Starting phenix.real_space_refine on Fri Dec 27 20:45:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubv_42106/12_2024/8ubv_42106.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubv_42106/12_2024/8ubv_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_42106/12_2024/8ubv_42106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubv_42106/12_2024/8ubv_42106.map" model { file = "/net/cci-nas-00/data/ceres_data/8ubv_42106/12_2024/8ubv_42106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubv_42106/12_2024/8ubv_42106.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 6.29, per 1000 atoms: 0.95 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: 1.75 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.81 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: 1.73 Time building geometry restraints manager: 2.02 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: 8.350 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.910 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.900 ------------------------------------------------------------------------------- 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 6682 Z= 0.329 Angle : 1.001 20.400 8978 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 : 24.13 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.002 TRP B 577 HIS 0.008 0.002 HIS H 514 PHE 0.015 0.002 PHE C 112 TYR 0.015 0.002 TYR H 420 ARG 0.000 0.000 ARG H 397 *********************** 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 : 0.837 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: 0.1591 time to fit residues: 40.9329 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 : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 0.0970 chunk 49 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 372 GLN B 473 GLN B 541 ASN ** B 593 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5826 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6682 Z= 0.222 Angle : 0.753 10.412 8978 Z= 0.402 Chirality : 0.046 0.198 1092 Planarity : 0.004 0.077 1117 Dihedral : 5.815 35.873 848 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.26 % Favored : 88.63 % Rotamer: Outliers : 3.75 % Allowed : 8.91 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.27), residues: 844 helix: -1.48 (0.29), residues: 283 sheet: -2.39 (0.58), residues: 71 loop : -2.97 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 626 HIS 0.006 0.002 HIS H 470 PHE 0.013 0.002 PHE H 511 TYR 0.013 0.001 TYR H 598 ARG 0.000 0.000 ARG I 28 *********************** 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 155 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 399 MET cc_start: 0.1131 (pmm) cc_final: 0.0778 (ptp) REVERT: B 524 MET cc_start: 0.6257 (tmm) cc_final: 0.5743 (ttp) REVERT: B 554 ASP cc_start: 0.7589 (t0) cc_final: 0.7186 (t70) REVERT: B 578 ILE cc_start: 0.6544 (mp) cc_final: 0.5643 (mp) REVERT: C 78 GLU cc_start: 0.8691 (pm20) cc_final: 0.8402 (pm20) REVERT: C 85 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7148 (mm-30) REVERT: H 439 LEU cc_start: 0.7083 (tp) cc_final: 0.6827 (tp) REVERT: H 440 LEU cc_start: 0.5666 (mt) cc_final: 0.5328 (mt) REVERT: H 509 LYS cc_start: 0.6999 (mttt) cc_final: 0.6400 (mmtm) REVERT: H 524 MET cc_start: 0.5067 (ptp) cc_final: 0.4622 (ptp) REVERT: H 617 MET cc_start: 0.3434 (pmm) cc_final: 0.3146 (pmm) REVERT: H 645 LEU cc_start: 0.8241 (mm) cc_final: 0.8029 (mm) outliers start: 29 outliers final: 28 residues processed: 145 average time/residue: 0.1541 time to fit residues: 31.6149 Evaluate side-chains 120 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 424 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5902 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6682 Z= 0.217 Angle : 0.739 10.383 8978 Z= 0.392 Chirality : 0.045 0.155 1092 Planarity : 0.003 0.057 1117 Dihedral : 5.633 36.196 848 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.74 % Favored : 86.26 % Rotamer: Outliers : 3.88 % Allowed : 7.62 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.27), residues: 844 helix: -1.23 (0.30), residues: 275 sheet: -2.73 (0.53), residues: 87 loop : -2.87 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 626 HIS 0.007 0.001 HIS B 535 PHE 0.011 0.001 PHE H 511 TYR 0.010 0.001 TYR H 598 ARG 0.000 0.000 ARG H 384 *********************** 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 150 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 399 MET cc_start: 0.0516 (pmm) cc_final: 0.0090 (ptp) REVERT: B 524 MET cc_start: 0.6495 (tmm) cc_final: 0.6016 (ttp) REVERT: B 534 ILE cc_start: 0.7386 (mm) cc_final: 0.7019 (mm) REVERT: C 78 GLU cc_start: 0.8813 (pm20) cc_final: 0.8497 (pm20) REVERT: H 399 MET cc_start: 0.3313 (mpp) cc_final: 0.1548 (mtp) REVERT: H 439 LEU cc_start: 0.6944 (tp) cc_final: 0.6700 (tp) REVERT: H 509 LYS cc_start: 0.7097 (mttt) cc_final: 0.6312 (mmtm) REVERT: H 617 MET cc_start: 0.3674 (pmm) cc_final: 0.3419 (pmm) outliers start: 30 outliers final: 29 residues processed: 140 average time/residue: 0.1614 time to fit residues: 31.7514 Evaluate side-chains 129 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 36 optimal weight: 0.2980 chunk 51 optimal weight: 0.0670 chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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** C 43 GLN H 424 GLN ** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN ** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 592 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5875 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6682 Z= 0.192 Angle : 0.711 9.913 8978 Z= 0.382 Chirality : 0.045 0.174 1092 Planarity : 0.003 0.048 1117 Dihedral : 5.512 37.223 848 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.32 % Favored : 87.56 % Rotamer: Outliers : 4.01 % Allowed : 5.81 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.28), residues: 844 helix: -1.23 (0.30), residues: 276 sheet: -2.24 (0.54), residues: 81 loop : -2.86 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 626 HIS 0.005 0.001 HIS C 116 PHE 0.015 0.001 PHE I 112 TYR 0.010 0.001 TYR H 598 ARG 0.000 0.000 ARG H 421 *********************** 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: 31 poor density : 111 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 399 MET cc_start: 0.0562 (pmm) cc_final: 0.0193 (ptp) REVERT: B 534 ILE cc_start: 0.7434 (mm) cc_final: 0.7032 (mm) REVERT: B 578 ILE cc_start: 0.6908 (mp) cc_final: 0.6655 (mp) REVERT: C 78 GLU cc_start: 0.8807 (pm20) cc_final: 0.8543 (pm20) REVERT: C 97 ILE cc_start: 0.7701 (pt) cc_final: 0.7429 (pt) REVERT: H 439 LEU cc_start: 0.6828 (tp) cc_final: 0.6622 (tp) REVERT: H 448 GLN cc_start: 0.5790 (tp40) cc_final: 0.5197 (tp40) REVERT: H 509 LYS cc_start: 0.7073 (mttt) cc_final: 0.6269 (mmtm) REVERT: H 617 MET cc_start: 0.3844 (pmm) cc_final: 0.3641 (pmm) outliers start: 31 outliers final: 29 residues processed: 132 average time/residue: 0.1566 time to fit residues: 29.5280 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 : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.9980 chunk 46 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 41 optimal weight: 0.3980 chunk 72 optimal weight: 3.9990 chunk 20 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: B 473 GLN B 498 GLN B 535 HIS ** 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** I 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6682 Z= 0.206 Angle : 0.733 11.390 8978 Z= 0.388 Chirality : 0.045 0.171 1092 Planarity : 0.003 0.051 1117 Dihedral : 5.512 36.536 848 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.10 % Favored : 85.90 % Rotamer: Outliers : 3.75 % Allowed : 5.81 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.28), residues: 844 helix: -1.18 (0.30), residues: 269 sheet: -2.29 (0.54), residues: 82 loop : -2.80 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 626 HIS 0.008 0.001 HIS B 535 PHE 0.016 0.001 PHE I 112 TYR 0.010 0.001 TYR H 598 ARG 0.000 0.000 ARG H 370 *********************** 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 : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 399 MET cc_start: 0.0747 (pmm) cc_final: 0.0419 (ptp) REVERT: B 507 SER cc_start: 0.7726 (p) cc_final: 0.7478 (m) REVERT: B 524 MET cc_start: 0.7082 (ttp) cc_final: 0.5923 (ttp) REVERT: C 78 GLU cc_start: 0.8789 (pm20) cc_final: 0.8578 (pm20) REVERT: H 439 LEU cc_start: 0.6725 (tp) cc_final: 0.6077 (pp) REVERT: H 448 GLN cc_start: 0.5453 (tp40) cc_final: 0.4892 (tp40) REVERT: H 509 LYS cc_start: 0.7079 (mttt) cc_final: 0.6109 (mmtt) outliers start: 29 outliers final: 29 residues processed: 130 average time/residue: 0.1480 time to fit residues: 27.8085 Evaluate side-chains 124 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 8.9990 chunk 73 optimal weight: 0.0670 chunk 16 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 67 optimal weight: 0.0030 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 overall best weight: 0.6730 ------------------------------------------------------------------------------- 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** C 