Starting phenix.real_space_refine on Wed Apr 30 00:47:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l2e_62773/04_2025/9l2e_62773.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l2e_62773/04_2025/9l2e_62773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l2e_62773/04_2025/9l2e_62773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l2e_62773/04_2025/9l2e_62773.map" model { file = "/net/cci-nas-00/data/ceres_data/9l2e_62773/04_2025/9l2e_62773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l2e_62773/04_2025/9l2e_62773.cif" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.169 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 48 5.16 5 C 5680 2.51 5 N 1624 2.21 5 O 1712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9064 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1133 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 2, 'TRANS': 136} Restraints were copied for chains: C, B, E, D, G, F, H Time building chain proxies: 4.40, per 1000 atoms: 0.49 Number of scatterers: 9064 At special positions: 0 Unit cell: (105.848, 105.848, 62.216, 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 48 16.00 O 1712 8.00 N 1624 7.00 C 5680 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: 2.52 Conformation dependent library (CDL) restraints added in 1.1 seconds 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 0 sheets defined 83.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 426 through 437 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 447 through 455 Processing helix chain 'A' and resid 459 through 476 removed outlier: 3.507A pdb=" N PHE A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.865A pdb=" N TRP A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 removed outlier: 3.692A pdb=" N ARG A 499 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 496 through 500' Processing helix chain 'A' and resid 501 through 508 removed outlier: 3.742A pdb=" N CYS A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 518 removed outlier: 3.705A pdb=" N LEU A 515 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS A 516 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 531 through 545 Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 413 through 424 Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 447 through 455 Processing helix chain 'B' and resid 459 through 476 removed outlier: 3.506A pdb=" N PHE B 476 " --> pdb=" O GLU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 495 removed outlier: 3.866A pdb=" N TRP B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 removed outlier: 3.692A pdb=" N ARG B 499 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN B 500 " --> pdb=" O ARG B 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 496 through 500' Processing helix chain 'B' and resid 501 through 508 removed outlier: 3.742A pdb=" N CYS B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 518 removed outlier: 3.704A pdb=" N LEU B 515 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS B 516 " --> pdb=" O SER B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 Processing helix chain 'B' and resid 531 through 545 Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 413 through 424 Processing helix chain 'C' and resid 426 through 437 Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 447 through 455 Processing helix chain 'C' and resid 459 through 476 removed outlier: 3.506A pdb=" N PHE C 476 " --> pdb=" O GLU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 495 removed outlier: 3.866A pdb=" N TRP C 490 " --> pdb=" O ASN C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 500 removed outlier: 3.693A pdb=" N ARG C 499 " --> pdb=" O PRO C 496 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN C 500 " --> pdb=" O ARG C 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 496 through 500' Processing helix chain 'C' and resid 501 through 508 removed outlier: 3.742A pdb=" N CYS C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 518 removed outlier: 3.705A pdb=" N LEU C 515 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS C 516 " --> pdb=" O SER C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 531 through 545 Processing helix chain 'D' and resid 408 through 412 Processing helix chain 'D' and resid 413 through 424 Processing helix chain 'D' and resid 426 through 437 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 447 through 455 Processing helix chain 'D' and resid 459 through 476 removed outlier: 3.507A pdb=" N PHE D 476 " --> pdb=" O GLU D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 495 removed outlier: 3.866A pdb=" N TRP D 490 " --> pdb=" O ASN D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 500 removed outlier: 3.692A pdb=" N ARG D 499 " --> pdb=" O PRO D 496 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN D 500 " --> pdb=" O ARG D 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 496 through 500' Processing helix chain 'D' and resid 501 through 508 removed outlier: 3.741A pdb=" N CYS D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 518 removed outlier: 3.706A pdb=" N LEU D 515 " --> pdb=" O ARG D 512 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N HIS D 516 " --> pdb=" O SER D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 531 through 545 Processing helix chain 'E' and resid 408 through 412 Processing helix chain 'E' and resid 413 through 424 Processing helix chain 'E' and resid 426 through 437 Processing helix chain 'E' and resid 439 through 445 Processing helix chain 'E' and resid 447 through 455 Processing helix chain 'E' and resid 459 through 476 removed outlier: 3.506A pdb=" N PHE E 476 " --> pdb=" O GLU E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 495 removed outlier: 3.866A pdb=" N TRP E 490 " --> pdb=" O ASN E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 500 removed outlier: 3.692A pdb=" N ARG E 499 " --> pdb=" O PRO E 496 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN E 500 " --> pdb=" O ARG E 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 496 through 500' Processing helix chain 'E' and resid 501 through 508 removed outlier: 3.742A pdb=" N CYS E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 518 removed outlier: 3.705A pdb=" N LEU E 515 " --> pdb=" O ARG E 512 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS E 516 " --> pdb=" O SER E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 526 Processing helix chain 'E' and resid 531 through 545 Processing helix chain 'F' and resid 408 through 412 Processing helix chain 'F' and resid 413 through 424 Processing helix chain 'F' and resid 426 