Starting phenix.real_space_refine on Wed Sep 17 14:09:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l2e_62773/09_2025/9l2e_62773.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l2e_62773/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9l2e_62773/09_2025/9l2e_62773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l2e_62773/09_2025/9l2e_62773.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l2e_62773/09_2025/9l2e_62773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l2e_62773/09_2025/9l2e_62773.map" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C, D, E, F, G, H Time building chain proxies: 0.93, per 1000 atoms: 0.10 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: 0.59 Conformation dependent library (CDL) restraints added in 315.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.30 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: 1.25 Time building geometry restraints manager: 0.78 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' 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: 5.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.130 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.930 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG B 463 TYR 0.010 0.002 TYR H 503 PHE 0.012 0.002 PHE H 467 TRP 0.017 0.002 TRP B 412 HIS 0.003 0.001 HIS D 516 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9232) covalent geometry : angle 0.58162 (12432) hydrogen bonds : bond 0.16882 ( 512) hydrogen bonds : angle 5.86197 ( 1440) *********************** 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 : 0.356 Fit side-chains REVERT: A 486 ASN cc_start: 0.8012 (t0) cc_final: 0.7167 (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: 0.7831 time to fit residues: 209.7404 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 : 0.361 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.0170 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.190005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.169838 restraints weight = 9315.041| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.36 r_work: 0.3729 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1166 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= 0.143 Angle : 0.530 6.267 12432 Z= 0.286 Chirality : 0.037 0.106 1352 Planarity : 0.004 0.026 1600 Dihedral : 6.301 54.332 1263 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.73 % Allowed : 28.33 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.28), residues: 1096 helix: 1.17 (0.19), residues: 776 sheet: None (None), residues: 0 loop : 2.57 (0.43), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 463 TYR 0.011 0.001 TYR E 503 PHE 0.009 0.002 PHE C 433 TRP 0.009 0.001 TRP C 412 HIS 0.002 0.001 HIS G 516 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9232) covalent geometry : angle 0.52986 (12432) hydrogen bonds : bond 0.05076 ( 512) hydrogen bonds : angle 5.15919 ( 1440) *********************** 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 295 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 258 time to evaluate : 0.401 Fit side-chains REVERT: A 414 GLU cc_start: 0.7461 (mp0) cc_final: 0.7120 (mt-10) REVERT: A 446 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7423 (tt) REVERT: A 486 ASN cc_start: 0.8239 (t0) cc_final: 0.7452 (t0) REVERT: A 489 ASP cc_start: 0.7823 (m-30) cc_final: 0.7243 (p0) REVERT: A 494 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7612 (mt) REVERT: A 515 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7504 (mt) REVERT: B 446 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7563 (tt) REVERT: B 515 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7479 (mt) REVERT: C 446 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7457 (tt) REVERT: C 520 GLU cc_start: 0.7801 (tp30) cc_final: 0.7503 (tp30) REVERT: D 446 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7582 (tt) REVERT: D 515 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7555 (mt) REVERT: E 414 GLU cc_start: 0.7387 (mp0) cc_final: 0.7113 (mt-10) REVERT: E 446 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7371 (tt) REVERT: E 486 ASN cc_start: 0.8254 (t0) cc_final: 0.7486 (t0) REVERT: E 489 ASP cc_start: 0.7815 (m-30) cc_final: 0.7264 (p0) REVERT: E 515 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7472 (mt) REVERT: F 446 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7566 (tt) REVERT: F 489 ASP cc_start: 0.7745 (m-30) cc_final: 0.7367 (p0) REVERT: F 515 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7471 (mt) REVERT: G 414 GLU cc_start: 0.7468 (mp0) cc_final: 0.7194 (mt-10) REVERT: G 446 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7376 (tt) REVERT: G 486 ASN cc_start: 0.8194 (t0) cc_final: 0.7377 (t0) REVERT: G 489 ASP cc_start: 0.7746 (m-30) cc_final: 0.7211 (p0) REVERT: G 515 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7489 (mt) REVERT: H 446 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7595 (tt) REVERT: H 515 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7496 (mt) outliers start: 37 outliers final: 4 residues processed: 267 average time/residue: 0.7779 time to fit residues: 218.1269 Evaluate side-chains 256 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 494 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain B residue 446 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 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 454 ASP 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 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 515 