43 GLN H 424 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** ** H 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5939 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6682 Z= 0.208 Angle : 0.742 10.079 8978 Z= 0.395 Chirality : 0.045 0.177 1092 Planarity : 0.003 0.045 1117 Dihedral : 5.569 37.783 848 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.74 % Favored : 86.26 % Rotamer: Outliers : 3.88 % Allowed : 3.62 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.27), residues: 844 helix: -1.18 (0.30), residues: 270 sheet: -2.15 (0.55), residues: 77 loop : -2.88 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 626 HIS 0.006 0.001 HIS C 116 PHE 0.012 0.001 PHE I 112 TYR 0.008 0.001 TYR H 598 ARG 0.000 0.000 ARG I 28 *********************** 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 152 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: B 399 MET cc_start: 0.0694 (pmm) cc_final: 0.0433 (ptp) REVERT: B 524 MET cc_start: 0.6986 (ttp) cc_final: 0.5921 (ttp) REVERT: C 19 ASN cc_start: 0.7034 (t0) cc_final: 0.6443 (p0) REVERT: H 439 LEU cc_start: 0.6685 (tp) cc_final: 0.6020 (pt) REVERT: H 448 GLN cc_start: 0.5444 (tp40) cc_final: 0.5116 (tp40) REVERT: H 509 LYS cc_start: 0.7408 (mttt) cc_final: 0.6144 (mmtt) outliers start: 30 outliers final: 29 residues processed: 143 average time/residue: 0.1630 time to fit residues: 32.7025 Evaluate side-chains 127 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 80 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 424 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** ** H 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6682 Z= 0.203 Angle : 0.742 10.905 8978 Z= 0.395 Chirality : 0.046 0.165 1092 Planarity : 0.003 0.041 1117 Dihedral : 5.669 37.682 848 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 14.22 % Favored : 85.66 % Rotamer: Outliers : 3.75 % Allowed : 3.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.27), residues: 844 helix: -1.22 (0.30), residues: 271 sheet: -2.25 (0.55), residues: 82 loop : -2.86 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 626 HIS 0.012 0.001 HIS I 116 PHE 0.018 0.002 PHE I 112 TYR 0.007 0.001 TYR H 598 ARG 0.000 0.000 ARG I 62 *********************** 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: 29 poor density : 109 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 399 MET cc_start: 0.0832 (pmm) cc_final: 0.0625 (ptp) REVERT: B 524 MET cc_start: 0.7122 (ttp) cc_final: 0.5836 (ttp) REVERT: C 19 ASN cc_start: 0.7072 (t0) cc_final: 0.6490 (p0) REVERT: H 439 LEU cc_start: 0.6618 (tp) cc_final: 0.5958 (pt) REVERT: H 448 GLN cc_start: 0.5428 (tp40) cc_final: 0.5195 (tp40) REVERT: H 509 LYS cc_start: 0.7525 (mttt) cc_final: 0.6046 (mmtt) REVERT: I 112 PHE cc_start: 0.6540 (m-80) cc_final: 0.5958 (m-80) outliers start: 29 outliers final: 29 residues processed: 129 average time/residue: 0.1486 time to fit residues: 27.3356 Evaluate side-chains 129 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 0.0970 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 424 GLN H 444 HIS ** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6682 Z= 0.216 Angle : 0.751 10.390 8978 Z= 0.400 Chirality : 0.046 0.194 1092 Planarity : 0.003 0.040 1117 Dihedral : 5.707 39.745 848 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.74 % Favored : 86.14 % Rotamer: Outliers : 3.75 % Allowed : 3.49 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.27), residues: 844 helix: -1.29 (0.29), residues: 277 sheet: -2.36 (0.53), residues: 82 loop : -2.86 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 626 HIS 0.007 0.001 HIS I 116 PHE 0.019 0.002 PHE C 112 TYR 0.009 0.001 TYR H 598 ARG 0.000 0.000 ARG H 421 *********************** 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 139 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 507 SER cc_start: 0.8109 (p) cc_final: 0.7520 (p) REVERT: B 524 MET cc_start: 0.7091 (ttp) cc_final: 0.5878 (ttp) REVERT: C 19 ASN cc_start: 0.7129 (t0) cc_final: 0.6545 (p0) REVERT: H 439 LEU cc_start: 0.6553 (tp) cc_final: 0.5899 (pt) REVERT: H 448 GLN cc_start: 0.5428 (tp40) cc_final: 0.5207 (tp40) REVERT: H 509 LYS cc_start: 0.7548 (mttt) cc_final: 0.6073 (mmtt) REVERT: H 651 MET cc_start: 0.2626 (tmm) cc_final: 0.2328 (tmm) REVERT: I 112 PHE cc_start: 0.6549 (m-80) cc_final: 0.6023 (m-80) outliers start: 29 outliers final: 29 residues processed: 130 average time/residue: 0.1586 time to fit residues: 29.9252 Evaluate side-chains 130 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 