Starting phenix.real_space_refine on Thu Mar 6 08:26:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k8b_22725/03_2025/7k8b_22725.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k8b_22725/03_2025/7k8b_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/cci-nas-00/data/ceres_data/7k8b_22725/03_2025/7k8b_22725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k8b_22725/03_2025/7k8b_22725.map" model { file = "/net/cci-nas-00/data/ceres_data/7k8b_22725/03_2025/7k8b_22725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k8b_22725/03_2025/7k8b_22725.cif" } 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. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.45, per 1000 atoms: 0.62 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 - 3.00 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: 1.37 Conformation dependent library (CDL) restraints added in 747.4 milliseconds 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: 0.62 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: 1.93 Time building geometry restraints manager: 1.62 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: 0.00 - 2.62: 7540 2.62 - 5.23: 131 5.23 - 7.85: 19 7.85 - 10.46: 1 10.46 - 13.08: 2 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 3.040 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 3.040 nonbonded pdb=" OE1 GLU A 93 " pdb=" N ASN A 162 " model vdw 2.324 3.120 nonbonded pdb=" O LYS A 480 " pdb=" OG1 THR A 483 " model vdw 2.335 3.040 ... (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: 0.070 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.240 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:14.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.210 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.570 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: 0.8191 time to fit residues: 103.8275 Evaluate side-chains 106 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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: 1.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 34 optimal weight: 0.4980 chunk 42 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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** A 746 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.241277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.224217 restraints weight = 7808.589| |-----------------------------------------------------------------------------| r_work (start): 0.4476 rms_B_bonded: 2.30 r_work: 0.4397 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5654 Z= 0.223 Angle : 0.729 11.006 7693 Z= 0.371 Chirality : 0.045 0.173 918 Planarity : 0.006 0.096 973 Dihedral : 5.439 54.142 772 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.04 % Allowed : 12.67 % Favored : 84.29 % 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: -0.95 (0.32), residues: 722 helix: -0.12 (0.24), residues: 482 sheet: -1.44 (0.78), residues: 39 loop : -1.44 (0.46), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 5 HIS 0.004 0.001 HIS A 68 PHE 0.026 0.002 PHE A 241 TYR 0.056 0.003 TYR A 30 ARG 0.012 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 125 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 5 TRP cc_start: 0.7882 (t-100) cc_final: 0.7678 (t-100) REVERT: A 20 MET cc_start: 0.5139 (tpt) cc_final: 0.4902 (tpt) REVERT: A 137 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8322 (mm) REVERT: A 229 MET cc_start: 0.6753 (ppp) cc_final: 0.6540 (pp-130) REVERT: A 284 MET cc_start: 0.6821 (mmm) cc_final: 0.6584 (mmt) REVERT: A 382 ARG cc_start: 0.5946 (mtp180) cc_final: 0.5699 (tpt90) REVERT: A 743 LYS cc_start: 0.6667 (tptm) cc_final: 0.6219 (tppt) outliers start: 18 outliers final: 6 residues processed: 114 average time/residue: 0.7615 time to fit residues: 92.8334 Evaluate side-chains 109 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 617 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 53 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.234439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.217041 restraints weight = 7855.727| |-----------------------------------------------------------------------------| r_work (start): 0.4411 rms_B_bonded: 2.27 r_work: 0.4333 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5654 Z= 0.331 Angle : 0.798 12.504 7693 Z= 0.411 Chirality : 0.048 0.169 918 Planarity : 0.006 0.062 973 Dihedral : 5.798 46.113 772 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.56 % Allowed : 16.39 % Favored : 79.05 % 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: -1.19 (0.31), residues: 722 helix: -0.30 (0.24), residues: 476 sheet: -1.48 (0.78), residues: 33 loop : -1.53 (0.46), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 736 HIS 0.004 0.002 HIS A 101 PHE 0.019 0.003 PHE A 241 TYR 0.041 0.003 TYR A 30 ARG 0.004 