Starting phenix.real_space_refine on Tue Mar 3 13:47:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k8b_22725/03_2026/7k8b_22725.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k8b_22725/03_2026/7k8b_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_2026/7k8b_22725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k8b_22725/03_2026/7k8b_22725.map" model { file = "/net/cci-nas-00/data/ceres_data/7k8b_22725/03_2026/7k8b_22725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k8b_22725/03_2026/7k8b_22725.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.35, per 1000 atoms: 0.24 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: 0.49 Conformation dependent library (CDL) restraints added in 389.3 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: 0.16 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: 0.87 Time building geometry restraints manager: 0.65 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: 0.060 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: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.880 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:8.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.590 ------------------------------------------------------------------------------- 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= 0.311 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG A 453 TYR 0.023 0.002 TYR A 151 PHE 0.021 0.002 PHE A 241 TRP 0.013 0.001 TRP A 86 HIS 0.004 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 5654) covalent geometry : angle 0.82691 ( 7693) hydrogen bonds : bond 0.13778 ( 348) hydrogen bonds : angle 5.75003 ( 1020) *********************** 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 : 0.185 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: 0.3602 time to fit residues: 45.5044 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 : 0.140 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 = 0.4619 r_free = 0.4619 target = 0.240808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.223707 restraints weight = 7870.121| |-----------------------------------------------------------------------------| r_work (start): 0.4468 rms_B_bonded: 2.30 r_work: 0.4389 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6265 moved from start: 0.1269 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= 0.161 Angle : 0.730 10.852 7693 Z= 0.372 Chirality : 0.045 0.169 918 Planarity : 0.006 0.091 973 Dihedral : 5.471 55.916 772 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.87 % Allowed : 12.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.32), residues: 722 helix: -0.10 (0.24), residues: 480 sheet: -1.49 (0.77), residues: 39 loop : -1.49 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 230 TYR 0.051 0.002 TYR A 30 PHE 0.026 0.002 PHE A 241 TRP 0.014 0.002 TRP A 5 HIS 0.004 0.002 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 5654) covalent geometry : angle 0.72987 ( 7693) hydrogen bonds : bond 0.04707 ( 348) hydrogen bonds : angle 4.95333 ( 1020) *********************** 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 123 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 5 TRP cc_start: 0.7811 (t-100) cc_final: 0.7568 (t-100) REVERT: A 20 MET cc_start: 0.5145 (tpt) cc_final: 0.4909 (tpt) REVERT: A 137 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8332 (mm) REVERT: A 229 MET cc_start: 0.6776 (ppp) cc_final: 0.6527 (pp-130) REVERT: A 284 MET cc_start: 0.6805 (mmm) cc_final: 0.6588 (mmt) REVERT: A 382 ARG cc_start: 0.5966 (mtp180) cc_final: 0.5719 (tpt90) REVERT: A 743 LYS cc_start: 0.6658 (tptm) cc_final: 0.6212 (tppt) outliers start: 17 outliers final: 7 residues processed: 112 average time/residue: 0.3547 time to fit residues: 42.2474 Evaluate side-chains 109 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 30.0000 chunk 68 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 = 0.4591 r_free = 0.4591 target = 0.237498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.219823 restraints weight = 7926.208| |-----------------------------------------------------------------------------| r_work (start): 0.4443 rms_B_bonded: 2.33 r_work: 0.4363 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.1756 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= 0.178 Angle : 0.739 12.566 7693 Z= 0.375 Chirality : 0.045 0.173 918 Planarity : 0.005 0.060 973 Dihedral : 5.434 42.718 772 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.05 % Allowed : 16.39 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.32), residues: 722 helix: -0.12 (0.24), residues: 476 sheet: -1.35 (0.80), residues: 33 loop : -1.48 (0.45), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 