Starting phenix.real_space_refine on Fri Aug 22 18:01:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubv_42106/08_2025/8ubv_42106.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubv_42106/08_2025/8ubv_42106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ubv_42106/08_2025/8ubv_42106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubv_42106/08_2025/8ubv_42106.map" model { file = "/net/cci-nas-00/data/ceres_data/8ubv_42106/08_2025/8ubv_42106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubv_42106/08_2025/8ubv_42106.cif" } resolution = 4.1 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= -0.001 sd= 0.008 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 56 5.16 5 C 4210 2.51 5 N 1085 2.21 5 O 1252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6603 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2509 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 4, 'TRANS': 319} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'ARG:plan': 16} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 792 Classifications: {'peptide': 102} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 98} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2500 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 4, 'TRANS': 318} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ARG:plan': 15} Unresolved non-hydrogen planarities: 42 Chain: "I" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 802 Classifications: {'peptide': 103} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 99} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 1.81, per 1000 atoms: 0.27 Number of scatterers: 6603 At special positions: 0 Unit cell: (89.16, 121.852, 67.613, 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 56 16.00 O 1252 8.00 N 1085 7.00 C 4210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 396 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS I 109 " distance=2.03 Simple disulfide: pdb=" SG CYS C 109 " - pdb=" SG CYS I 107 " distance=2.05 Simple disulfide: pdb=" SG CYS H 396 " - pdb=" SG CYS H 422 " distance=2.03 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: 0.52 Conformation dependent library (CDL) restraints added in 407.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1624 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 40.0% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'B' and resid 377 through 382 removed outlier: 4.156A pdb=" N ILE B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 409 removed outlier: 4.724A pdb=" N LEU B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 436 removed outlier: 3.967A pdb=" N ILE B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 463 removed outlier: 3.557A pdb=" N CYS B 463 " --> pdb=" O LEU B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 488 removed outlier: 4.209A pdb=" N GLY B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 510 removed outlier: 3.721A pdb=" N LYS B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 510 " --> pdb=" O GLN B 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 505 through 510' Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.679A pdb=" N VAL B 533 " --> pdb=" O THR B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 538 Processing helix chain 'B' and resid 554 through 565 Processing helix chain 'B' and resid 580 through 588 removed outlier: 4.354A pdb=" N VAL B 584 " --> pdb=" O ASN B 580 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA B 588 " --> pdb=" O VAL B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 616 removed outlier: 3.509A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 642 removed outlier: 3.758A pdb=" N ALA B 635 " --> pdb=" O THR B 631 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN B 640 " --> pdb=" O THR B 636 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER B 642 " --> pdb=" O ILE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 668 removed outlier: 4.533A pdb=" N VAL B 665 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLN B 666 " --> pdb=" O GLU B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 686 Processing helix chain 'C' and resid 18 through 29 Processing helix chain 'C' and resid 49 through 56 removed outlier: 3.611A pdb=" N ALA C 53 " --> pdb=" O ARG C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 64 removed outlier: 3.600A pdb=" N ARG C 62 " --> pdb=" O TYR C 58 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 94 Proline residue: C 86 - end of helix removed outlier: 4.179A pdb=" N GLN C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'H' and resid 377 through 382 removed outlier: 3.840A pdb=" N ILE H 381 " --> pdb=" O LEU H 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 400 through 