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 38 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 500 GLN F 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.184745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.164398 restraints weight = 9119.079| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.32 r_work: 0.3663 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 9232 Z= 0.260 Angle : 0.682 6.713 12432 Z= 0.365 Chirality : 0.045 0.118 1352 Planarity : 0.005 0.028 1600 Dihedral : 6.886 59.787 1256 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 7.86 % Allowed : 23.99 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.27), residues: 1096 helix: 0.90 (0.19), residues: 776 sheet: None (None), residues: 0 loop : 1.97 (0.42), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 465 TYR 0.015 0.002 TYR G 503 PHE 0.013 0.003 PHE E 433 TRP 0.004 0.001 TRP C 412 HIS 0.002 0.001 HIS C 530 Details of bonding type rmsd covalent geometry : bond 0.00584 ( 9232) covalent geometry : angle 0.68249 (12432) hydrogen bonds : bond 0.06787 ( 512) hydrogen bonds : angle 5.71132 ( 1440) *********************** 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 316 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 238 time to evaluate : 0.416 Fit side-chains REVERT: A 446 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7475 (tt) REVERT: A 486 ASN cc_start: 0.8290 (t0) cc_final: 0.8086 (t0) REVERT: A 515 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7439 (mt) REVERT: B 414 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7301 (mt-10) REVERT: B 446 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7692 (tt) REVERT: B 515 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7523 (mt) REVERT: C 446 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7427 (tt) REVERT: C 515 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7396 (mt) REVERT: D 446 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7734 (tt) REVERT: D 515 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7551 (mt) REVERT: E 414 GLU cc_start: 0.7528 (mp0) cc_final: 0.7190 (mt-10) REVERT: E 446 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7484 (tt) REVERT: E 457 MET cc_start: 0.6699 (mtt) cc_final: 0.6401 (mmt) REVERT: E 486 ASN cc_start: 0.8286 (t0) cc_final: 0.8081 (t0) REVERT: E 515 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7428 (mt) REVERT: F 446 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7695 (tt) REVERT: F 515 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7502 (mt) REVERT: G 414 GLU cc_start: 0.7559 (mp0) cc_final: 0.7233 (mt-10) REVERT: G 446 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7443 (tt) REVERT: G 457 MET cc_start: 0.6707 (mtt) cc_final: 0.6399 (mmt) REVERT: G 486 ASN cc_start: 0.8228 (t0) cc_final: 0.8011 (t0) REVERT: G 515 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7445 (mt) REVERT: H 446 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7729 (tt) REVERT: H 515 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7536 (mt) outliers start: 78 outliers final: 32 residues processed: 274 average time/residue: 0.7474 time to fit residues: 215.3107 Evaluate side-chains 278 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 230 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 513 SER 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 462 THR 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 B residue 540 THR Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 454 ASP 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 494 LEU 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 513 SER 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 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 454 ASP Chi-restraints excluded: chain G residue 462 THR Chi-restraints excluded: chain G residue 487 LEU Chi-restraints excluded: chain G residue 513 SER 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 513 SER Chi-restraints excluded: chain H residue 515 LEU Chi-restraints excluded: chain H residue 540 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 59 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 95 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.193866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.174877 restraints weight = 9587.868| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 1.30 r_work: 0.3822 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1700 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= 0.159 Angle : 0.567 6.826 12432 Z= 0.297 Chirality : 0.038 0.108 1352 Planarity : 0.004 0.027 1600 Dihedral : 6.622 59.061 1256 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 6.05 % Allowed : 26.01 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.27), residues: 1096 helix: 0.98 (0.19), residues: 776 sheet: None (None), residues: 0 loop : 1.92 (0.42), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 463 TYR 0.013 0.002 TYR A 503 PHE 0.012 0.002 PHE C 433 TRP 0.002 0.001 TRP C 412 HIS 0.002 0.001 HIS B 516 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9232) covalent geometry : angle 0.56700 (12432) hydrogen bonds : bond 0.05166 ( 512) hydrogen bonds : angle 5.32896 ( 1440) *********************** 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 293 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 233 time to evaluate : 0.419 Fit side-chains REVERT: A 414 GLU cc_start: 0.7470 (mp0) cc_final: 0.7132 (mt-10) REVERT: A 446 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7404 (tt) REVERT: A 515 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7532 (mt) REVERT: B 414 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: B 446 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7670 (tt) REVERT: B 450 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: B 515 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7531 (mt) REVERT: C 446 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7366 (tt) REVERT: C 515 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7429 (mt) REVERT: D 414 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7326 (mt-10) REVERT: D 446 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7688 (tt) REVERT: D 450 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6671 (mp0) REVERT: D 515 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7569 (mt) REVERT: E 414 GLU cc_start: 0.7445 (mp0) cc_final: 0.7166 (mt-10) REVERT: E 446 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7428 (tt) REVERT: E 457 MET cc_start: 0.6694 (mtt) cc_final: 0.6444 (mmt) REVERT: E 515 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7512 (mt) REVERT: F 414 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7325 (mt-10) REVERT: F 446 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7665 (tt) REVERT: F 450 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6653 (mp0) REVERT: F 489 ASP cc_start: 0.7820 (m-30) cc_final: 0.7519 (p0) REVERT: F 515 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7564 (mt) REVERT: G 414 GLU cc_start: 0.7455 (mp0) cc_final: 0.7191 (mt-10) REVERT: G 446 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7383 (tt) REVERT: G 457 MET cc_start: 0.6661 (mtt) cc_final: 0.6426 (mmt) REVERT: G 515 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7526 (mt) REVERT: H 414 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: H 446 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7682 (tt) REVERT: H 450 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6647 (mp0) REVERT: H 515 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7546 (mt) outliers start: 60 outliers final: 21 residues processed: 260 average time/residue: 0.7108 time to fit residues: 194.9113 Evaluate side-chains 267 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 513 SER 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 450 GLU Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 462 THR 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 414 GLU 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 462 THR 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 513 SER 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 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 513 SER Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 540 THR Chi-restraints excluded: chain H residue 414 GLU Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 450 GLU Chi-restraints excluded: chain H residue 454 ASP 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 98 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 0.0970 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 95 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.195740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.176686 restraints weight = 9510.621| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.30 r_work: 0.3831 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 9232 Z= 0.133 Angle : 0.532 6.654 12432 Z= 0.276 Chirality : 0.037 0.109 1352 Planarity : 0.004 0.029 1600 Dihedral : 6.462 59.490 1256 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.33 % Allowed : 27.92 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.27), residues: 1096 helix: 1.21 (0.19), residues: 768 sheet: None (None), residues: 0 loop : 1.92 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 465 TYR 0.011 0.001 TYR A 503 PHE 0.010 0.002 PHE G 433 TRP 0.003 0.001 TRP A 420 HIS 0.002 0.000 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9232) covalent geometry : angle 0.53167 (12432) hydrogen bonds : bond 0.04617 ( 512) hydrogen bonds : angle 5.08372 ( 1440) *********************** 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 272 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 0.385 Fit side-chains REVERT: A 414 GLU cc_start: 0.7362 (mp0) cc_final: 0.7087 (mt-10) REVERT: A 446 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7361 (tt) REVERT: A 515 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7548 (mt) REVERT: B 414 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: B 446 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7628 (tt) REVERT: B 450 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6719 (mp0) REVERT: C 446 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7322 (tt) REVERT: C 457 MET cc_start: 0.6574 (mtt) cc_final: 0.6367 (mmt) REVERT: D 414 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: D 446 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7658 (tt) REVERT: D 515 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7573 (mt) REVERT: E 414 GLU cc_start: 0.7355 (mp0) cc_final: 0.7109 (mt-10) REVERT: E 446 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7359 (tt) REVERT: E 515 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7507 (mt) REVERT: F 414 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7391 (mt-10) REVERT: F 446 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7627 (tt) REVERT: F 450 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6678 (mp0) REVERT: F 486 ASN cc_start: 0.8203 (t0) cc_final: 0.7619 (t0) REVERT: F 489 ASP cc_start: 