230 TYR 0.042 0.002 TYR A 30 PHE 0.019 0.002 PHE A 241 TRP 0.015 0.002 TRP A 736 HIS 0.003 0.002 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 5654) covalent geometry : angle 0.73884 ( 7693) hydrogen bonds : bond 0.04572 ( 348) hydrogen bonds : angle 4.93387 ( 1020) *********************** 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 134 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 5 TRP cc_start: 0.7882 (t-100) cc_final: 0.7605 (t-100) REVERT: A 20 MET cc_start: 0.5186 (tpt) cc_final: 0.4954 (tpt) REVERT: A 99 LYS cc_start: 0.6374 (mmmt) cc_final: 0.6156 (tptp) REVERT: A 137 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8316 (mm) REVERT: A 229 MET cc_start: 0.6405 (ppp) cc_final: 0.6175 (pp-130) REVERT: A 230 ARG cc_start: 0.5600 (OUTLIER) cc_final: 0.4998 (ptp-110) REVERT: A 521 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6400 (mt-10) REVERT: A 570 ILE cc_start: 0.7907 (tt) cc_final: 0.7630 (tt) REVERT: A 743 LYS cc_start: 0.6675 (tptm) cc_final: 0.6244 (tppt) outliers start: 24 outliers final: 13 residues processed: 119 average time/residue: 0.3509 time to fit residues: 44.4103 Evaluate side-chains 121 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 27 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.4625 r_free = 0.4625 target = 0.241585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.224022 restraints weight = 7944.732| |-----------------------------------------------------------------------------| r_work (start): 0.4470 rms_B_bonded: 2.34 r_work: 0.4388 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5654 Z= 0.133 Angle : 0.705 13.177 7693 Z= 0.346 Chirality : 0.043 0.147 918 Planarity : 0.005 0.054 973 Dihedral : 4.960 26.962 772 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.05 % Allowed : 18.58 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.32), residues: 722 helix: 0.05 (0.24), residues: 477 sheet: -1.00 (0.77), residues: 39 loop : -1.34 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 230 TYR 0.028 0.002 TYR A 30 PHE 0.031 0.002 PHE A 241 TRP 0.010 0.001 TRP A 736 HIS 0.003 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 5654) covalent geometry : angle 0.70480 ( 7693) hydrogen bonds : bond 0.03906 ( 348) hydrogen bonds : angle 4.72905 ( 1020) *********************** 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 132 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 TRP cc_start: 0.8007 (t-100) cc_final: 0.7758 (t-100) REVERT: A 20 MET cc_start: 0.5333 (tpt) cc_final: 0.5067 (tpt) REVERT: A 137 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8231 (mm) REVERT: A 230 ARG cc_start: 0.5406 (mtm110) cc_final: 0.5075 (ptp-110) REVERT: A 271 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6635 (mm-30) REVERT: A 516 ILE cc_start: 0.6677 (pt) cc_final: 0.6164 (tt) REVERT: A 532 GLU cc_start: 0.7273 (tp30) cc_final: 0.6117 (pt0) REVERT: A 570 ILE cc_start: 0.7866 (tt) cc_final: 0.7615 (tt) REVERT: A 743 LYS cc_start: 0.6602 (tptm) cc_final: 0.6263 (tppt) outliers start: 24 outliers final: 12 residues processed: 120 average time/residue: 0.3749 time to fit residues: 47.7726 Evaluate side-chains 120 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TYR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 427 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 = 0.4597 r_free = 0.4597 target = 0.238564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.220901 restraints weight = 8087.086| |-----------------------------------------------------------------------------| r_work (start): 0.4445 rms_B_bonded: 2.36 r_work: 0.4363 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5654 Z= 0.155 Angle : 0.718 12.807 7693 Z= 0.357 Chirality : 0.044 0.200 918 Planarity : 0.005 0.052 973 Dihedral : 4.921 17.433 771 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.07 % Allowed : 19.93 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.32), residues: 722 helix: 0.04 (0.24), residues: 479 sheet: -1.12 (0.75), residues: 39 loop : -1.25 (0.47), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 230 TYR 0.025 0.002 TYR A 30 PHE 0.018 0.002 PHE A 134 TRP 0.018 0.001 TRP A 736 HIS 0.003 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5654) covalent geometry : angle 0.71815 ( 7693) hydrogen bonds : bond 0.04099 ( 348) hydrogen bonds : angle 4.75121 ( 1020) *********************** 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 : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TRP cc_start: 0.7933 (t-100) cc_final: 0.7700 (t-100) REVERT: A 20 MET cc_start: 0.5359 (tpt) cc_final: 0.5090 (tpt) REVERT: A 137 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8323 (mm) REVERT: A 516 ILE cc_start: 0.6653 (pt) cc_final: 0.6108 (tt) REVERT: A 570 ILE cc_start: 0.7875 (tt) cc_final: 0.7605 (tt) REVERT: A 743 LYS cc_start: 0.6584 (tptm) cc_final: 0.6277 (tppt) REVERT: A 751 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7957 (pp) outliers start: 30 outliers final: 16 residues processed: 118 average time/residue: 0.3548 time to fit residues: 44.6101 Evaluate side-chains 119 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 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 417 ILE 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 627 LEU 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 29 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.234289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.217062 restraints weight = 7890.400| |-----------------------------------------------------------------------------| r_work (start): 0.4409 rms_B_bonded: 2.26 r_work: 0.4332 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5654 Z= 0.216 Angle : 0.800 13.109 7693 Z= 0.403 Chirality : 0.048 0.163 918 Planarity : 0.006 0.051 973 Dihedral : 5.412 19.451 771 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 5.91 % Allowed : 20.78 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.32), residues: 722 helix: -0.04 (0.24), residues: 466 sheet: -1.26 (0.79), residues: 31 loop : -1.38 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 281 TYR 0.022 0.002 TYR A 30 PHE 0.017 0.002 PHE A 134 TRP 0.034 0.002 TRP A 736 HIS 0.004 0.002 HIS A 558 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 5654) covalent geometry : angle 0.79962 ( 7693) hydrogen bonds : bond 0.04730 ( 348) hydrogen bonds : angle 5.04099 ( 1020) *********************** 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 144 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.5471 (tpt) cc_final: 0.5201 (tpt) REVERT: A 99 LYS cc_start: 0.6530 (mmmt) cc_final: 0.6284 (tptp) REVERT: A 132 HIS cc_start: 0.6191 (OUTLIER) cc_final: 0.5980 (m90) REVERT: A 137 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8423 (mm) REVERT: A 476 ASP cc_start: 0.5130 (OUTLIER) cc_final: 0.4799 (p0) REVERT: A 516 ILE cc_start: 0.6741 (pt) cc_final: 0.6148 (tt) REVERT: A 743 LYS cc_start: 0.6666 (tptm) cc_final: 0.6406 (tppt) REVERT: A 751 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8045 (pp) outliers start: 35 outliers final: 20 residues processed: 128 average time/residue: 0.3246 time to fit residues: 44.3819 Evaluate side-chains 131 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 132 HIS Chi-restraints excluded: chain A residue 137 ILE 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 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 612 VAL Chi-restraints excluded: chain A residue 627 LEU 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 43 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.0470 chunk 44 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 54 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.7682 ------------------------------------------------------------------------------- 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 = 0.4601 r_free = 0.4601 target = 0.238934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.221584 restraints weight = 8098.732| |-----------------------------------------------------------------------------| r_work (start): 0.4452 rms_B_bonded: 2.35 r_work: 0.4374 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5654 Z= 0.140 Angle : 0.736 11.509 7693 Z= 0.362 Chirality : 0.044 0.165 918 Planarity : 0.005 0.047 973 Dihedral : 4.996 18.220 771 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.56 % Allowed : 22.64 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.32), residues: 722 helix: 0.05 (0.24), residues: 470 sheet: -0.46 (0.85), residues: 34 loop : -1.41 (0.45), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 453 TYR 0.024 0.001 TYR A 30 PHE 0.030 0.001 PHE A 241 TRP 0.024 0.002 TRP A 5 HIS 0.005 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 5654) covalent geometry : angle 0.73626 ( 7693) hydrogen bonds : bond 0.04064 ( 348) hydrogen bonds : angle 4.82472 ( 1020) *********************** 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 135 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 TRP cc_start: 0.7955 (t-100) cc_final: 0.7725 (t-100) REVERT: A 20 MET cc_start: 0.5403 (tpt) cc_final: 0.5121 (tpt) REVERT: A 99 LYS cc_start: 0.6295 (mmmt) cc_final: 0.6074 (tptp) REVERT: A 137 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8409 (mm) REVERT: A 184 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: A 516 ILE cc_start: 0.6741 (pt) cc_final: 0.6174 (tt) REVERT: A 557 ILE