409 removed outlier: 4.632A pdb=" N LEU H 407 " --> pdb=" O GLY H 403 " (cutoff:3.500A) Processing helix chain 'H' and resid 427 through 436 Processing helix chain 'H' and resid 452 through 463 removed outlier: 4.060A pdb=" N LEU H 456 " --> pdb=" O THR H 452 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS H 457 " --> pdb=" O ASP H 453 " (cutoff:3.500A) Processing helix chain 'H' and resid 479 through 488 removed outlier: 3.545A pdb=" N ILE H 483 " --> pdb=" O ASP H 479 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY H 488 " --> pdb=" O VAL H 484 " (cutoff:3.500A) Processing helix chain 'H' and resid 504 through 508 Processing helix chain 'H' and resid 529 through 536 removed outlier: 4.038A pdb=" N VAL H 533 " --> pdb=" O THR H 529 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU H 536 " --> pdb=" O GLY H 532 " (cutoff:3.500A) Processing helix chain 'H' and resid 554 through 565 Processing helix chain 'H' and resid 580 through 591 removed outlier: 4.494A pdb=" N VAL H 584 " --> pdb=" O ASN H 580 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA H 588 " --> pdb=" O VAL H 584 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS H 589 " --> pdb=" O GLU H 585 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU H 590 " --> pdb=" O VAL H 586 " (cutoff:3.500A) Processing helix chain 'H' and resid 607 through 616 removed outlier: 3.908A pdb=" N ALA H 611 " --> pdb=" O TYR H 607 " (cutoff:3.500A) Processing helix chain 'H' and resid 631 through 642 removed outlier: 3.679A pdb=" N ALA H 635 " --> pdb=" O THR H 631 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN H 640 " --> pdb=" O THR H 636 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER H 642 " --> pdb=" O ILE H 638 " (cutoff:3.500A) Processing helix chain 'H' and resid 659 through 668 removed outlier: 5.122A pdb=" N VAL H 665 " --> pdb=" O VAL H 661 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLN H 666 " --> pdb=" O GLU H 662 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 29 Processing helix chain 'I' and resid 49 through 56 removed outlier: 3.740A pdb=" N ALA I 53 " --> pdb=" O ARG I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 65 removed outlier: 3.702A pdb=" N SER I 61 " --> pdb=" O SER I 57 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG I 62 " --> pdb=" O TYR I 58 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLY I 65 " --> pdb=" O SER I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 94 Proline residue: I 86 - end of helix Processing helix chain 'I' and resid 103 through 107 Processing sheet with id=AA1, first strand: chain 'B' and resid 570 through 571 removed outlier: 3.600A pdb=" N LEU B 597 " --> pdb=" O THR B 621 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 43 through 47 Processing sheet with id=AA3, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.718A pdb=" N LEU I 98 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 443 through 444 removed outlier: 4.204A pdb=" N HIS H 470 " --> pdb=" O VAL H 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'H' and resid 494 through 496 removed outlier: 6.265A pdb=" N ILE H 495 " --> pdb=" O GLY H 522 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU H 571 " --> pdb=" O GLU H 596 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR H 598 " --> pdb=" O LEU H 571 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU H 597 " --> pdb=" O ASP H 623 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 43 through 47 177 hydrogen bonds defined for protein. 495 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.87 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2155 1.34 - 1.47: 1353 1.47 - 1.59: 3104 1.59 - 1.71: 0 1.71 - 1.83: 70 Bond restraints: 6682 Sorted by residual: bond pdb=" CD2 TRP H 577 " pdb=" CE2 TRP H 577 " ideal model delta sigma weight residual 1.409 1.445 -0.036 1.70e-02 3.46e+03 4.60e+00 bond pdb=" CD2 TRP H 626 " pdb=" CE2 TRP H 626 " ideal model delta sigma weight residual 1.409 1.445 -0.036 1.70e-02 3.46e+03 4.37e+00 bond pdb=" CD2 TRP B 577 " pdb=" CE2 TRP B 577 " ideal model delta sigma weight residual 1.409 1.444 -0.035 1.70e-02 3.46e+03 4.24e+00 bond pdb=" CD2 TRP B 626 " pdb=" CE2 TRP B 626 " ideal model delta sigma weight residual 1.409 1.444 -0.035 1.70e-02 3.46e+03 4.20e+00 bond pdb=" CD2 TRP H 577 " pdb=" CE3 TRP H 577 " ideal model delta sigma weight residual 1.398 1.429 -0.031 1.60e-02 3.91e+03 3.74e+00 ... (remaining 6677 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 8909 4.08 - 8.16: 61 8.16 - 12.24: 4 12.24 - 16.32: 3 16.32 - 20.40: 1 Bond angle restraints: 8978 Sorted by residual: angle pdb=" C VAL C 115 " pdb=" N HIS C 116 " pdb=" CA HIS C 116 " ideal model delta sigma weight residual 121.70 