0.7811 (m-30) cc_final: 0.7527 (p0) REVERT: G 414 GLU cc_start: 0.7384 (mp0) cc_final: 0.7140 (mt-10) REVERT: G 446 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7338 (tt) REVERT: G 515 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7498 (mt) REVERT: H 414 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7364 (mt-10) REVERT: H 446 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7643 (tt) REVERT: H 515 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7553 (mt) outliers start: 33 outliers final: 6 residues processed: 255 average time/residue: 0.7208 time to fit residues: 193.6856 Evaluate side-chains 242 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 217 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 513 SER 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 450 GLU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 513 SER Chi-restraints excluded: chain D residue 414 GLU 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 513 SER 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 F residue 450 GLU Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 513 SER Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain H residue 414 GLU Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 515 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.192893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.173675 restraints weight = 9481.096| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.29 r_work: 0.3790 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9232 Z= 0.176 Angle : 0.563 6.164 12432 Z= 0.302 Chirality : 0.039 0.106 1352 Planarity : 0.004 0.029 1600 Dihedral : 6.575 59.068 1256 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 5.04 % Allowed : 25.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.27), residues: 1096 helix: 1.08 (0.19), residues: 776 sheet: None (None), residues: 0 loop : 1.82 (0.41), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 465 TYR 0.013 0.002 TYR E 503 PHE 0.010 0.002 PHE G 433 TRP 0.004 0.001 TRP B 412 HIS 0.001 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9232) covalent geometry : angle 0.56281 (12432) hydrogen bonds : bond 0.05241 ( 512) hydrogen bonds : angle 5.26207 ( 1440) *********************** 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 279 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 0.424 Fit side-chains REVERT: A 446 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7486 (tt) REVERT: A 515 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7495 (mt) REVERT: B 414 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7310 (mt-10) REVERT: B 446 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7659 (tt) REVERT: B 450 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: B 515 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7623 (mt) REVERT: C 446 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7483 (tt) REVERT: D 414 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7323 (mt-10) REVERT: D 446 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7663 (tt) REVERT: D 515 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7636 (mt) REVERT: E 414 GLU cc_start: 0.7366 (mp0) cc_final: 0.7096 (mt-10) REVERT: E 446 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7499 (tt) REVERT: E 515 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7501 (mt) REVERT: F 414 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: F 446 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7641 (tt) REVERT: F 450 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6697 (mp0) REVERT: F 515 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7629 (mt) REVERT: G 414 GLU cc_start: 0.7395 (mp0) cc_final: 0.7125 (mt-10) REVERT: G 446 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7490 (tt) REVERT: G 515 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7494 (mt) REVERT: H 414 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: H 446 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7647 (tt) REVERT: H 515 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7612 (mt) outliers start: 50 outliers final: 22 residues processed: 254 average time/residue: 0.6952 time to fit residues: 186.3238 Evaluate side-chains 271 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 228 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 ASP 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 414 GLU Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 540 THR 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 462 THR Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 540 THR 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 D residue 540 THR Chi-restraints excluded: chain E residue 441 ASP 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 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 462 THR Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 540 THR Chi-restraints excluded: chain G residue 441 ASP Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 487 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 17 optimal weight: 0.0980 chunk 14 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 31 optimal weight: 0.0970 chunk 98 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.195294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.176064 restraints weight = 9535.674| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 1.31 r_work: 0.3835 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9232 Z= 0.129 Angle : 0.499 6.293 12432 Z= 0.268 Chirality : 0.036 0.109 1352 Planarity : 0.004 0.028 1600 Dihedral : 6.442 59.329 1256 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.63 % Allowed : 26.31 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.27), residues: 1096 helix: 1.26 (0.19), residues: 768 sheet: None (None), residues: 0 loop : 1.82 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 463 TYR 0.011 0.001 TYR C 503 PHE 0.009 0.002 PHE G 433 TRP 0.003 0.001 TRP F 490 HIS 0.001 0.000 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9232) covalent geometry : angle 0.49939 (12432) hydrogen bonds : bond 0.04486 ( 512) hydrogen bonds : angle 5.01235 ( 1440) *********************** 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 270 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 0.356 Fit side-chains REVERT: A 414 GLU cc_start: 0.7329 (mp0) cc_final: 0.7037 (mt-10) REVERT: A 446 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7343 (tt) REVERT: A 457 MET cc_start: 0.6315 (mmt) cc_final: 0.5833 (mmt) REVERT: A 489 ASP cc_start: 0.7850 (m-30) cc_final: 0.7356 (p0) REVERT: A 515 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7498 (mt) REVERT: B 414 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: B 446 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7635 (tt) REVERT: B 450 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: B 515 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7601 (mt) REVERT: C 446 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7326 (tt) REVERT: C 457 MET cc_start: 0.6654 (mtt) cc_final: 0.6356 (mmt) REVERT: C 489 ASP cc_start: 0.7808 (m-30) cc_final: 0.7320 (p0) REVERT: D 414 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7328 (mt-10) REVERT: D 446 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7640 (tt) REVERT: D 515 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7612 (mt) REVERT: E 414 GLU cc_start: 0.7370 (mp0) cc_final: 0.7112 (mt-10) REVERT: E 446 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7336 (tt) REVERT: E 489 ASP cc_start: 0.7773 (m-30) cc_final: 0.7346 (p0) REVERT: E 515 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7521 (mt) REVERT: F 414 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: F 446 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7624 (tt) REVERT: F 450 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6654 (mp0) REVERT: G 414 GLU cc_start: 0.7379 (mp0) cc_final: 0.7115 (mt-10) REVERT: G 446 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7344 (tt) REVERT: G 489 ASP cc_start: 0.7794 (m-30) cc_final: 0.7377 (p0) REVERT: G 515 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7508 (mt) REVERT: H 414 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7329 (mt-10) REVERT: H 446 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7631 (tt) REVERT: H 515 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7599 (mt) outliers start: 36 outliers final: 11 residues processed: 255 average time/residue: 0.7574 time to fit residues: 202.9130 Evaluate side-chains 257 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 450 GLU 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 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 487 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 83 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 47 optimal weight: 0.0970 chunk 65 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.1580 ------------------------------------------------------------------------------- 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 = 0.4127 r_free = 0.4127 target = 0.192042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.172873 restraints weight = 9545.159| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.29 r_work: 0.3807 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9232 Z= 0.194 Angle : 0.579 5.313 12432 Z= 0.313 Chirality : 0.040 0.125 1352 Planarity : 0.004 0.029 1600 Dihedral : 6.618 59.135 1256 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.24 % Allowed : 24.90 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.27), residues: 1096 helix: 1.04 (0.19), residues: 776 sheet: None (None), residues: 0 loop : 1.69 (0.41), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 465 TYR 0.013 0.002 TYR E 503 PHE 0.011 0.003 PHE C 433 TRP 0.005 0.001 TRP F 412 HIS 0.002 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 9232) covalent geometry : angle 0.57911 (12432) hydrogen bonds : bond 0.05423 ( 512) hydrogen bonds : angle 5.29431 ( 1440) *********************** 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 280 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 228 time to evaluate : 0.399 Fit side-chains REVERT: A 446 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7537 (tt) REVERT: A 515 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7507 (mt) REVERT: B 414 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7311 (mt-10) REVERT: B 446 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7644 (tt) REVERT: B 450 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: B 515 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7631 (mt) REVERT: C 446 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7520 (tt) REVERT: D 414 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: D 446 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7629 (tt) REVERT: D 515 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7618 (mt) REVERT: E 414 GLU cc_start: 0.7423 (mp0) cc_final: 0.7147 (mt-10) REVERT: E 446 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7522 (tt) REVERT: E 515 