0.001 ARG A 13 *********************** 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 141 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 5 TRP cc_start: 0.7872 (t-100) cc_final: 0.7660 (t-100) REVERT: A 20 MET cc_start: 0.5253 (tpt) cc_final: 0.5018 (tpt) REVERT: A 137 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8339 (mm) REVERT: A 230 ARG cc_start: 0.5636 (OUTLIER) cc_final: 0.5222 (ptp-110) REVERT: A 284 MET cc_start: 0.7040 (mmm) cc_final: 0.6348 (mmt) REVERT: A 521 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6466 (mt-10) REVERT: A 704 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8455 (tp) REVERT: A 743 LYS cc_start: 0.6759 (tptm) cc_final: 0.6352 (tppt) outliers start: 27 outliers final: 12 residues processed: 125 average time/residue: 0.7289 time to fit residues: 97.4195 Evaluate side-chains 124 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 230 ARG Chi-restraints excluded: chain A residue 282 THR 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 409 LEU Chi-restraints excluded: chain A residue 427 ILE 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 612 VAL Chi-restraints excluded: chain A residue 617 SER 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 60 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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** ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.241370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.224048 restraints weight = 8106.793| |-----------------------------------------------------------------------------| r_work (start): 0.4477 rms_B_bonded: 2.38 r_work: 0.4398 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5654 Z= 0.191 Angle : 0.713 13.734 7693 Z= 0.350 Chirality : 0.043 0.166 918 Planarity : 0.005 0.053 973 Dihedral : 5.043 26.451 772 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.21 % Allowed : 19.59 % Favored : 77.20 % 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: -0.82 (0.32), residues: 722 helix: -0.03 (0.24), residues: 479 sheet: -0.68 (0.82), residues: 34 loop : -1.48 (0.46), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 741 HIS 0.009 0.001 HIS A 239 PHE 0.015 0.001 PHE A 241 TYR 0.029 0.002 TYR A 30 ARG 0.004 0.000 ARG A 230 *********************** 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 123 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 TRP cc_start: 0.7906 (t-100) cc_final: 0.7589 (t-100) REVERT: A 20 MET cc_start: 0.5282 (tpt) cc_final: 0.5006 (tpt) REVERT: A 137 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8319 (mm) REVERT: A 230 ARG cc_start: 0.5334 (mtm110) cc_final: 0.4993 (ptp-110) REVERT: A 271 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6668 (mm-30) REVERT: A 516 ILE cc_start: 0.6809 (OUTLIER) cc_final: 0.6420 (OUTLIER) REVERT: A 532 GLU cc_start: 0.7290 (tp30) cc_final: 0.6101 (pt0) REVERT: A 557 ILE cc_start: 0.7320 (OUTLIER) cc_final: 0.7004 (mp) REVERT: A 743 LYS cc_start: 0.6575 (tptm) cc_final: 0.6255 (tppt) outliers start: 19 outliers final: 11 residues processed: 111 average time/residue: 0.8431 time to fit residues: 99.5276 Evaluate side-chains 117 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 184 GLU Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 516 ILE 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 612 VAL Chi-restraints excluded: chain A residue 639 ILE 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 61 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 33 optimal weight: 40.0000 chunk 66 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 13 optimal weight: 0.0570 chunk 54 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 overall best weight: 4.0106 ------------------------------------------------------------------------------- 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 = 0.4584 r_free = 0.4584 target = 0.236955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.219826 restraints weight = 7878.107| |-----------------------------------------------------------------------------| r_work (start): 0.4432 rms_B_bonded: 2.26 r_work: 0.4355 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5654 Z= 0.255 Angle : 0.747 13.400 7693 Z= 0.371 Chirality : 0.045 0.193 918 Planarity : 0.005 0.052 973 Dihedral : 5.107 19.985 771 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 5.07 % Allowed : 20.78 % Favored : 74.16 % 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: -0.03 (0.24), residues: 479 sheet: -1.33 (0.77), residues: 33 loop : -1.19 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 736 HIS 0.004 0.001 HIS A 239 PHE 0.034 0.002 PHE A 241 TYR 0.025 0.002 TYR A 30 ARG 0.004 0.001 ARG A 230 *********************** 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 134 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TRP