142.10 -20.40 1.80e+00 3.09e-01 1.28e+02 angle pdb=" N VAL C 110 " pdb=" CA VAL C 110 " pdb=" C VAL C 110 " ideal model delta sigma weight residual 112.29 104.74 7.55 9.40e-01 1.13e+00 6.45e+01 angle pdb=" C VAL I 115 " pdb=" N HIS I 116 " pdb=" CA HIS I 116 " ideal model delta sigma weight residual 121.70 135.92 -14.22 1.80e+00 3.09e-01 6.24e+01 angle pdb=" N VAL H 373 " pdb=" CA VAL H 373 " pdb=" C VAL H 373 " ideal model delta sigma weight residual 113.53 107.63 5.90 9.80e-01 1.04e+00 3.63e+01 angle pdb=" N ILE H 389 " pdb=" CA ILE H 389 " pdb=" C ILE H 389 " ideal model delta sigma weight residual 113.71 109.15 4.56 9.50e-01 1.11e+00 2.30e+01 ... (remaining 8973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 3545 17.56 - 35.13: 445 35.13 - 52.69: 119 52.69 - 70.25: 22 70.25 - 87.81: 11 Dihedral angle restraints: 4142 sinusoidal: 1670 harmonic: 2472 Sorted by residual: dihedral pdb=" CB CYS B 396 " pdb=" SG CYS B 396 " pdb=" SG CYS B 422 " pdb=" CB CYS B 422 " ideal model delta sinusoidal sigma weight residual 93.00 165.99 -72.99 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS H 396 " pdb=" SG CYS H 396 " pdb=" SG CYS H 422 " pdb=" CB CYS H 422 " ideal model delta sinusoidal sigma weight residual 93.00 160.39 -67.39 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CA ILE B 485 " pdb=" C ILE B 485 " pdb=" N ALA B 486 " pdb=" CA ALA B 486 " ideal model delta harmonic sigma weight residual 180.00 145.21 34.79 0 5.00e+00 4.00e-02 4.84e+01 ... (remaining 4139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 748 0.048 - 0.096: 266 0.096 - 0.144: 67 0.144 - 0.192: 10 0.192 - 0.239: 1 Chirality restraints: 1092 Sorted by residual: chirality pdb=" CB ILE B 578 " pdb=" CA ILE B 578 " pdb=" CG1 ILE B 578 " pdb=" CG2 ILE B 578 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA GLU C 111 " pdb=" N GLU C 111 " pdb=" C GLU C 111 " pdb=" CB GLU C 111 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.01e-01 chirality pdb=" CA LYS H 450 " pdb=" N LYS H 450 " pdb=" C LYS H 450 " pdb=" CB LYS H 450 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.56e-01 ... (remaining 1089 not shown) Planarity restraints: 1117 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU I 41 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C GLU I 41 " -0.026 2.00e-02 2.50e+03 pdb=" O GLU I 41 " 0.010 2.00e-02 2.50e+03 pdb=" N GLY I 42 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 106 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" C VAL I 106 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL I 106 " 0.009 2.00e-02 2.50e+03 pdb=" N CYS I 107 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 111 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C GLU C 111 " -0.025 2.00e-02 2.50e+03 pdb=" O GLU C 111 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE C 112 " 0.008 2.00e-02 2.50e+03 ... (remaining 1114 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 71 2.54 - 3.13: 5632 3.13 - 3.72: 10034 3.72 - 4.31: 13698 4.31 - 4.90: 21477 Nonbonded interactions: 50912 Sorted by model distance: nonbonded pdb=" O GLN H 592 " pdb=" OG1 THR H 618 " model vdw 1.956 3.040 nonbonded pdb=" O ILE B 619 " pdb=" OG SER B 644 " model vdw 2.076 3.040 nonbonded pdb=" OD1 ASN C 25 " pdb=" NZ LYS C 29 " model vdw 2.086 3.120 nonbonded pdb=" OG1 THR H 452 " pdb=" OE1 GLU H 454 " model vdw 2.105 3.040 nonbonded pdb=" O LYS H 566 " pdb=" ND2 ASN H 593 " model vdw 2.117 3.120 ... (remaining 50907 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 363 through 685) selection = chain 'H' } ncs_group { reference = chain 'C' selection = (chain 'I' and resid 17 through 118) } 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 group one per residue 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: 7.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.550 Find NCS groups from input model: 0.100 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5692 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6686 Z= 0.238 Angle : 1.002 20.400 8986 Z= 0.562 Chirality : 0.051 0.239 1092 Planarity : 0.003 0.023 1117 Dihedral : 17.196 87.815 2506 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 24.