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7478 (mt) REVERT: F 446 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7626 (tt) REVERT: F 450 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: F 489 ASP cc_start: 0.7738 (m-30) cc_final: 0.7463 (p0) REVERT: F 515 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7622 (mt) REVERT: G 414 GLU cc_start: 0.7437 (mp0) cc_final: 0.7158 (mt-10) REVERT: G 446 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7528 (tt) REVERT: G 489 ASP cc_start: 0.7924 (m-30) cc_final: 0.7464 (p0) REVERT: G 515 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7480 (mt) REVERT: H 446 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7597 (tt) REVERT: H 515 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7626 (mt) outliers start: 52 outliers final: 27 residues processed: 255 average time/residue: 0.6975 time to fit residues: 187.2865 Evaluate side-chains 272 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 450 GLU 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 430 CYS 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 515 LEU Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain C residue 430 CYS Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 462 THR 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 454 ASP Chi-restraints excluded: chain D residue 462 THR Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 540 THR 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 E residue 540 THR 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 515 LEU Chi-restraints excluded: chain G residue 430 CYS Chi-restraints excluded: chain G residue 446 LEU 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 430 CYS Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 454 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 95 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.193897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.174892 restraints weight = 9499.758| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 1.29 r_work: 0.3831 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1915 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= 0.148 Angle : 0.529 5.392 12432 Z= 0.285 Chirality : 0.037 0.108 1352 Planarity : 0.004 0.028 1600 Dihedral : 6.534 58.838 1256 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.03 % Allowed : 25.50 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.27), residues: 1096 helix: 1.04 (0.19), residues: 776 sheet: None (None), residues: 0 loop : 1.73 (0.41), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 465 TYR 0.011 0.002 TYR A 503 PHE 0.010 0.002 PHE E 433 TRP 0.004 0.001 TRP F 490 HIS 0.001 0.000 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9232) covalent geometry : angle 0.52924 (12432) hydrogen bonds : bond 0.04797 ( 512) hydrogen bonds : angle 5.15161 ( 1440) *********************** 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 263 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 0.424 Fit side-chains REVERT: A 446 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7439 (tt) REVERT: A 457 MET cc_start: 0.6315 (mmt) cc_final: 0.5901 (mmt) REVERT: A 489 ASP cc_start: 0.7867 (m-30) cc_final: 0.7368 (p0) REVERT: A 515 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7502 (mt) REVERT: B 446 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7632 (tt) REVERT: B 450 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6691 (mp0) REVERT: B 515 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7639 (mt) REVERT: C 446 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7500 (tt) REVERT: C 489 ASP cc_start: 0.7817 (m-30) cc_final: 0.7339 (p0) REVERT: D 414 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7273 (mt-10) REVERT: D 446 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7608 (tt) REVERT: D 450 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: D 515 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7635 (mt) REVERT: E 414 GLU cc_start: 0.7422 (mp0) cc_final: 0.7149 (mt-10) REVERT: E 446 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7430 (tt) REVERT: E 489 ASP cc_start: 0.7818 (m-30) cc_final: 0.7353 (p0) REVERT: E 515 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7506 (mt) REVERT: F 446 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7625 (tt) REVERT: F 450 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: F 489 ASP cc_start: 0.7699 (m-30) cc_final: 0.7408 (p0) REVERT: F 515 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7627 (mt) REVERT: G 414 GLU cc_start: 0.7471 (mp0) cc_final: 0.7191 (mt-10) REVERT: G 446 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7431 (tt) REVERT: G 489 ASP cc_start: 0.7831 (m-30) cc_final: 0.7401 (p0) REVERT: G 515 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7471 (mt) REVERT: H 446 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7610 (tt) REVERT: H 450 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6773 (mp0) REVERT: H 515 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7626 (mt) outliers start: 40 outliers final: 15 residues processed: 248 average time/residue: 0.7444 time to fit residues: 194.1820 Evaluate side-chains 257 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 222 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 450 GLU 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 C residue 540 THR 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 450 GLU Chi-restraints excluded: chain D residue 462 THR Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 540 THR 