cc_start: 0.7348 (OUTLIER) cc_final: 0.6950 (mp) REVERT: A 570 ILE cc_start: 0.7926 (tt) cc_final: 0.7699 (tt) REVERT: A 743 LYS cc_start: 0.6531 (tptm) cc_final: 0.6167 (tppt) REVERT: A 751 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7934 (pp) outliers start: 27 outliers final: 16 residues processed: 119 average time/residue: 0.3508 time to fit residues: 44.5922 Evaluate side-chains 126 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 137 ILE 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 417 ILE 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 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 627 LEU 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 45 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 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 = 0.4557 r_free = 0.4557 target = 0.233878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.216877 restraints weight = 7880.342| |-----------------------------------------------------------------------------| r_work (start): 0.4394 rms_B_bonded: 2.23 r_work: 0.4318 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.2672 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= 0.231 Angle : 0.834 12.065 7693 Z= 0.419 Chirality : 0.049 0.206 918 Planarity : 0.006 0.051 973 Dihedral : 5.436 19.772 771 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 5.91 % Allowed : 21.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.32), residues: 722 helix: -0.12 (0.24), residues: 471 sheet: -1.24 (0.79), residues: 31 loop : -1.29 (0.47), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 281 TYR 0.027 0.002 TYR A 30 PHE 0.023 0.002 PHE A 241 TRP 0.032 0.003 TRP A 736 HIS 0.003 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 5654) covalent geometry : angle 0.83436 ( 7693) hydrogen bonds : bond 0.04779 ( 348) hydrogen bonds : angle 5.13397 ( 1020) *********************** 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 140 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TRP cc_start: 0.7908 (t-100) cc_final: 0.7566 (t-100) REVERT: A 20 MET cc_start: 0.5468 (tpt) cc_final: 0.5174 (tpt) REVERT: A 99 LYS cc_start: 0.6599 (mmmt) cc_final: 0.6377 (tptp) REVERT: A 137 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8435 (mm) REVERT: A 382 ARG cc_start: 0.6128 (mtp180) cc_final: 0.5710 (mtp180) REVERT: A 476 ASP cc_start: 0.5329 (OUTLIER) cc_final: 0.4907 (p0) REVERT: A 743 LYS cc_start: 0.6619 (tptm) cc_final: 0.6237 (tppt) REVERT: A 751 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8048 (pp) outliers start: 35 outliers final: 23 residues processed: 122 average time/residue: 0.3358 time to fit residues: 43.8132 Evaluate side-chains 131 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 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 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 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 612 VAL Chi-restraints excluded: chain A residue 627 LEU 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 49 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.4587 r_free = 0.4587 target = 0.237537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.220431 restraints weight = 7981.701| |-----------------------------------------------------------------------------| r_work (start): 0.4440 rms_B_bonded: 2.30 r_work: 0.4360 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.2654 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= 0.155 Angle : 0.773 11.376 7693 Z= 0.378 Chirality : 0.044 0.164 918 Planarity : 0.005 0.046 973 Dihedral : 5.115 16.872 771 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.39 % Allowed : 23.82 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.32), residues: 722 helix: 0.06 (0.24), residues: 469 sheet: -0.44 (0.91), residues: 26 loop : -1.42 (0.45), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 453 TYR 0.026 0.002 TYR A 30 PHE 0.023 0.001 PHE A 241 TRP 0.027 0.002 TRP A 736 HIS 0.002 0.001 HIS A 558 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 5654) covalent geometry : angle 0.77328 ( 7693) hydrogen bonds : bond 0.04221 ( 348) hydrogen bonds : angle 4.90364 ( 1020) *********************** 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 135 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TRP cc_start: 0.7953 (t-100) cc_final: 0.7721 (t-100) REVERT: A 99 LYS cc_start: 0.6354 (mmmt) cc_final: 0.6149 (tptp) REVERT: A 137 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8395 (mm) REVERT: A 160 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: A 557 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.6921 (mp) REVERT: A 743 LYS cc_start: 0.6507 (tptm) cc_final: 0.6187 (tppt) REVERT: A 751 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7932 (pp) outliers start: 26 outliers final: 18 residues processed: 121 average time/residue: 0.3516 time to fit residues: 45.3621 Evaluate side-chains 130 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 137 ILE Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 324 MET 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 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 627 LEU 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 35 optimal weight: 0.4980 chunk 47 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 66 optimal weight: 0.0970 chunk 39 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.8582 ------------------------------------------------------------------------------- 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 = 0.4603 r_free = 0.4603 target = 0.239519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.222168 restraints weight = 7982.236| |-----------------------------------------------------------------------------| r_work (start): 0.4455 rms_B_bonded: 2.34 r_work: 0.4378 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.2755 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= 0.148 Angle : 0.774 11.154 7693 Z= 0.378 Chirality : 0.045 0.231 918 Planarity : 0.005 0.044 973 Dihedral : 5.022 16.434 771 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.39 % Allowed : 24.49 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.32), residues: 722 helix: 0.12 (0.24), residues: 470 sheet: -0.15 (0.88), residues: 33 loop : -1.40 (0.46), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 453 TYR 0.025 0.002 TYR A 30 PHE 0.029 0.001 PHE A 241 TRP 0.023 0.002 TRP A 736 HIS 0.006 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 5654) covalent geometry : angle 0.77392 ( 7693) hydrogen bonds : bond 0.04112 ( 348) hydrogen bonds : angle 4.83719 ( 1020) ********************** 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 135 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LYS cc_start: 0.6293 (mmmt) cc_final: 0.6067 (tptp) REVERT: A 137 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8411 (mm) REVERT: A 160 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7271 (tm-30) REVERT: A 271 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6749 (mm-30) REVERT: A 476 ASP cc_start: 0.5408 (OUTLIER) cc_final: 0.5111 (p0) REVERT: A 516 ILE cc_start: 0.6782 (pt) cc_final: 0.6209 (tt) REVERT: A 557 ILE cc_start: 0.7392 (OUTLIER) cc_final: 0.6887 (mt) REVERT: A 570 ILE cc_start: 0.8000 (tt) cc_final: 0.7722 (tp) REVERT: A 743 LYS cc_start: 0.6487 (tptm) cc_final: 0.6191 (tppt) REVERT: A 751 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7891 (pp) outliers start: 26 outliers final: 19 residues processed: 122 average time/residue: 0.3442 time to fit residues: 44.7588 Evaluate side-chains 132 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 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 324 MET 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 521 GLU Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 627 LEU 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 38 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 51 optimal weight: 0.0970 chunk 58 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 0.0070 overall best weight: 1.0202 ------------------------------------------------------------------------------- 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 = 0.4620 r_free = 0.4620 target = 0.241431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.224311 restraints weight = 8005.284| |-----------------------------------------------------------------------------| r_work (start): 0.4479 rms_B_bonded: 2.32 r_work: 0.4400 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5654 Z= 0.140 Angle : 0.779 11.094 7693 Z= 0.375 Chirality : 0.045 0.191 918 Planarity : 0.005 0.043 973 Dihedral : 4.907 16.661 771 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.73 % Allowed : 24.49 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.32), residues: 722 helix: 0.12 (0.24), residues: 470 sheet: 0.08 (0.90), residues: 33 loop : -1.36 (0.46), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 453 TYR 0.024 0.001 TYR A 30 PHE 0.008 0.001 PHE A 449 TRP 0.032 0.002 TRP A 5 HIS 0.008 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 5654) covalent geometry : angle 0.77927 ( 7693) hydrogen bonds : bond 0.03871 ( 348) hydrogen bonds : angle 4.72266 ( 1020) =============================================================================== Job complete usr+sys time: 1508.43 seconds wall clock time: 26 minutes 29.09 seconds (1589.09 seconds total)