT: A 570 ILE cc_start: 0.7816 (tt) cc_final: 0.7575 (tp) REVERT: A 656 GLU cc_start: 0.6503 (pt0) cc_final: 0.6275 (pt0) REVERT: A 751 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7638 (pp) outliers start: 22 outliers final: 18 residues processed: 117 average time/residue: 0.8283 time to fit residues: 103.1669 Evaluate side-chains 123 residues out of total 592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 751 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 8.9990 chunk 8 optimal weight: 0.0870 chunk 15 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 chunk 58 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.241939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.224625 restraints weight = 7937.198| |-----------------------------------------------------------------------------| r_work (start): 0.4474 rms_B_bonded: 2.33 r_work: 0.4394 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5654 Z= 0.208 Angle : 0.774 10.822 7693 Z= 0.372 Chirality : 0.044 0.231 918 Planarity : 0.004 0.041 973 Dihedral : 4.745 18.948 771 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.89 % Allowed : 26.86 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.32), residues: 722 helix: 0.25 (0.24), residues: 472 sheet: -0.13 (0.88), residues: 33 loop : -1.31 (0.45), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 5 HIS 0.007 0.001 HIS A 239 PHE 0.038 0.002 PHE A 134 TYR 0.011 0.001 TYR A 151 ARG 0.002 0.000 ARG A 281 =============================================================================== Job complete usr+sys time: 2117.20 seconds wall clock time: 38 minutes 20.36 seconds (2300.36 seconds total)