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 16.00 % Favored : 83.89 % Rotamer: Outliers : 3.88 % Allowed : 1.94 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.69 (0.26), residues: 844 helix: -1.64 (0.30), residues: 257 sheet: -2.52 (0.58), residues: 73 loop : -3.02 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG H 397 TYR 0.015 0.002 TYR H 420 PHE 0.015 0.002 PHE C 112 TRP 0.009 0.002 TRP B 577 HIS 0.008 0.002 HIS H 514 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 6682) covalent geometry : angle 1.00091 ( 8978) SS BOND : bond 0.00755 ( 4) SS BOND : angle 2.06190 ( 8) hydrogen bonds : bond 0.18636 ( 177) hydrogen bonds : angle 9.39307 ( 495) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 399 MET cc_start: 0.0872 (pmm) cc_final: 0.0136 (ptp) REVERT: B 554 ASP cc_start: 0.7503 (t0) cc_final: 0.7185 (t70) REVERT: H 375 ASP cc_start: 0.5060 (p0) cc_final: 0.4718 (p0) REVERT: H 439 LEU cc_start: 0.7060 (tp) cc_final: 0.6219 (pp) REVERT: H 449 ASP cc_start: 0.6818 (m-30) cc_final: 0.6613 (m-30) REVERT: H 471 PHE cc_start: 0.7028 (m-80) cc_final: 0.6621 (m-10) REVERT: H 524 MET cc_start: 0.5915 (ptp) cc_final: 0.5334 (ptp) REVERT: H 645 LEU cc_start: 0.8286 (mm) cc_final: 0.8070 (mm) REVERT: I 70 GLU cc_start: 0.6926 (tt0) cc_final: 0.6531 (tm-30) outliers start: 30 outliers final: 30 residues processed: 188 average time/residue: 0.0722 time to fit residues: 18.7753 Evaluate side-chains 126 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.0770 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 372 GLN B 473 GLN B 541 ASN ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN ** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 576 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.217360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.192883 restraints weight = 20174.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.192139 restraints weight = 18096.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.192194 restraints weight = 17191.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.192417 restraints weight = 15954.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.192500 restraints weight = 15685.310| |-----------------------------------------------------------------------------| r_work (final): 0.4583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5422 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6686 Z= 0.148 Angle : 0.733 10.411 8986 Z= 0.393 Chirality : 0.045 0.184 1092 Planarity : 0.004 0.075 1117 Dihedral : 5.713 35.446 848 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.26 % Favored : 88.63 % Rotamer: Outliers : 3.88 % Allowed : 8.53 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.40 (0.27), residues: 844 helix: -1.32 (0.29), residues: 274 sheet: -2.33 (0.58), residues: 71 loop : -2.93 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG H 614 TYR 0.012 0.001 TYR H 598 PHE 0.009 0.001 PHE I 59 TRP 0.007 0.001 TRP B 626 HIS 0.007 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6682) covalent geometry : angle 0.73195 ( 8978) SS BOND : bond 0.00390 ( 4) SS BOND : angle 1.71721 ( 8) hydrogen bonds : bond 0.02951 ( 177) hydrogen bonds : angle 6.60288 ( 495) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 399 MET cc_start: 0.1030 (pmm) cc_final: 0.0516 (ptp) REVERT: B 524 MET cc_start: 0.5731 (tmm) cc_final: 0.4999 (ttp) REVERT: B 578 ILE cc_start: 0.6328 (mp) cc_final: 0.5186 (mp) REVERT: H 439 LEU cc_start: 0.6653 (tp) cc_final: 0.6416 (tp) REVERT: H 509 LYS cc_start: 0.6912 (mttt) cc_final: 0.6607 (mmtm) REVERT: H 524 MET cc_start: 0.4955 (ptp) cc_final: 0.4546 (ptp) REVERT: H 617 MET cc_start: 0.3235 (pmm) cc_final: 0.2866 (pmm) outliers start: 30 outliers final: 28 residues processed: 147 average time/residue: 0.0666 time to fit residues: 13.9772 Evaluate side-chains 128 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.212715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.185184 restraints weight = 18666.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.183852 restraints weight = 16872.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.183861 restraints weight = 15797.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.184073 restraints weight = 15087.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.184265 restraints weight = 14510.904| |-----------------------------------------------------------------------------| r_work (final): 0.4546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5543 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6686 Z= 0.149 Angle : 0.728 10.484 8986 Z= 0.388 Chirality : 0.045 0.162 1092 Planarity : 0.003 0.055 1117 Dihedral : 5.596 35.523 848 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.39 % Favored : 86.49 % Rotamer: Outliers : 3.88 % Allowed : 6.98 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -3.30 (0.28), residues: 844 helix: -1.10 (0.31), residues: 268 sheet: -2.64 (0.52), residues: 91 loop : -2.86 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG H 564 TYR 0.010 0.001 TYR H 598 PHE 0.009 0.001 PHE H 511 TRP 0.005 0.001 TRP B 626 HIS 0.006 0.001 HIS B 535 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6682) covalent geometry : angle 0.72738 ( 8978) SS BOND : bond 0.00162 ( 4) SS