through 437 Processing helix chain 'F' and resid 439 through 445 Processing helix chain 'F' and resid 447 through 455 Processing helix chain 'F' and resid 459 through 476 removed outlier: 3.506A pdb=" N PHE F 476 " --> pdb=" O GLU F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 495 removed outlier: 3.865A pdb=" N TRP F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 500 removed outlier: 3.693A pdb=" N ARG F 499 " --> pdb=" O PRO F 496 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN F 500 " --> pdb=" O ARG F 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 496 through 500' Processing helix chain 'F' and resid 501 through 508 removed outlier: 3.742A pdb=" N CYS F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 512 through 518 removed outlier: 3.705A pdb=" N LEU F 515 " --> pdb=" O ARG F 512 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS F 516 " --> pdb=" O SER F 513 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 526 Processing helix chain 'F' and resid 531 through 545 Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 413 through 424 Processing helix chain 'G' and resid 426 through 437 Processing helix chain 'G' and resid 439 through 445 Processing helix chain 'G' and resid 447 through 455 Processing helix chain 'G' and resid 459 through 476 removed outlier: 3.506A pdb=" N PHE G 476 " --> pdb=" O GLU G 472 " (cutoff:3.500A) Processing helix chain 'G' and resid 486 through 495 removed outlier: 3.866A pdb=" N TRP G 490 " --> pdb=" O ASN G 486 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 500 removed outlier: 3.691A pdb=" N ARG G 499 " --> pdb=" O PRO G 496 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN G 500 " --> pdb=" O ARG G 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 496 through 500' Processing helix chain 'G' and resid 501 through 508 removed outlier: 3.741A pdb=" N CYS G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 518 removed outlier: 3.706A pdb=" N LEU G 515 " --> pdb=" O ARG G 512 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS G 516 " --> pdb=" O SER G 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 526 Processing helix chain 'G' and resid 531 through 545 Processing helix chain 'H' and resid 408 through 412 Processing helix chain 'H' and resid 413 through 424 Processing helix chain 'H' and resid 426 through 437 Processing helix chain 'H' and resid 439 through 445 Processing helix chain 'H' and resid 447 through 455 Processing helix chain 'H' and resid 459 through 476 removed outlier: 3.506A pdb=" N PHE H 476 " --> pdb=" O GLU H 472 " (cutoff:3.500A) Processing helix chain 'H' and resid 486 through 495 removed outlier: 3.866A pdb=" N TRP H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 500 removed outlier: 3.693A pdb=" N ARG H 499 " --> pdb=" O PRO H 496 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN H 500 " --> pdb=" O ARG H 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 496 through 500' Processing helix chain 'H' and resid 501 through 508 removed outlier: 3.742A pdb=" N CYS H 508 " --> pdb=" O GLY H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 512 through 518 removed outlier: 3.706A pdb=" N LEU H 515 " --> pdb=" O ARG H 512 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS H 516 " --> pdb=" O SER H 513 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 526 Processing helix chain 'H' and resid 531 through 545 512 hydrogen bonds defined for protein. 1440 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3072 1.34 - 1.46: 1596 1.46 - 1.57: 4500 1.57 - 1.69: 0 1.69 - 1.80: 64 Bond restraints: 9232 Sorted by residual: bond pdb=" N TYR C 429 " pdb=" CA TYR C 429 " ideal model delta sigma weight residual 1.457 1.444 0.013 1.35e-02 5.49e+03 9.24e-01 bond pdb=" N TYR G 429 " pdb=" CA TYR G 429 " ideal model delta sigma weight residual 1.457 1.444 0.013 1.35e-02 5.49e+03 9.10e-01 bond pdb=" N TYR E 429 " pdb=" CA TYR E 429 " ideal model delta sigma weight residual 1.457 1.444 0.013 1.35e-02 5.49e+03 9.10e-01 bond pdb=" N TYR D 429 " pdb=" CA TYR D 429 " ideal model delta sigma weight residual 1.457 1.444 0.013 1.35e-02 5.49e+03 8.95e-01 bond pdb=" N TYR A 429 " pdb=" CA TYR A 429 " ideal model delta sigma weight residual 1.457 1.445 0.013 1.35e-02 5.49e+03 8.60e-01 ... (remaining 9227 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 11836 1.22 - 2.44: 516 2.44 - 3.67: 56 3.67 - 4.89: 8 4.89 - 6.11: 16 Bond angle restraints: 12432 Sorted by residual: angle pdb=" C VAL F 409 " pdb=" CA VAL F 409 " pdb=" CB VAL F 409 " ideal model delta sigma weight residual 114.35 111.65 2.70 1.06e+00 8.90e-01 6.51e+00 angle pdb=" C VAL C 409 " pdb=" CA VAL C 409 " pdb=" CB VAL C 409 " ideal model delta sigma weight residual 114.35 111.67 2.68 1.06e+00 8.90e-01 6.41e+00 angle pdb=" C VAL D 409 " pdb=" CA VAL D 409 " pdb=" CB VAL D 409 " ideal model delta sigma weight residual 114.35 111.68 2.67 1.06e+00 8.90e-01 6.34e+00 angle pdb=" C VAL A 409 " pdb=" CA VAL A 409 " pdb=" CB VAL A 409 " ideal model delta sigma weight residual 114.35 111.69 2.66 1.06e+00 8.90e-01 6.32e+00 angle pdb=" C VAL B 409 " pdb=" CA VAL B 409 " pdb=" CB VAL B 409 " ideal model delta sigma weight residual 114.35 111.70 2.65 1.06e+00 8.90e-01 6.26e+00 ... (remaining 12427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 4560 17.11 - 34.21: 656 34.21 - 51.32: 224 51.32 - 68.43: 80 68.43 - 85.53: 40 Dihedral angle restraints: 5560 sinusoidal: 2344 harmonic: 3216 Sorted by residual: dihedral pdb=" CA LEU B 514 " pdb=" CB LEU B 514 " pdb=" CG LEU B 514 " pdb=" CD1 LEU B 514 " ideal model delta sinusoidal sigma weight residual 60.00 119.34 -59.34 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LEU F 514 " pdb=" CB LEU F 514 " pdb=" CG LEU F 514 " pdb=" CD1 LEU F 514 " ideal model delta sinusoidal sigma weight residual 60.00 119.30 -59.30 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LEU A 514 " pdb=" CB LEU A 514 " pdb=" CG LEU A 514 " pdb=" CD1 LEU A 514 " ideal model delta sinusoidal sigma weight residual 60.00 119.29 -59.29 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 562 0.021 - 0.042: 445 0.042 - 0.062: 208 0.062 - 0.083: 86 0.083 - 0.104: 51 Chirality restraints: 1352 Sorted by residual: chirality pdb=" CA PRO B 410 " pdb=" N PRO B 410 " pdb=" C PRO B 410 " pdb=" CB PRO B 410 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.10 2.00e-01 2.50e+01 2.70e-01 chirality pdb=" CA PRO H 410 " pdb=" N PRO H 410 " pdb=" C PRO H 410 " pdb=" CB PRO H 410 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.10 2.00e-01 2.50e+01 2.69e-01 chirality pdb=" CA ILE H 529 " pdb=" N ILE H 529 " pdb=" C ILE