79 optimal weight: 0.0020 chunk 48 optimal weight: 0.4980 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 424 GLN ** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6682 Z= 0.199 Angle : 0.747 10.137 8978 Z= 0.398 Chirality : 0.046 0.190 1092 Planarity : 0.003 0.038 1117 Dihedral : 5.771 40.380 848 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.51 % Favored : 86.37 % Rotamer: Outliers : 3.75 % Allowed : 1.55 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.27), residues: 844 helix: -1.25 (0.30), residues: 280 sheet: -2.33 (0.54), residues: 82 loop : -2.85 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 626 HIS 0.007 0.001 HIS C 116 PHE 0.018 0.002 PHE C 112 TYR 0.008 0.001 TYR H 598 ARG 0.000 0.000 ARG H 548 *********************** 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 133 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 524 MET cc_start: 0.7119 (ttp) cc_final: 0.5843 (ttp) REVERT: H 439 LEU cc_start: 0.6590 (tp) cc_final: 0.5956 (pt) REVERT: H 509 LYS cc_start: 0.7463 (mttt) cc_final: 0.6689 (mmtm) REVERT: H 651 MET cc_start: 0.2605 (tmm) cc_final: 0.2251 (tmm) REVERT: I 112 PHE cc_start: 0.6604 (m-80) cc_final: 0.6131 (m-80) outliers start: 29 outliers final: 29 residues processed: 124 average time/residue: 0.1468 time to fit residues: 26.4616 Evaluate side-chains 124 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 83 optimal weight: 0.0770 chunk 77 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 424 GLN ** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 567 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** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 moved from start: 0.6402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6682 Z= 0.201 Angle : 0.758 12.736 8978 Z= 0.397 Chirality : 0.046 0.191 1092 Planarity : 0.003 0.038 1117 Dihedral : 5.686 41.767 848 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % Rotamer: Outliers : 3.75 % Allowed : 1.55 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.28), residues: 844 helix: -1.23 (0.30), residues: 280 sheet: -2.33 (0.54), residues: 82 loop : -2.82 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 626 HIS 0.009 0.001 HIS C 116 PHE 0.020 0.002 PHE C 112 TYR 0.008 0.001 TYR H 598 ARG 0.000 0.000 ARG H 646 ********************** 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 136 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 524 MET cc_start: 0.7094 (ttp) cc_final: 0.5825 (ttp) REVERT: H 439 LEU cc_start: 0.6582 (tp) cc_final: 0.5938 (pt) REVERT: H 448 GLN cc_start: 0.5403 (tm-30) cc_final: 0.5051 (mt0) REVERT: H 449 ASP cc_start: 0.7521 (m-30) cc_final: 0.6844 (m-30) REVERT: H 509 LYS cc_start: 0.7478 (mttt) cc_final: 0.5970 (mmtt) REVERT: I 112 PHE cc_start: 0.6572 (m-80) cc_final: 0.6160 (m-80) outliers start: 29 outliers final: 29 residues processed: 127 average time/residue: 0.1431 time to fit residues: 26.3152 Evaluate side-chains 122 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 66 optimal weight: 0.0030 chunk 27 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 3 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 overall best weight: 0.3990 ------------------------------------------------------------------------------- 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 424 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.208849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.181099 restraints weight = 17798.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.181054 restraints weight = 17319.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.181492 restraints weight = 15625.947| |-----------------------------------------------------------------------------| r_work (final): 0.4508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5591 moved from start: 0.6542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6682 Z= 0.190 Angle : 0.748 12.084 8978 Z= 0.392 Chirality : 0.046 0.189 1092 Planarity : 0.003 0.038 1117 Dihedral : 5.611 41.275 848 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 3.75 % Allowed : 1.55 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.28), residues: 844 helix: -1.16 (0.30), residues: 278 sheet: -2.23 (0.55), residues: 82 loop : -2.81 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 626 HIS 0.010 0.001 HIS C 116 PHE 0.018 0.001 PHE H 523 TYR 0.007 0.001 TYR H 598 ARG 0.000 0.000 ARG H 564 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1914.76 seconds wall clock time: 36 minutes 31.18 seconds (2191.18 seconds total)