BOND : angle 1.26585 ( 8) hydrogen bonds : bond 0.02923 ( 177) hydrogen bonds : angle 6.08008 ( 495) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 399 MET cc_start: 0.0292 (pmm) cc_final: -0.0261 (ptp) REVERT: B 524 MET cc_start: 0.5978 (tmm) cc_final: 0.4985 (ttp) REVERT: C 111 GLU cc_start: 0.7764 (pm20) cc_final: 0.7411 (pm20) REVERT: H 399 MET cc_start: 0.3224 (mpp) cc_final: 0.1932 (ptp) REVERT: H 439 LEU cc_start: 0.6380 (tp) cc_final: 0.5816 (pp) REVERT: H 509 LYS cc_start: 0.7054 (mttt) cc_final: 0.6592 (mmtm) REVERT: H 617 MET cc_start: 0.3296 (pmm) cc_final: 0.2973 (pmm) outliers start: 30 outliers final: 29 residues processed: 143 average time/residue: 0.0659 time to fit residues: 13.5569 Evaluate side-chains 126 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 11 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 0.3980 chunk 81 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 30 optimal weight: 0.0770 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 473 GLN ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.210318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.178616 restraints weight = 18232.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.180239 restraints weight = 14627.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.181445 restraints weight = 12573.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.181931 restraints weight = 11389.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.181931 restraints weight = 10785.078| |-----------------------------------------------------------------------------| r_work (final): 0.4532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5586 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6686 Z= 0.152 Angle : 0.718 10.096 8986 Z= 0.387 Chirality : 0.045 0.175 1092 Planarity : 0.003 0.048 1117 Dihedral : 5.557 35.296 848 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.15 % Favored : 86.85 % Rotamer: Outliers : 3.88 % Allowed : 7.11 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -3.27 (0.28), residues: 844 helix: -1.19 (0.31), residues: 275 sheet: -2.14 (0.56), residues: 81 loop : -2.90 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG H 494 TYR 0.008 0.001 TYR H 520 PHE 0.008 0.001 PHE H 511 TRP 0.006 0.001 TRP H 626 HIS 0.008 0.001 HIS B 535 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6682) covalent geometry : angle 0.71669 ( 8978) SS BOND : bond 0.00593 ( 4) SS BOND : angle 1.36878 ( 8) hydrogen bonds : bond 0.03035 ( 177) hydrogen bonds : angle 5.94520 ( 495) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 399 MET cc_start: 0.0338 (pmm) cc_final: 0.0062 (ptp) REVERT: B 534 ILE cc_start: 0.7732 (mm) cc_final: 0.7436 (mm) REVERT: H 399 MET cc_start: 0.3567 (mpp) cc_final: 0.1838 (mtm) REVERT: H 439 LEU cc_start: 0.6345 (tp) cc_final: 0.5857 (pp) REVERT: H 509 LYS cc_start: 0.7216 (mttt) cc_final: 0.6375 (mmtt) REVERT: H 617 MET cc_start: 0.3455 (pmm) cc_final: 0.3230 (pmm) outliers start: 30 outliers final: 29 residues processed: 132 average time/residue: 0.0680 time to fit residues: 12.7696 Evaluate side-chains 120 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 0.0020 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN B 506 GLN ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.209768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.183158 restraints weight = 18303.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.181877 restraints weight = 18385.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.182517 restraints weight = 15905.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.182617 restraints weight = 13925.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.183174 restraints weight = 13488.636| |-----------------------------------------------------------------------------| r_work (final): 0.4528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5538 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6686 Z= 0.144 Angle : 0.728 11.307 8986 Z= 0.389 Chirality : 0.045 0.169 1092 Planarity : 0.003 0.050 1117 Dihedral : 5.557 36.425 848 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.27 % Favored : 86.61 % Rotamer: Outliers : 3.75 % Allowed : 4.52 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -3.27 (0.28), residues: 844 helix: -1.15 (0.30), residues: 272 sheet: -2.31 (0.54), residues: 81 loop : -2.88 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG H 397 TYR 0.009 0.001 TYR H 598 PHE 0.010 0.001 PHE H 511 TRP 0.005 0.001 TRP B 626 HIS 0.006 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6682) covalent geometry : angle 0.72636 ( 8978) SS BOND : bond 0.00227 ( 4) SS BOND : angle 1.76474 ( 8) hydrogen bonds : bond 0.02886 ( 177) hydrogen bonds : angle 5.83863 ( 495) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 524 MET cc_start: 0.6218 (ttp) cc_final: 0.5327 (ttp) REVERT: H 399 MET cc_start: 0.4050 (mpp) cc_final: 0.2202 (mtm) REVERT: H 439 LEU cc_start: 0.6246 (tp) cc_final: 0.5853 (pp) REVERT: H 449 ASP cc_start: 0.6986 (m-30) cc_final: 0.6610 (m-30) REVERT: H 509 LYS cc_start: 0.7468 (mttt) cc_final: 0.6277 (mmtt) REVERT: H 617 MET cc_start: 0.3483 (pmm) cc_final: 0.3240 (pmm) outliers start: 29 outliers final: 29 residues processed: 130 average time/residue: 0.0687 time to fit residues: 12.8100 Evaluate side-chains 123 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 0.0010 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 535 HIS ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 372 GLN H 444 HIS ** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN ** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 592 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.205388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.178987 restraints weight = 18369.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.178003 restraints weight = 19376.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.179195 restraints weight = 16632.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.179175 restraints weight = 13504.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.179264 restraints weight = 13012.537| |-----------------------------------------------------------------------------| r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5642 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6686 Z= 0.171 Angle : 0.793 10.555 8986 Z= 0.420 Chirality : 0.047 0.178 1092 Planarity : 0.004 0.043 1117 Dihedral : 5.834 41.176 848 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.10 % Favored : 85.90 % Rotamer: Outliers : 3.75 % Allowed : 6.20 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -3.45 (0.27), residues: 844 helix: -1.24 (0.30), residues: 270 sheet: -2.37 (0.54), residues: 84 loop : -3.03 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG H 540 TYR 0.009 0.001 TYR H 420 PHE 0.011 0.002 PHE C 112 TRP 0.010 0.002 TRP H 626 HIS 0.011 0.002 HIS B 535 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 6682) covalent geometry : angle 0.79087 ( 8978) SS BOND : bond 0.00560 ( 4) SS BOND : angle 1.89975 ( 8) hydrogen bonds : bond 0.03597 ( 177) hydrogen bonds : angle 5.96226 ( 495) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 524 MET cc_start: 0.6416 (ttp) cc_final: 0.5522 (ttp) REVERT: C 19 ASN cc_start: 0.6467 (t0) cc_final: 0.6193 (p0) REVERT: H 439 LEU cc_start: 0.6216 (tp) cc_final: 0.5813 (pt) REVERT: H 509 LYS cc_start: 0.7652 (mttt) cc_final: 0.6390 (mmtt) REVERT: H 551 THR cc_start: 0.5758 (p) cc_final: 0.5558 (p) REVERT: H 563 LYS cc_start: 0.7388 (mtpp) cc_final: 0.6851 (mmtt) REVERT: H 610 ILE cc_start: 0.6170 (pt) cc_final: 0.5951 (mm) outliers start: 29 outliers final: 29 residues processed: 136 average time/residue: 0.0705 time to fit residues: 13.5202 Evaluate side-chains 123 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 30 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 0.0020 chunk 44 optimal weight: 1.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 567 ASN ** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.207042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.177100 restraints weight = 18475.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.178400 restraints weight = 15583.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.178975 restraints weight = 13779.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.179032 restraints weight = 13346.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.179282 restraints weight = 12436.771| |-----------------------------------------------------------------------------| r_work (final): 0.4496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5695 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6686 Z= 0.156 Angle : 0.766 10.868 8986 Z= 0.406 Chirality : 0.046 0.182 1092 Planarity : 0.003 0.040 1117 Dihedral : 5.835 37.541 848 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.45 % Favored : 85.55 % Rotamer: Outliers : 3.88 % Allowed : 2.84 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -3.41 (0.27), residues: 844 helix: -1.34 (0.30), residues: 271 sheet: -2.12 (0.54), residues: 82 loop : -2.97 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG H 384 TYR 0.007 0.001 TYR H 598 PHE 0.015 0.001 PHE C 45 TRP 0.006 0.001 TRP B 626 HIS 0.006 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 6682) covalent geometry : angle 0.76431 ( 8978) SS BOND : bond 0.00518 ( 4) SS BOND : angle 2.04042 ( 8) hydrogen bonds : bond 0.03151 ( 