H 529 " pdb=" CB ILE H 529 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.68e-01 ... (remaining 1349 not shown) Planarity restraints: 1600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 441 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" CG ASP C 441 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASP C 441 " 0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP C 441 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 441 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" CG ASP F 441 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASP F 441 " 0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP F 441 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 441 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" CG ASP B 441 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASP B 441 " -0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP B 441 " -0.007 2.00e-02 2.50e+03 ... (remaining 1597 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 96 2.62 - 3.19: 7746 3.19 - 3.76: 14900 3.76 - 4.33: 20786 4.33 - 4.90: 34392 Nonbonded interactions: 77920 Sorted by model distance: nonbonded pdb=" OG SER A 459 " pdb=" OD2 ASP H 454 " model vdw 2.047 3.040 nonbonded pdb=" OD2 ASP E 454 " pdb=" OG SER F 459 " model vdw 2.085 3.040 nonbonded pdb=" OD2 ASP G 454 " pdb=" OG SER H 459 " model vdw 2.095 3.040 nonbonded pdb=" OD2 ASP F 454 " pdb=" OG SER G 459 " model vdw 2.106 3.040 nonbonded pdb=" OD2 ASP D 454 " pdb=" OG SER E 459 " model vdw 2.118 3.040 ... (remaining 77915 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'H' } 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: 38.640 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.300 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9232 Z= 0.157 Angle : 0.582 6.110 12432 Z= 0.334 Chirality : 0.038 0.104 1352 Planarity : 0.004 0.026 1600 Dihedral : 20.563 85.535 3480 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.81 % Allowed : 31.25 % Favored : 66.94 % 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: 1.27 (0.26), residues: 1096 helix: 0.88 (0.19), residues: 808 sheet: None (None), residues: 0 loop : 1.16 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 412 HIS 0.003 0.001 HIS D 516 PHE 0.012 0.002 PHE H 467 TYR 0.010 0.002 TYR H 503 ARG 0.004 0.000 ARG B 463 Details of bonding type rmsd hydrogen bonds : bond 0.16882 ( 512) hydrogen bonds : angle 5.86197 ( 1440) covalent geometry : bond 0.00334 ( 9232) covalent geometry : angle 0.58162 (12432) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 247 time to evaluate : 1.269 Fit side-chains REVERT: A 486 ASN cc_start: 0.8012 (t0) cc_final: 0.7168 (t0) REVERT: A 489 ASP cc_start: 0.7241 (m-30) cc_final: 0.6925 (p0) REVERT: C 520 GLU cc_start: 0.7642 (tp30) cc_final: 0.7414 (tp30) REVERT: E 486 ASN cc_start: 0.8079 (t0) cc_final: 0.7375 (t0) REVERT: E 489 ASP cc_start: 0.7201 (m-30) cc_final: 0.6950 (p0) REVERT: G 486 ASN cc_start: 0.8015 (t0) cc_final: 0.7264 (t0) REVERT: G 489 ASP cc_start: 0.7195 (m-30) cc_final: 0.6926 (p0) outliers start: 18 outliers final: 15 residues processed: 255 average time/residue: 1.9253 time to fit residues: 516.0868 Evaluate side-chains 247 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 232 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 462 THR Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 462 THR Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 462 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 42 optimal weight: 0.3980 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN B 436 GLN C 436 GLN D 436 GLN E 436 GLN F 436 GLN G 436 GLN H 436 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.188795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.168712 restraints weight = 9176.375| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.34 r_work: 0.3712 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9232 Z= 0.161 Angle : 0.553 6.129 12432 Z= 0.299 Chirality : 0.039 0.105 1352 Planarity : 0.004 0.025 1600 Dihedral : 6.444 55.404 1263 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.94 % Allowed : 27.02 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.28), residues: 1096 helix: 1.11 (0.19), residues: 776 sheet: None (None), residues: 0 loop : 2.48 (0.43), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 412 HIS 0.002 0.001 HIS G 516 PHE 0.009 0.002 PHE E 433 TYR 0.012 0.002 TYR E 503 ARG 0.003 0.000 ARG C 463 Details of bonding type rmsd hydrogen bonds : bond 0.05357 ( 512) hydrogen bonds : angle 5.26988 ( 1440) covalent geometry : bond 0.00343 ( 9232) covalent geometry : angle 0.55272 (12432) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 251 time to evaluate : 1.168 Fit side-chains REVERT: A 446 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7400 (tt) REVERT: A 486 ASN cc_start: 0.8267 (t0) cc_final: 0.7442 (t0) REVERT: A 489 ASP cc_start: 0.7876 (m-30) cc_final: 0.7268 (p0) REVERT: A 515 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7501 (mt) REVERT: B 446 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7648 (tt) REVERT: B 515 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7488 (mt) REVERT: C 446 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7434 (tt) REVERT: C 520 GLU cc_start: 0.7801 (tp30) cc_final: 0.7491 (tp30) REVERT: D 446 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7660 (tt) REVERT: D 489 ASP cc_start: 0.7718 (m-30) cc_final: 0.7413 (p0) REVERT: D 515 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7569 (mt) REVERT: E 414 GLU cc_start: 0.7414 (mp0) cc_final: 0.7139 (mt-10) REVERT: E 446 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7379 (tt) REVERT: E 486 ASN cc_start: 0.8245 (t0) cc_final: 0.7429 (t0) REVERT: E 489 ASP cc_start: 0.7878 (m-30) cc_final: 0.7281 (p0) REVERT: E 515 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7482 (mt) REVERT: F 446 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7652 (tt) REVERT: F 489 ASP cc_start: 0.7755 (m-30) cc_final: 0.7400 (p0) REVERT: F 515 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7491 (mt) REVERT: G 414 GLU cc_start: 0.7475 (mp0) cc_final: 0.7187 (mt-10) REVERT: G 446 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7341 (tt) REVERT: G 486 ASN cc_start: 0.8197 (t0) cc_final: 0.7326 (t0) REVERT: G 489 ASP cc_start: 0.7802 (m-30) cc_final: 0.7231 (p0) REVERT: G 515 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7496 (mt) REVERT: H 446 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7672 (tt) REVERT: H 489 ASP cc_start: 0.7725 (m-30) cc_final: 0.7420 (p0) REVERT: H 515 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7522 (mt) outliers start: 49 outliers final: 13 residues processed: 267 average time/residue: 1.6823 time to fit residues: 472.1642 Evaluate side-chains 256 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 540 THR Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 540 THR Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 462 THR Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 540 THR Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 540 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 8 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 0.0470 chunk 70 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.194708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.175759 restraints weight = 9604.371| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.30 r_work: 0.3823 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9232 Z= 0.152 Angle : 0.541 6.625 12432 Z= 0.286 Chirality : 0.038 0.106 1352 Planarity : 0.004 0.027 1600 Dihedral : 6.313 56.930 1258 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 5.44 % Allowed : 27.12 % Favored : 67.44 % 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: 2.08 (0.27), residues: 1096 helix: 1.18 (0.19), residues: 776 sheet: None (None), residues: 0 loop : 2.33 (0.42), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 412 HIS 0.002 0.001 HIS A 516 PHE 0.010 0.002 PHE C 433 TYR 0.011 0.002 TYR A 503 ARG 0.003 0.000 ARG C 517 Details of bonding type rmsd hydrogen bonds : bond 0.05137 ( 512) hydrogen bonds : angle 5.17953 ( 1440) covalent geometry : bond 0.00318 ( 9232) covalent geometry : angle 0.54131 (12432) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 247 time to evaluate : 1.017 Fit side-chains REVERT: A 414 GLU cc_start: 0.7428 (mp0) cc_final: 0.7139 (mt-10) REVERT: A 446 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7319 (tt) REVERT: A 515 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7534 (mt) REVERT: B 414 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7385 (mt-10) REVERT: B 446 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7589 (tt) REVERT: B 515 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7512 (mt) REVERT: C 446 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7358 (tt) REVERT: C 515 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7374 (mt) REVERT: D 446 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7585 (tt) REVERT: D 489 ASP cc_start: 0.7880 (m-30) cc_final: 0.7501 (p0) REVERT: D 515 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7604 (mt) REVERT: E 414 GLU cc_start: 0.7436 (mp0) cc_final: 0.7183 (mt-10) REVERT: E 446 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7342 (tt) REVERT: E 486 ASN cc_start: 0.8328 (t0) cc_final: 0.8111 (t0) REVERT: E 515 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7524 (mt) REVERT: F 414 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7408 (mt-10) REVERT: F 446 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7572 (tt) REVERT: F 489 ASP cc_start: 0.7897 (m-30) cc_final: 0.7517 (p0) REVERT: F 515 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7536 (mt) REVERT: G 414 GLU cc_start: 0.7359 (mp0) cc_final: 0.7124 (mt-10) REVERT: G 446 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7279 (tt) REVERT: G 486 ASN cc_start: 0.8281 (t0) cc_final: 0.8062 (t0) REVERT: G 515 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7521 (mt) REVERT: H 446 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7600 (tt) REVERT: H 489 ASP cc_start: 0.7761 (m-30) cc_final: 0.7496 (p0) REVERT: H 515 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7563 (mt) outliers start: 54 outliers final: 10 residues processed: 266 average time/residue: 1.4845 time to fit residues: 415.4330 Evaluate side-chains 262 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 236 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 513 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 462 THR Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 513 SER Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 462 THR Chi-restraints excluded: chain H residue 513 SER Chi-restraints excluded: chain H residue 515 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 40 optimal weight: 0.0040 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.0980 chunk 94 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.193688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.174693 restraints weight = 9499.440| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.30 r_work: 0.3818 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9232 Z= 0.177 Angle : 0.581 6.615 12432 Z= 0.305 Chirality : 0.039 0.106 1352 Planarity : 0.004 0.028 1600 Dihedral : 6.489 58.679 1256 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 6.15 % Allowed : 25.50 % Favored : 68.35 % 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: 1.91 (0.27), residues: 1096 helix: 1.13 (0.19), residues: 776 sheet: None (None), residues: 0 loop : 2.05 (0.41), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 412 HIS 0.001 0.001 HIS C 516 PHE 0.011 0.002 PHE C 433 TYR 0.012 0.002 TYR A 503 ARG 0.003 0.000 ARG A 465 Details of bonding type rmsd hydrogen bonds : bond 0.05298 ( 512) hydrogen bonds : angle 5.30354 ( 1440) covalent geometry : bond 0.00383 ( 9232) covalent geometry : angle 0.58093 (12432) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 233 time to evaluate : 1.156 Fit side-chains REVERT: A 446 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7394 (tt) REVERT: A 515 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7505 (mt) REVERT: B 414 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7375 (mt-10) REVERT: B 446 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7666 (tt) REVERT: B 450 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: B 515 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7536 (mt) REVERT: C 446 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7364 (tt) REVERT: C 457 MET cc_start: 0.6619 (mtt) cc_final: 0.6387 (mmt) REVERT: C 515 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7366 (mt) REVERT: D 446 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7659 (tt) REVERT: D 515 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7594 (mt) REVERT: E 414 GLU cc_start: 0.7421 (mp0) cc_final: 0.7155 (mt-10) REVERT: E 446 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7404 (tt) REVERT: E 515 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7491 (mt) REVERT: F 414 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: F 446 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7642 (tt) REVERT: F 450 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6681 (mp0) REVERT: F 515 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7567 (mt) REVERT: G 414 GLU cc_start: 0.7437 (mp0) cc_final: 0.7180 (mt-10) REVERT: G 446 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7352 (tt) REVERT: G 486 ASN cc_start: 0.8268 (t0) cc_final: 0.8067 (t0) REVERT: G 515 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7497 (mt) REVERT: H 446 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7661 (tt) REVERT: H 515 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7551 (mt) outliers start: 61 outliers final: 25 residues processed: 258 average time/residue: 1.3892 time to fit residues: 378.6281 Evaluate side-chains 275 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 230 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 513 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 462 THR Chi-restraints excluded: chain D residue 513 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 540 THR Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain F residue 414 GLU Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 450 GLU Chi-restraints excluded: chain F residue 454 ASP Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain F residue 513 SER Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 540 THR Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 462 THR Chi-restraints excluded: chain G residue 487 LEU Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 540 THR Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 462 THR Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 540 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 92 optimal weight: 0.0020 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 66 optimal weight: 0.0970 chunk 56 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.198097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.179197 restraints weight = 9455.085| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.30 r_work: 0.3856 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 9232 Z= 0.114 Angle : 0.499 6.458 12432 Z= 0.257 Chirality : 0.036 0.110 1352 Planarity : 0.003 0.030 1600 Dihedral : 6.252 58.291 1256 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.73 % Allowed : 27.72 % Favored : 68.55 % 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: 2.26 (0.27), residues: 1096 helix: 1.41 (0.19), residues: 768 sheet: None (None), residues: 0 loop : 2.10 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 490 HIS 0.002 0.000 HIS C 516 PHE 0.009 0.001 PHE E 433 TYR 0.009 0.001 TYR C 429 ARG 0.002 0.000 ARG D 463 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 512) hydrogen bonds : angle 4.90509 ( 1440) covalent geometry : bond 0.00226 ( 9232) covalent geometry : angle 0.49852 (12432) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 261 time to evaluate : 1.026 Fit side-chains REVERT: A 414 GLU cc_start: 0.7260 (mp0) cc_final: 0.7035 (mt-10) REVERT: A 446 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7293 (tt) REVERT: A 494 LEU cc_start: 0.7655 (tp) cc_final: 0.7260 (mp) REVERT: A 515 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7512 (mt) REVERT: B 414 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7393 (mt-10) REVERT: B 446 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7521 (tt) REVERT: C 446 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7240 (tt) REVERT: D 414 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7413 (mt-10) REVERT: D 446 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7530 (tt) REVERT: D 489 ASP cc_start: 0.7788 (m-30) cc_final: 0.7437 (p0) REVERT: D 515 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7617 (mt) REVERT: E 414 GLU cc_start: 0.7355 (mp0) cc_final: 0.7144 (mt-10) REVERT: E 424 ILE cc_start: 0.6909 (pt) cc_final: 0.6679 (pt) REVERT: E 446 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7302 (tt) REVERT: E 515 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7517 (mt) REVERT: F 414 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7394 (mt-10) REVERT: F 446 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7517 (tt) REVERT: F 480 SER cc_start: 0.8636 (m) cc_final: 0.8428 (p) REVERT: F 489 ASP cc_start: 0.7744 (m-30) cc_final: 0.7430 (p0) REVERT: G 414 GLU cc_start: 0.7348 (mp0) cc_final: 0.7146 (mt-10) REVERT: G 424 ILE cc_start: 0.6914 (pt) cc_final: 0.6683 (pt) REVERT: G 446 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7252 (tt) REVERT: G 515 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7498 (mt) REVERT: H 414 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7432 (mt-10) REVERT: H 446 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7518 (tt) REVERT: H 489 ASP cc_start: 0.7780 (m-30) cc_final: 0.7484 (p0) outliers start: 37 outliers final: 0 residues processed: 282 average time/residue: 1.3159 time to fit residues: 392.2797 Evaluate side-chains 240 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 226 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 414 GLU Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain H residue 446 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 3 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 38 optimal weight: 0.1980 chunk 90 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.194272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.175267 restraints weight = 9379.206| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 1.30 r_work: 0.3820 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9232 Z= 0.149 Angle : 0.520 6.009 12432 Z= 0.280 Chirality : 0.037 0.106 1352 Planarity : 0.004 0.029 1600 Dihedral : 6.313 58.221 1256 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.03 % Allowed : 27.02 % Favored : 68.95 % 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: 2.09 (0.27), residues: 1096 helix: 1.32 (0.19), residues: 776 sheet: None (None), residues: 0 loop : 1.95 (0.41), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 420 HIS 0.002 0.000 HIS C 516 PHE 0.009 0.002 PHE G 433 TYR 0.012 0.002 TYR C 503 ARG 0.002 0.000 ARG G 465 Details of bonding type rmsd hydrogen bonds : bond 0.04759 ( 512) hydrogen bonds : angle 5.07647 ( 1440) covalent geometry : bond 0.00315 ( 9232) covalent geometry : angle 0.51952 (12432) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 230 time to evaluate : 1.033 Fit side-chains REVERT: A 414 GLU cc_start: 0.7257 (mp0) cc_final: 0.6997 (mt-10) REVERT: A 446 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7394 (tt) REVERT: A 489 ASP cc_start: 0.7834 (m-30) cc_final: 0.7406 (p0) REVERT: A 515 