cc_start: 0.7833 (t-100) cc_final: 0.7555 (t-100) REVERT: A 20 MET cc_start: 0.5334 (tpt) cc_final: 0.5069 (tpt) REVERT: A 137 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8360 (mm) REVERT: A 284 MET cc_start: 0.6371 (tpp) cc_final: 0.5924 (mmt) REVERT: A 516 ILE cc_start: 0.6743 (OUTLIER) cc_final: 0.6287 (mp) REVERT: A 743 LYS cc_start: 0.6632 (tptm) cc_final: 0.6369 (tppt) REVERT: A 751 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7932 (pp) outliers start: 30 outliers final: 17 residues processed: 119 average time/residue: 0.8543 time to fit residues: 108.0656 Evaluate side-chains 121 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 30 TYR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 184 GLU 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 427 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 516 ILE 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 595 MET 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 21 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 10 optimal weight: 0.0670 chunk 6 optimal weight: 6.9990 overall best weight: 5.0126 ------------------------------------------------------------------------------- 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** A 746 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.234239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.216965 restraints weight = 7880.242| |-----------------------------------------------------------------------------| r_work (start): 0.4411 rms_B_bonded: 2.28 r_work: 0.4336 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.2445 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= 0.290 Angle : 0.788 13.459 7693 Z= 0.392 Chirality : 0.046 0.157 918 Planarity : 0.005 0.052 973 Dihedral : 5.360 20.136 771 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 5.91 % Allowed : 21.11 % Favored : 72.97 % 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: -0.89 (0.32), residues: 722 helix: -0.07 (0.24), residues: 470 sheet: -1.09 (0.81), residues: 31 loop : -1.40 (0.45), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 736 HIS 0.004 0.001 HIS A 558 PHE 0.018 0.002 PHE A 241 TYR 0.023 0.002 TYR A 30 ARG 0.003 0.001 ARG A 281 *********************** 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 145 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TRP cc_start: 0.7769 (t-100) cc_final: 0.7461 (t-100) REVERT: A 20 MET cc_start: 0.5415 (tpt) cc_final: 0.5138 (tpt) REVERT: A 132 HIS cc_start: 0.6230 (OUTLIER) cc_final: 0.5991 (m90) REVERT: A 137 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8434 (mm) REVERT: A 476 ASP cc_start: 0.5058 (OUTLIER) cc_final: 0.4698 (p0) REVERT: A 516 ILE cc_start: 0.6784 (OUTLIER) cc_final: 0.6329 (mp) REVERT: A 743 LYS cc_start: 0.6662 (tptm) cc_final: 0.6409 (tppt) REVERT: A 751 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7995 (pp) outliers start: 35 outliers final: 20 residues processed: 128 average time/residue: 0.7672 time to fit residues: 105.1393 Evaluate side-chains 125 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 30 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 184 GLU 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 427 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 516 ILE 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 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 69 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 46 optimal weight: 0.0980 chunk 65 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- 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 = 0.4570 r_free = 0.4570 target = 0.235346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.218348 restraints weight = 7865.293| |-----------------------------------------------------------------------------| r_work (start): 0.4416 rms_B_bonded: 2.26 r_work: 0.4338 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.2547 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= 0.268 Angle : 0.779 12.737 7693 Z= 0.385 Chirality : 0.046 0.164 918 Planarity : 0.005 0.049 973 Dihedral : 5.300 20.113 771 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 6.25 % Allowed : 21.79 % Favored : 71.96 % 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: -0.78 (0.32), residues: 722 helix: -0.00 (0.24), residues: 465 sheet: -0.53 (0.89), residues: 26 loop : -1.38 (0.45), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 736 HIS 0.026 0.003 HIS A 239 PHE 0.016 0.002 PHE A 134 TYR 0.026 0.002 TYR A 30 ARG 0.003 0.000 ARG A 281 *********************** 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 to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TRP cc_start: 0.7822 (t-100) cc_final: 0.7574 (t-100) REVERT: A 20 MET cc_start: 0.5412 (tpt) cc_final: 0.5110 (tpt) REVERT: A 132 HIS cc_start: 