177) hydrogen bonds : angle 5.93423 ( 495) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 524 MET cc_start: 0.6484 (ttp) cc_final: 0.5519 (ttp) REVERT: H 439 LEU cc_start: 0.6324 (tp) cc_final: 0.5872 (pp) REVERT: H 448 GLN cc_start: 0.5084 (tp40) cc_final: 0.4681 (tp40) REVERT: H 509 LYS cc_start: 0.7651 (mttt) cc_final: 0.7034 (mmtm) REVERT: H 651 MET cc_start: 0.3677 (tmm) cc_final: 0.3467 (tmm) outliers start: 30 outliers final: 29 residues processed: 129 average time/residue: 0.0754 time to fit residues: 13.7655 Evaluate side-chains 116 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 63 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 GLN ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 567 ASN ** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.200919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.175030 restraints weight = 18742.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.175127 restraints weight = 15824.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.175086 restraints weight = 14418.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.175179 restraints weight = 14586.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.175176 restraints weight = 14051.345| |-----------------------------------------------------------------------------| r_work (final): 0.4421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6686 Z= 0.187 Angle : 0.836 10.497 8986 Z= 0.440 Chirality : 0.048 0.177 1092 Planarity : 0.004 0.041 1117 Dihedral : 6.155 41.757 848 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 15.52 % Favored : 84.36 % Rotamer: Outliers : 4.01 % Allowed : 2.97 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -3.55 (0.27), residues: 844 helix: -1.45 (0.28), residues: 283 sheet: -2.71 (0.52), residues: 89 loop : -2.97 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG H 397 TYR 0.010 0.001 TYR H 420 PHE 0.022 0.003 PHE I 112 TRP 0.012 0.002 TRP H 626 HIS 0.013 0.002 HIS I 116 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 6682) covalent geometry : angle 0.83442 ( 8978) SS BOND : bond 0.00449 ( 4) SS BOND : angle 1.96570 ( 8) hydrogen bonds : bond 0.03808 ( 177) hydrogen bonds : angle 6.13434 ( 495) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 482 MET cc_start: 0.2760 (ttp) cc_final: 0.1876 (mtp) REVERT: B 524 MET cc_start: 0.6629 (ttp) cc_final: 0.5688 (ttp) REVERT: C 111 GLU cc_start: 0.7970 (pm20) cc_final: 0.7673 (pm20) REVERT: H 439 LEU cc_start: 0.6170 (tp) cc_final: 0.5742 (pt) REVERT: H 448 GLN cc_start: 0.5335 (tp40) cc_final: 0.4982 (tp40) REVERT: H 509 LYS cc_start: 0.7754 (mttt) cc_final: 0.6513 (mmtt) REVERT: H 563 LYS cc_start: 0.7490 (mtpp) cc_final: 0.7226 (mmmt) REVERT: H 651 MET cc_start: 0.3756 (tmm) cc_final: 0.3333 (tmm) outliers start: 31 outliers final: 30 residues processed: 131 average time/residue: 0.0695 time to fit residues: 12.8538 Evaluate side-chains 123 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 70 optimal weight: 0.0980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 567 ASN ** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.205334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.181133 restraints weight = 18414.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.180034 restraints weight = 18272.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.180970 restraints weight = 15563.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.181169 restraints weight = 13141.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.181222 restraints weight = 13820.832| |-----------------------------------------------------------------------------| r_work (final): 0.4511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5604 moved from start: 0.6534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6686 Z= 0.155 Angle : 0.781 12.614 8986 Z= 0.409 Chirality : 0.047 0.172 1092 Planarity : 0.003 0.039 1117 Dihedral : 5.949 40.228 848 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.03 % Favored : 86.85 % Rotamer: Outliers : 3.88 % Allowed : 2.33 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -3.41 (0.27), residues: 844 helix: -1.32 (0.29), residues: 281 sheet: -1.95 (0.59), residues: 72 loop : -3.04 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG I 28 TYR 0.007 0.001 TYR H 420 PHE 0.019 0.002 PHE C 45 TRP 0.007 0.001 TRP B 626 HIS 0.008 0.002 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6682) covalent geometry : angle 0.78049 ( 8978) SS BOND : bond 0.00370 ( 4) SS BOND : angle 1.53953 ( 8) hydrogen bonds : bond 0.03121 ( 177) hydrogen bonds : angle 5.91956 ( 495) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 482 MET cc_start: 0.3150 (ttp) cc_final: 0.2340 (mtp) REVERT: B 524 MET cc_start: 