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7553 (mt) REVERT: B 414 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7346 (mt-10) REVERT: B 446 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7592 (tt) REVERT: B 515 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7662 (mt) REVERT: C 446 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7370 (tt) REVERT: D 414 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: D 446 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7585 (tt) REVERT: D 489 ASP cc_start: 0.7772 (m-30) cc_final: 0.7382 (p0) REVERT: D 515 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7738 (mt) REVERT: E 414 GLU cc_start: 0.7343 (mp0) cc_final: 0.7104 (mt-10) REVERT: E 446 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7381 (tt) REVERT: E 489 ASP cc_start: 0.7794 (m-30) cc_final: 0.7339 (p0) REVERT: E 515 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7541 (mt) REVERT: F 414 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7377 (mt-10) REVERT: F 446 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7573 (tt) REVERT: F 450 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: F 489 ASP cc_start: 0.7786 (m-30) cc_final: 0.7414 (p0) REVERT: G 414 GLU cc_start: 0.7345 (mp0) cc_final: 0.7099 (mt-10) REVERT: G 446 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7388 (tt) REVERT: G 515 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7533 (mt) REVERT: H 414 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7391 (mt-10) REVERT: H 446 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7574 (tt) outliers start: 40 outliers final: 10 residues processed: 257 average time/residue: 1.4786 time to fit residues: 400.2535 Evaluate side-chains 258 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 231 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain C residue 430 CYS Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 430 CYS Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain E residue 430 CYS Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 414 GLU Chi-restraints excluded: chain F residue 430 CYS Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 450 GLU Chi-restraints excluded: chain G residue 430 CYS Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain H residue 430 CYS Chi-restraints excluded: chain H residue 446 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 92 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.195037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.175922 restraints weight = 9498.848| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 1.31 r_work: 0.3825 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9232 Z= 0.134 Angle : 0.495 5.868 12432 Z= 0.267 Chirality : 0.036 0.107 1352 Planarity : 0.003 0.028 1600 Dihedral : 6.291 58.512 1256 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.73 % Allowed : 27.62 % Favored : 68.65 % 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: 2.16 (0.27), residues: 1096 helix: 1.37 (0.19), residues: 768 sheet: None (None), residues: 0 loop : 1.96 (0.39), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 490 HIS 0.002 0.000 HIS C 516 PHE 0.009 0.002 PHE G 433 TYR 0.011 0.001 TYR A 503 ARG 0.002 0.000 ARG H 465 Details of bonding type rmsd hydrogen bonds : bond 0.04512 ( 512) hydrogen bonds : angle 4.98204 ( 1440) covalent geometry : bond 0.00276 ( 9232) covalent geometry : angle 0.49517 (12432) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 1.064 Fit side-chains REVERT: A 414 GLU cc_start: 0.7250 (mp0) cc_final: 0.7005 (mt-10) REVERT: A 446 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7366 (tt) REVERT: A 457 MET cc_start: 0.6149 (mmt) cc_final: 0.5757 (mmt) REVERT: A 515 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7533 (mt) REVERT: B 414 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7376 (mt-10) REVERT: B 446 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7604 (tt) REVERT: B 515 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7628 (mt) REVERT: C 446 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7335 (tt) REVERT: C 489 ASP cc_start: 0.7874 (m-30) cc_final: 0.7387 (p0) REVERT: D 414 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7399 (mt-10) REVERT: D 446 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7601 (tt) REVERT: D 489 ASP cc_start: 0.7773 (m-30) cc_final: 0.7351 (p0) REVERT: D 515 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7697 (mt) REVERT: E 414 GLU cc_start: 0.7325 (mp0) cc_final: 0.7094 (mt-10) REVERT: E 446 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7359 (tt) REVERT: E 457 MET cc_start: 0.6157 (mmt) cc_final: 0.5554 (mmt) REVERT: E 515 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7514 (mt) REVERT: F 414 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7397 (mt-10) REVERT: F 446 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7575 (tt) REVERT: F 450 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6580 (mp0) REVERT: F 486 ASN cc_start: 0.8247 (t0) cc_final: 0.7581 (t0) REVERT: F 489 ASP cc_start: 0.7734 (m-30) cc_final: 0.7356 (p0) REVERT: F 515 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7711 (mt) REVERT: G 414 GLU cc_start: 0.7389 (mp0) cc_final: 0.7136 (mt-10) REVERT: G 446 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7374 (tt) REVERT: G 457 MET cc_start: 0.6192 (mmt) cc_final: 0.5568 (mmt) REVERT: G 489 ASP cc_start: 0.7828 (m-30) cc_final: 0.7407 (p0) REVERT: G 515 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7485 (mt) REVERT: H 414 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: H 446 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7566 (tt) REVERT: H 486 ASN cc_start: 0.8166 (t0) cc_final: 0.7767 (t0) REVERT: H 489 ASP cc_start: 0.7699 (m-30) cc_final: 0.7415 (p0) REVERT: H 515 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7744 (mt) outliers start: 37 outliers final: 10 residues processed: 243 average time/residue: 1.5867 time to fit residues: 406.1670 Evaluate side-chains 242 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 213 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain C residue 430 CYS Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 430 CYS Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain E residue 430 CYS Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 414 GLU Chi-restraints excluded: chain F residue 430 CYS Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 450 GLU Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain G residue 430 CYS Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain H residue 414 GLU Chi-restraints