0.6183 (OUTLIER) cc_final: 0.5959 (m90) REVERT: A 137 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8450 (mm) REVERT: A 416 ILE cc_start: 0.6714 (pt) cc_final: 0.6203 (pp) REVERT: A 476 ASP cc_start: 0.4969 (OUTLIER) cc_final: 0.4657 (p0) REVERT: A 516 ILE cc_start: 0.6752 (OUTLIER) cc_final: 0.6370 (mt) REVERT: A 710 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7720 (mp) REVERT: A 743 LYS cc_start: 0.6620 (tptm) cc_final: 0.6243 (tppt) REVERT: A 751 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7998 (pp) outliers start: 37 outliers final: 23 residues processed: 120 average time/residue: 0.8040 time to fit residues: 102.9317 Evaluate side-chains 128 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 30 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 132 HIS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 311 PHE 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 460 VAL 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 516 ILE 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 612 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 710 ILE 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 60 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 2 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 = 0.4573 r_free = 0.4573 target = 0.235848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.218571 restraints weight = 7886.795| |-----------------------------------------------------------------------------| r_work (start): 0.4412 rms_B_bonded: 2.29 r_work: 0.4336 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5654 Z= 0.267 Angle : 0.786 12.220 7693 Z= 0.388 Chirality : 0.046 0.159 918 Planarity : 0.005 0.048 973 Dihedral : 5.279 20.647 771 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 6.08 % Allowed : 21.45 % Favored : 72.47 % 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: -0.07 (0.24), residues: 474 sheet: -0.48 (0.91), residues: 26 loop : -1.39 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 736 HIS 0.016 0.002 HIS A 239 PHE 0.016 0.002 PHE A 241 TYR 0.026 0.002 TYR A 30 ARG 0.004 0.000 ARG A 281 *********************** 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 139 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TRP cc_start: 0.7867 (t-100) cc_final: 0.7588 (t-100) REVERT: A 20 MET cc_start: 0.5385 (tpt) cc_final: 0.5093 (tpt) REVERT: A 137 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8453 (mm) REVERT: A 160 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7283 (tm-30) REVERT: A 382 ARG cc_start: 0.6150 (mtp180) cc_final: 0.5774 (mtp180) REVERT: A 476 ASP cc_start: 0.5144 (OUTLIER) cc_final: 0.4741 (p0) REVERT: A 516 ILE cc_start: 0.6732 (OUTLIER) cc_final: 0.6311 (mp) REVERT: A 743 LYS cc_start: 0.6590 (tptm) cc_final: 0.6241 (tppt) REVERT: A 751 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8000 (pp) outliers start: 36 outliers final: 26 residues processed: 123 average time/residue: 0.7621 time to fit residues: 100.0740 Evaluate side-chains 133 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 30 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 160 GLN Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 311 PHE 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 460 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 516 ILE 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 594 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 713 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 39 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 6 optimal weight: 0.2980 chunk 42 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- 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** ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.237155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.220009 restraints weight = 7974.739| |-----------------------------------------------------------------------------| r_work (start): 0.4429 rms_B_bonded: 2.29 r_work: 0.4351 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5654 Z= 0.224 Angle : 0.778 11.493 7693 Z= 0.378 Chirality : 0.045 0.171 918 Planarity : 0.005 0.045 973 Dihedral : 5.128 21.841 771 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 5.74 % Allowed : 22.30 % Favored : 71.96 % 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: -0.77 (0.32), residues: 722 helix: -0.02 (0.24), residues: 472 sheet: -0.35 (0.94), residues: 26 loop : -1.37 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 736 HIS 0.006 0.001 HIS A 239 PHE 0.014 0.001 PHE A 134 TYR 0.025 0.002 TYR A 30 ARG 0.003 0.000 ARG A 281 *********************** 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 144 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TRP cc_start: 0.7851 (t-100) cc_final: 0.7599 (t-100) REVERT: A 20 MET cc_start: 0.5392 (tpt) cc_final: 0.5090 (tpt) REVERT: A 137 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8431 (mm) REVERT: A 160 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: A 284 MET cc_start: 0.6412 (mmm) cc_final: 0.4945 (mmt) REVERT: A 476 ASP cc_start: 0.5071 (OUTLIER) cc_final: 0.4762 (p0) REVERT: A 516 ILE cc_start: 0.6738 (OUTLIER) cc_final: 0.6312 (mt) REVERT: A 520 LEU cc_start: 0.6119 (OUTLIER) cc_final: 0.5281 (tt) REVERT: A 743 LYS cc_start: 0.6523 (tptm) cc_final: 0.6206 (tppt) REVERT: A 751 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7928 (pp) outliers start: 34 outliers final: 23 residues processed: 127 average time/residue: 0.8065 time to fit residues: 109.0605 Evaluate side-chains 136 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 30 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 160 GLN Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 315 ILE 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 460 VAL 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 516 ILE Chi-restraints excluded: chain A residue 520 LEU 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 594 LEU Chi-restraints excluded: chain A residue 595 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 41 optimal weight: 0.4980 chunk 64 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- 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 = 0.4582 r_free = 0.4582 target = 0.236952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.219665 restraints weight = 7909.026| |-----------------------------------------------------------------------------| r_work (start): 0.4430 rms_B_bonded: 2.29 r_work: 0.4351 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5654 Z= 0.245 Angle : 0.803 11.312 7693 Z= 0.392 Chirality : 0.046 0.175 918 Planarity : 0.005 0.047 973 Dihedral : 5.128 21.336 771 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 5.41 % Allowed : 23.65 % Favored : 70.95 % 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: -0.79 (0.32), residues: 722 helix: -0.04 (0.24), residues: 472 sheet: -0.42 (0.95), residues: 26 loop : -1.37 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 736 HIS 0.010 0.002 HIS A 239 PHE 0.014 0.002 PHE A 134 TYR 0.025 0.002 TYR A 30 ARG 0.002 0.000 ARG A 281 ********************** 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 140 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TRP cc_start: 0.7822 (t-100) cc_final: 0.7565 (t-100) REVERT: A 137 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8399 (mm) REVERT: A 160 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: A 284 MET cc_start: 0.6574 (mmm) cc_final: 0.5038 (mmt) REVERT: A 476 ASP cc_start: 0.5070 (OUTLIER) cc_final: 0.4697 (p0) REVERT: A 516 ILE cc_start: 0.6717 (OUTLIER) cc_final: 0.6395 (mt) REVERT: A 570 ILE cc_start: 0.7975 (tt) cc_final: 0.7711 (tp) REVERT: A 743 LYS cc_start: 0.6521 (tptm) cc_final: 0.6211 (tppt) REVERT: A 751 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7934 (pp) outliers start: 32 outliers final: 23 residues processed: 126 average time/residue: 0.7789 time to fit residues: 104.7169 Evaluate side-chains 136 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 30 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 160 GLN Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 315 ILE 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 460 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 516 ILE 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 594 LEU Chi-restraints excluded: chain A residue 595 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 25 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 50.0000 chunk 21 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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 = 0.4566 r_free = 0.4566 target = 0.235184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.217359 restraints weight = 8034.407| |-----------------------------------------------------------------------------| r_work (start): 0.4402 rms_B_bonded: 2.36 r_work: 0.4324 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 5654 Z= 0.314 Angle : 0.856 11.815 7693 Z= 0.424 Chirality : 0.049 0.227 918 Planarity : 0.006 0.051 973 Dihedral : 5.421 22.212 771 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 5.91 % Allowed : 23.65 % Favored : 70.44 % 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: -0.05 (0.24), residues: 463 sheet: -1.15 (0.82), residues: 31 loop : -1.31 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 736 HIS 0.010 0.002 HIS A 239 PHE 0.019 0.002 PHE A 134 TYR 0.026 0.002 TYR A 30 ARG 0.003 0.001 ARG A 677 =============================================================================== Job complete usr+sys time: 3271.58 seconds wall clock time: 56 minutes 42.66 seconds (3402.66 seconds total)