0.6454 (ttp) cc_final: 0.5536 (ttp) REVERT: H 439 LEU cc_start: 0.6192 (tp) cc_final: 0.5838 (pt) REVERT: H 448 GLN cc_start: 0.5045 (tp40) cc_final: 0.4838 (tp40) REVERT: H 509 LYS cc_start: 0.7656 (mttt) cc_final: 0.6353 (mmtt) outliers start: 30 outliers final: 30 residues processed: 124 average time/residue: 0.0637 time to fit residues: 11.4670 Evaluate side-chains 119 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 66 optimal weight: 0.0770 chunk 3 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 65 optimal weight: 0.0050 chunk 56 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.2952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 514 HIS ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN ** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 567 ASN ** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.207186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.176502 restraints weight = 18016.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.178277 restraints weight = 14366.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.179345 restraints weight = 12431.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.180044 restraints weight = 11224.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.180265 restraints weight = 10552.865| |-----------------------------------------------------------------------------| r_work (final): 0.4522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5633 moved from start: 0.6675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6686 Z= 0.143 Angle : 0.758 12.053 8986 Z= 0.396 Chirality : 0.046 0.165 1092 Planarity : 0.003 0.040 1117 Dihedral : 5.654 38.957 848 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.39 % Favored : 86.49 % Rotamer: Outliers : 3.88 % Allowed : 1.55 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.37 (0.27), residues: 844 helix: -1.19 (0.29), residues: 280 sheet: -2.75 (0.50), residues: 96 loop : -2.90 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG H 494 TYR 0.015 0.001 TYR H 598 PHE 0.020 0.002 PHE C 45 TRP 0.007 0.001 TRP B 626 HIS 0.010 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6682) covalent geometry : angle 0.75670 ( 8978) SS BOND : bond 0.00297 ( 4) SS BOND : angle 1.62318 ( 8) hydrogen bonds : bond 0.02941 ( 177) hydrogen bonds : angle 5.88626 ( 495) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 482 MET cc_start: 0.2492 (ttp) cc_final: 0.1985 (mtp) REVERT: B 524 MET cc_start: 0.6205 (ttp) cc_final: 0.5445 (ttp) REVERT: H 439 LEU cc_start: 0.6120 (tp) cc_final: 0.5657 (pt) REVERT: H 509 LYS cc_start: 0.7236 (mttt) cc_final: 0.6018 (mmtt) REVERT: H 651 MET cc_start: 0.3672 (tmm) cc_final: 0.3002 (tmm) outliers start: 30 outliers final: 29 residues processed: 128 average time/residue: 0.0652 time to fit residues: 12.1187 Evaluate side-chains 120 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.0070 chunk 55 optimal weight: 2.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 441 GLN ** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 567 ASN ** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.207511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.181242 restraints weight = 18208.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.180332 restraints weight = 16297.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.180917 restraints weight = 14631.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.181120 restraints weight = 13108.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.181326 restraints weight = 12405.792| |-----------------------------------------------------------------------------| r_work (final): 0.4506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5625 moved from start: 0.6856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6686 Z= 0.145 Angle : 0.755 12.059 8986 Z= 0.395 Chirality : 0.046 0.191 1092 Planarity : 0.003 0.038 1117 Dihedral : 5.645 38.975 848 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.63 % Favored : 86.26 % Rotamer: Outliers : 3.88 % Allowed : 1.68 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -3.35 (0.27), residues: 844 helix: -1.10 (0.30), residues: 277 sheet: -2.47 (0.56), residues: 86 loop : -2.99 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG H 540 TYR 0.012 0.001 TYR H 598 PHE 0.018 0.002 PHE C 45 TRP 0.007 0.001 TRP B 626 HIS 0.009 0.002 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6682) covalent geometry : angle 0.75375 ( 8978) SS BOND : bond 0.00277 ( 4) SS BOND : angle 1.52707 ( 8) hydrogen bonds : bond 0.02930 ( 177) hydrogen bonds : angle 5.78579 ( 495) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1458.92 seconds wall clock time: 26 minutes 1.49 seconds (1561.49 seconds total)