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 430 CYS Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 450 GLU Chi-restraints excluded: chain F residue 462 THR Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 540 THR Chi-restraints excluded: chain G residue 430 CYS Chi-restraints excluded: chain G residue 446 LEU 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 450 GLU 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 59 optimal weight: 0.0670 chunk 34 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 53 optimal weight: 0.0270 chunk 55 optimal weight: 0.0770 chunk 98 optimal weight: 0.9990 overall best weight: 0.3534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.197228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.178158 restraints weight = 9475.563| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.31 r_work: 0.3860 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 9232 Z= 0.115 Angle : 0.482 5.849 12432 Z= 0.258 Chirality : 0.035 0.110 1352 Planarity : 0.003 0.030 1600 Dihedral : 6.339 59.949 1256 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.02 % Allowed : 27.02 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.27), residues: 1096 helix: 1.40 (0.19), residues: 768 sheet: None (None), residues: 0 loop : 1.93 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 512 TYR 0.011 0.001 TYR C 429 PHE 0.008 0.001 PHE E 433 TRP 0.006 0.001 TRP E 420 HIS 0.003 0.000 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 9232) covalent geometry : angle 0.48177 (12432) hydrogen bonds : bond 0.04104 ( 512) hydrogen bonds : angle 4.86635 ( 1440) ********************** 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 265 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 0.374 Fit side-chains REVERT: A 414 GLU cc_start: 0.7286 (mp0) cc_final: 0.7012 (mt-10) REVERT: A 446 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7342 (tt) REVERT: A 454 ASP cc_start: 0.7199 (m-30) cc_final: 0.6868 (m-30) REVERT: A 457 MET cc_start: 0.6180 (mmt) cc_final: 0.5791 (mmt) REVERT: A 489 ASP cc_start: 0.7784 (m-30) cc_final: 0.7304 (p0) REVERT: A 515 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7522 (mt) REVERT: B 446 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7603 (tt) REVERT: B 489 ASP cc_start: 0.7670 (p0) cc_final: 0.7416 (m-30) REVERT: C 446 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7311 (tt) REVERT: C 489 ASP cc_start: 0.7819 (m-30) cc_final: 0.7370 (p0) REVERT: D 414 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7329 (mt-10) REVERT: D 446 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7634 (tt) REVERT: D 515 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7561 (mt) REVERT: E 414 GLU cc_start: 0.7296 (mp0) cc_final: 0.7056 (mt-10) REVERT: E 446 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7339 (tt) REVERT: E 457 MET cc_start: 0.6061 (mmt) cc_final: 0.5781 (mmt) REVERT: E 489 ASP cc_start: 0.7704 (m-30) cc_final: 0.7328 (p0) REVERT: E 515 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7483 (mt) REVERT: F 446 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7568 (tt) REVERT: F 489 ASP cc_start: 0.7597 (m-30) cc_final: 0.7386 (p0) REVERT: G 414 GLU cc_start: 0.7329 (mp0) cc_final: 0.7080 (mt-10) REVERT: G 446 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7339 (tt) REVERT: G 457 MET cc_start: 0.6074 (mmt) cc_final: 0.5782 (mmt) REVERT: G 489 ASP cc_start: 0.7786 (m-30) cc_final: 0.7337 (p0) REVERT: G 515 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7519 (mt) REVERT: H 446 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7636 (tt) REVERT: H 489 ASP cc_start: 0.7620 (p0) cc_final: 0.7383 (m-30) REVERT: H 515 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7553 (mt) outliers start: 30 outliers final: 10 residues processed: 256 average time/residue: 0.7598 time to fit residues: 204.0270 Evaluate side-chains 246 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 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 430 CYS Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain G residue 430 CYS Chi-restraints excluded: chain G residue 446 LEU 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 515 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 0.4980 chunk 85 optimal weight: 0.1980 chunk 92 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 522 GLN H 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.195996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.176845 restraints weight = 9358.286| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 1.29 r_work: 0.3838 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3718 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9232 Z= 0.131 Angle : 0.508 5.656 12432 Z= 0.275 Chirality : 0.036 0.108 1352 Planarity : 0.004 0.029 1600 Dihedral : 6.377 59.925 1256 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.82 % Allowed : 28.12 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.27), residues: 1096 helix: 1.39 (0.19), residues: 768 sheet: None (None), residues: 0 loop : 1.91 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 465 TYR 0.011 0.001 TYR A 503 PHE 0.009 0.002 PHE E 433 TRP 0.004 0.001 TRP F 490 HIS 0.001 0.000 HIS C 516 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9232) covalent geometry : angle 0.50815 (12432) hydrogen bonds : bond 0.04303 ( 512) hydrogen bonds : angle 4.92237 ( 1440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4608.02 seconds wall clock time: 79 minutes 10.88 seconds (4750.88 seconds total)