excluded: chain H residue 430 CYS Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 515 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 91 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 522 GLN D 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.192358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.173271 restraints weight = 9673.312| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.30 r_work: 0.3799 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9232 Z= 0.185 Angle : 0.562 5.423 12432 Z= 0.304 Chirality : 0.039 0.109 1352 Planarity : 0.004 0.029 1600 Dihedral : 6.546 59.966 1256 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.44 % Allowed : 26.21 % Favored : 69.35 % 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: 1.82 (0.27), residues: 1096 helix: 1.13 (0.19), residues: 776 sheet: None (None), residues: 0 loop : 1.83 (0.41), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 412 HIS 0.002 0.000 HIS C 516 PHE 0.010 0.002 PHE G 433 TYR 0.012 0.002 TYR A 503 ARG 0.003 0.000 ARG B 465 Details of bonding type rmsd hydrogen bonds : bond 0.05251 ( 512) hydrogen bonds : angle 5.23301 ( 1440) covalent geometry : bond 0.00403 ( 9232) covalent geometry : angle 0.56189 (12432) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 1.012 Fit side-chains REVERT: A 414 GLU cc_start: 0.7383 (mp0) cc_final: 0.7103 (mt-10) REVERT: A 446 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7405 (tt) REVERT: A 489 ASP cc_start: 0.7933 (m-30) cc_final: 0.7416 (p0) REVERT: A 515 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7551 (mt) REVERT: B 446 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7673 (tt) REVERT: B 515 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7621 (mt) REVERT: C 446 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7386 (tt) REVERT: D 446 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7668 (tt) REVERT: D 450 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: D 515 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7687 (mt) REVERT: E 414 GLU cc_start: 0.7395 (mp0) cc_final: 0.7124 (mt-10) REVERT: E 446 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7396 (tt) REVERT: E 489 ASP cc_start: 0.7921 (m-30) cc_final: 0.7408 (p0) REVERT: E 515 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7519 (mt) REVERT: F 446 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7662 (tt) REVERT: F 450 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6606 (mp0) REVERT: F 515 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7652 (mt) REVERT: G 414 GLU cc_start: 0.7403 (mp0) cc_final: 0.7131 (mt-10) REVERT: G 446 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7401 (tt) REVERT: G 515 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7509 (mt) REVERT: H 446 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7641 (tt) REVERT: H 489 ASP cc_start: 0.7801 (m-30) cc_final: 0.7487 (p0) REVERT: H 515 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7661 (mt) outliers start: 44 outliers final: 20 residues processed: 249 average time/residue: 1.5722 time to fit residues: 411.2553 Evaluate side-chains 257 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain C residue 430 CYS Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 430 CYS Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 454 ASP Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 430 CYS Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 450 GLU Chi-restraints excluded: chain F residue 454 ASP Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 450 GLU Chi-restraints excluded: chain G residue 487 LEU Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain H residue 430 CYS Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 454 ASP Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain H residue 515 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 28 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 0.0040 chunk 54 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 53 optimal weight: 0.0170 chunk 12 optimal weight: 3.9990 overall best weight: 0.4230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 522 GLN D 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.196204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.177010 restraints weight = 9452.752| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.33 r_work: 0.3841 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9232 Z= 0.120 Angle : 0.482 5.923 12432 Z= 0.260 Chirality : 0.036 0.109 1352 Planarity : 0.003 0.030 1600 Dihedral : 6.356 59.924 1256 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.33 % Allowed : 26.51 % Favored : 70.16 % 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: 2.10 (0.27), residues: 1096 helix: 1.32 (0.19), residues: 768 sheet: None (None), residues: 0 loop : 1.95 (0.39), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 490 HIS 0.002 0.000 HIS C 516 PHE 0.008 0.002 PHE G 433 TYR 0.010 0.001 TYR E 503 ARG 0.002 0.000 ARG B 463 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 512) hydrogen bonds : angle 4.94451 ( 1440) covalent geometry : bond 0.00240 ( 9232) covalent geometry : angle 0.48247 (12432) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 1.153 Fit side-chains REVERT: A 414 GLU cc_start: 0.7221 (mp0) cc_final: 0.6987 (mt-10) REVERT: A 446 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7335 (tt) REVERT: A 457 MET cc_start: 0.6112 (mmt) cc_final: 0.5820 (mmt) REVERT: A 489 ASP cc_start: 0.7834 (m-30) cc_final: 0.7373 (p0) REVERT: A 515 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7543 (mt) REVERT: B 446 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7622 (tt) REVERT: B 515 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7613 (mt) REVERT: C 446 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7307 (tt) REVERT: C 457 MET cc_start: 0.6172 (mmt) cc_final: 0.5591 (mmt) REVERT: C 489 ASP cc_start: 0.7828 (m-30) cc_final: 0.7374 (p0) REVERT: D 446 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7657 (tt) REVERT: D 489 ASP cc_start: 0.7727 (m-30) cc_final: 0.7475 (p0) REVERT: D 515 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7703 (mt) REVERT: E 414 GLU cc_start: 0.7326 (mp0) cc_final: 0.7087 (mt-10) REVERT: E 446 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7318 (tt) REVERT: E 457 MET cc_start: 0.6120 (mmt) cc_final: 0.5809 (mmt) REVERT: E 489 ASP cc_start: 0.7828 (m-30) cc_final: 0.7368 (p0) REVERT: E 515 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7552 (mt) REVERT: F 446 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7588 (tt) REVERT: F 486 ASN cc_start: 0.8151 (t0) cc_final: 0.7715 (t0) REVERT: F 489 ASP cc_start: 0.7698 (m-30) cc_final: 0.7353 (p0) REVERT: F 515 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7644 (mt) REVERT: G 414 GLU cc_start: 0.7394 (mp0) cc_final: 0.7138 (mt-10) REVERT: G 446 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7342 (tt) REVERT: G 457 MET cc_start: 0.6115 (mmt) cc_final: 0.5796 (mmt) REVERT: G 489 ASP cc_start: 0.7854 (m-30) cc_final: 0.7390 (p0) REVERT: G 515 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7529 (mt) REVERT: H 446 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7608 (tt) REVERT: H 486 ASN cc_start: 0.8261 (t0) cc_final: 0.7856 (t0) REVERT: H 489 ASP cc_start: 0.7734 (m-30) cc_final: 0.7484 (p0) REVERT: H 515 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7696 (mt) outliers start: 33 outliers final: 11 residues processed: 248 average time/residue: 1.6188 time to fit residues: 422.0146 Evaluate side-chains 242 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain C residue 430 CYS Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 430 CYS Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain E residue 430 CYS Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 430 CYS Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain G residue 430 CYS Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 450 GLU Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain H residue 430 CYS Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 515 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 84 optimal weight: 0.0060 chunk 63 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 61 optimal weight: 0.2980 chunk 81 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.194971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.175326 restraints weight = 9561.422| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.35 r_work: 0.3816 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9232 Z= 0.135 Angle : 0.500 5.446 12432 Z= 0.271 Chirality : 0.036 0.107 1352 Planarity : 0.003 0.029 1600 Dihedral : 6.317 59.910 1256 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.53 % Allowed : 27.12 % Favored : 69.35 % 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: 2.15 (0.27), residues: 1096 helix: 1.37 (0.19), residues: 768 sheet: None (None), residues: 0 loop : 1.94 (0.39), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 490 HIS 0.002 0.000 HIS H 516 PHE 0.009 0.002 PHE C 433 TYR 0.011 0.002 TYR C 503 ARG 0.002 0.000 ARG F 465 Details of bonding type rmsd hydrogen bonds : bond 0.04453 ( 512) hydrogen bonds : angle 4.96664 ( 1440) covalent geometry : bond 0.00282 ( 9232) covalent geometry : angle 0.50048 (12432) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2192 Ramachandran restraints generated. 1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 1.114 Fit side-chains REVERT: A 414 GLU cc_start: 0.7179 (mp0) cc_final: 0.6942 (mt-10) REVERT: A 446 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7370 (tt) REVERT: A 515 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7539 (mt) REVERT: B 446 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7638 (tt) REVERT: C 446 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7363 (tt) REVERT: C 489 ASP cc_start: 0.7866 (m-30) cc_final: 0.7378 (p0) REVERT: D 446 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7630 (tt) REVERT: D 489 ASP cc_start: 0.7749 (m-30) cc_final: 0.7418 (p0) REVERT: D 515 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7694 (mt) REVERT: E 414 GLU cc_start: 0.7277 (mp0) cc_final: 0.7046 (mt-10) REVERT: E 446 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7357 (tt) REVERT: E 457 MET cc_start: 0.6183 (mmt) cc_final: 0.5841 (mmt) REVERT: E 489 ASP cc_start: 0.7873 (m-30) cc_final: 0.7362 (p0) REVERT: E 515 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7526 (mt) REVERT: F 446 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7630 (tt) REVERT: F 486 ASN cc_start: 0.8138 (t0) cc_final: 0.7708 (t0) REVERT: F 489 ASP cc_start: 0.7715 (m-30) cc_final: 0.7369 (p0) REVERT: F 515 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7656 (mt) REVERT: G 414 GLU cc_start: 0.7351 (mp0) cc_final: 0.7099 (mt-10) REVERT: G 446 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7374 (tt) REVERT: G 457 MET cc_start: 0.6160 (mmt) cc_final: 0.5806 (mmt) REVERT: G 489 ASP cc_start: 0.7820 (m-30) cc_final: 0.7366 (p0) REVERT: G 515 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7524 (mt) REVERT: H 446 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7617 (tt) REVERT: H 515 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7672 (mt) outliers start: 35 outliers final: 13 residues processed: 248 average time/residue: 1.8821 time to fit residues: 489.6792 Evaluate side-chains 245 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 430 CYS Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 430 CYS Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain E residue 430 CYS Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 450 GLU Chi-restraints excluded: chain E residue 487 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 430 CYS Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain G residue 430 CYS Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 450 GLU Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain H residue 430 CYS Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain H residue 515 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 84 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.194524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.175812 restraints weight = 9471.572| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 1.26 r_work: 0.3816 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9232 Z= 0.146 Angle : 0.516 5.340 12432 Z= 0.281 Chirality : 0.037 0.114 1352 Planarity : 0.004 0.028 1600 Dihedral : 6.367 59.667 1256 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.12 % Allowed : 27.32 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.95 (0.27), residues: 1096 helix: 1.23 (0.19), residues: 776 sheet: None (None), residues: 0 loop : 1.87 (0.40), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 490 HIS 0.002 0.000 HIS C 516 PHE 0.009 0.002 PHE G 433 TYR 0.011 0.002 TYR A 503 ARG 0.002 0.000 ARG D 465 Details of bonding type rmsd hydrogen bonds : bond 0.04619 ( 512) hydrogen bonds : angle 5.02308 ( 1440) covalent geometry : bond 0.00308 ( 9232) covalent geometry : angle 0.51638 (12432) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9465.53 seconds wall clock time: 165 minutes 12.69 seconds (9912.69 seconds total)