Starting phenix.real_space_refine on Wed Jun 3 11:03:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9obv_70300/06_2026/9obv_70300.cif Found real_map, /net/cci-nas-00/data/ceres_data/9obv_70300/06_2026/9obv_70300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9obv_70300/06_2026/9obv_70300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9obv_70300/06_2026/9obv_70300.map" model { file = "/net/cci-nas-00/data/ceres_data/9obv_70300/06_2026/9obv_70300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9obv_70300/06_2026/9obv_70300.cif" } resolution = 3.21 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= 0.026 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 1 5.21 5 S 28 5.16 5 C 2570 2.51 5 N 568 2.21 5 O 679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3850 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 875 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 3, 'GLU:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 932 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 5, 'GLU:plan': 3, 'TYR:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 77 Chain: "C" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 875 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 3, 'GLU:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "D" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 932 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 5, 'GLU:plan': 3, 'TYR:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {' MG': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 1.08, per 1000 atoms: 0.28 Number of scatterers: 3850 At special positions: 0 Unit cell: (89.88, 74.472, 65.912, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 4 15.00 Mg 1 11.99 O 679 8.00 N 568 7.00 C 2570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 93.5 milliseconds 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 952 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 77.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.503A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 570 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 Processing helix chain 'A' and resid 626 through 657 removed outlier: 3.678A pdb=" N ILE A 631 " --> pdb=" O PHE A 627 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 838 removed outlier: 3.655A pdb=" N PHE A 817 " --> pdb=" O MET A 813 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 830 " --> pdb=" O ALA A 826 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 838 " --> pdb=" O GLU A 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 579 removed outlier: 3.748A pdb=" N LEU B 567 " --> pdb=" O PHE B 563 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 568 " --> pdb=" O VAL B 564 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 574 " --> pdb=" O SER B 570 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.671A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 656 removed outlier: 3.531A pdb=" N PHE B 638 " --> pdb=" O VAL B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 845 removed outlier: 4.037A pdb=" N PHE B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 583 removed outlier: 3.580A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL C 570 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 616 Processing helix chain 'C' and resid 626 through 657 removed outlier: 3.697A pdb=" N ILE C 631 " --> pdb=" O PHE C 627 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C 632 " --> pdb=" O SER C 628 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET C 641 " --> pdb=" O ALA C 637 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 838 removed outlier: 3.648A pdb=" N PHE C 817 " --> pdb=" O MET C 813 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 824 " --> pdb=" O VAL C 820 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL C 825 " --> pdb=" O ALA C 821 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 830 " --> pdb=" O ALA C 826 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE C 833 " --> pdb=" O PHE C 829 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS C 838 " --> pdb=" O GLU C 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 579 removed outlier: 3.750A pdb=" N LEU D 567 " --> pdb=" O PHE D 563 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 568 " --> pdb=" O VAL D 564 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 574 " --> pdb=" O SER D 570 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 removed outlier: 3.671A pdb=" N TRP D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 656 removed outlier: 3.535A pdb=" N PHE D 638 " --> pdb=" O VAL D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 845 removed outlier: 4.033A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 834 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: 0.50 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 568 1.32 - 1.44: 1050 1.44 - 1.56: 2216 1.56 - 1.68: 8 1.68 - 1.80: 56 Bond restraints: 3898 Sorted by residual: bond pdb=" C GLU B 552 " pdb=" N PRO B 553 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.18e+00 bond pdb=" C GLU D 552 " pdb=" N PRO D 553 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.13e+00 bond pdb=" CB PRO B 553 " pdb=" CG PRO B 553 " ideal model delta sigma weight residual 1.492 1.457 0.035 5.00e-02 4.00e+02 4.88e-01 bond pdb=" CB PRO D 553 " pdb=" CG PRO D 553 " ideal model delta sigma weight residual 1.492 1.457 0.035 5.00e-02 4.00e+02 4.80e-01 bond pdb=" C GLN A 556 " pdb=" N PRO A 557 " ideal model delta sigma weight residual 1.335 1.343 -0.009 1.28e-02 6.10e+03 4.71e-01 ... (remaining 3893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 5147 1.01 - 2.02: 102 2.02 - 3.02: 22 3.02 - 4.03: 5 4.03 - 5.04: 8 Bond angle restraints: 5284 Sorted by residual: angle pdb=" N ASP B 816 " pdb=" CA ASP B 816 " pdb=" C ASP B 816 " ideal model delta sigma weight residual 113.72 109.90 3.82 1.52e+00 4.33e-01 6.30e+00 angle pdb=" N ASP D 816 " pdb=" CA ASP D 816 " pdb=" C ASP D 816 " ideal model delta sigma weight residual 113.72 110.25 3.47 1.52e+00 4.33e-01 5.22e+00 angle pdb=" CA ASP D 816 " pdb=" C ASP D 816 " pdb=" N ASN D 817 " ideal model delta sigma weight residual 118.87 116.38 2.49 1.18e+00 7.18e-01 4.44e+00 angle pdb=" N GLU D 552 " pdb=" CA GLU D 552 " pdb=" C GLU D 552 " ideal model delta sigma weight residual 109.81 114.40 -4.59 2.21e+00 2.05e-01 4.32e+00 angle pdb=" N GLU B 552 " pdb=" CA GLU B 552 " pdb=" C GLU B 552 " ideal model delta sigma weight residual 109.81 114.35 -4.54 2.21e+00 2.05e-01 4.23e+00 ... (remaining 5279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.52: 2099 15.52 - 31.04: 110 31.04 - 46.57: 23 46.57 - 62.09: 21 62.09 - 77.61: 5 Dihedral angle restraints: 2258 sinusoidal: 802 harmonic: 1456 Sorted by residual: dihedral pdb=" C3 POV A 902 " pdb=" C31 POV A 902 " pdb=" O31 POV A 902 " pdb=" C32 POV A 902 " ideal model delta sinusoidal sigma weight residual 172.61 97.65 74.96 1 3.00e+01 1.11e-03 7.90e+00 dihedral pdb=" C3 POV B 902 " pdb=" C31 POV B 902 " pdb=" O31 POV B 902 " pdb=" C32 POV B 902 " ideal model delta sinusoidal sigma weight residual 172.61 98.78 73.83 1 3.00e+01 1.11e-03 7.70e+00 dihedral pdb=" C27 POV A 902 " pdb=" C28 POV A 902 " pdb=" C29 POV A 902 " pdb="C210 POV A 902 " ideal model delta sinusoidal sigma weight residual 127.48 -172.75 -59.77 1 3.00e+01 1.11e-03 5.30e+00 ... (remaining 2255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 360 0.025 - 0.049: 193 0.049 - 0.074: 67 0.074 - 0.098: 4 0.098 - 0.123: 6 Chirality restraints: 630 Sorted by residual: chirality pdb=" CA ILE A 619 " pdb=" N ILE A 619 " pdb=" C ILE A 619 " pdb=" CB ILE A 619 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 chirality pdb=" CA ILE C 619 " pdb=" N ILE C 619 " pdb=" C ILE C 619 " pdb=" CB ILE C 619 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 chirality pdb=" CA PRO B 553 " pdb=" N PRO B 553 " pdb=" C PRO B 553 " pdb=" CB PRO B 553 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.51e-01 ... (remaining 627 not shown) Planarity restraints: 620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 552 " 0.016 5.00e-02 4.00e+02 2.37e-02 9.02e-01 pdb=" N PRO B 553 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO B 553 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 553 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 552 " 0.015 5.00e-02 4.00e+02 2.31e-02 8.56e-01 pdb=" N PRO D 553 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO D 553 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 553 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 618 " 0.014 5.00e-02 4.00e+02 2.08e-02 6.91e-01 pdb=" N PRO B 619 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO B 619 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 619 " 0.012 5.00e-02 4.00e+02 ... (remaining 617 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1039 2.80 - 3.33: 3558 3.33 - 3.85: 5565 3.85 - 4.38: 6773 4.38 - 4.90: 11905 Nonbonded interactions: 28840 Sorted by model distance: nonbonded pdb=" OG1 THR B 626 " pdb=" O13 POV B 902 " model vdw 2.281 3.040 nonbonded pdb=" O ASN D 616 " pdb=" O HOH D 901 " model vdw 2.284 3.040 nonbonded pdb=" O ASN B 616 " pdb=" O HOH B1001 " model vdw 2.285 3.040 nonbonded pdb=" OG1 THR D 626 " pdb=" O13 POV A 902 " model vdw 2.287 3.040 nonbonded pdb=" OD1 ASN C 616 " pdb=" O HOH D 901 " model vdw 2.312 3.040 ... (remaining 28835 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 'A' and resid 551 through 901) selection = chain 'C' } ncs_group { reference = (chain 'B' and resid 546 through 845) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.370 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.400 Find NCS groups from input model: 0.060 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3898 Z= 0.118 Angle : 0.429 5.040 5284 Z= 0.230 Chirality : 0.033 0.123 630 Planarity : 0.003 0.024 620 Dihedral : 12.707 77.611 1306 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.60 % Allowed : 0.00 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.32), residues: 484 helix: -0.85 (0.22), residues: 372 sheet: None (None), residues: 0 loop : -2.09 (0.52), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 630 TYR 0.004 0.001 TYR A 647 PHE 0.008 0.001 PHE A 639 TRP 0.008 0.001 TRP B 610 HIS 0.001 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 3898) covalent geometry : angle 0.42905 / 0.23 ( 5284) hydrogen bonds : bond 0.30857 / 19.65 ( 278) hydrogen bonds : angle 7.39109 / 5.37 ( 834) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.135 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 66 average time/residue: 0.0382 time to fit residues: 3.6031 Evaluate side-chains 60 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 30.0000 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.162988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.120061 restraints weight = 4037.828| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.11 r_work: 0.2955 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3898 Z= 0.149 Angle : 0.494 5.295 5284 Z= 0.268 Chirality : 0.035 0.122 630 Planarity : 0.004 0.025 620 Dihedral : 13.799 80.699 678 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.36), residues: 484 helix: 1.27 (0.25), residues: 376 sheet: None (None), residues: 0 loop : -1.82 (0.56), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 630 TYR 0.005 0.001 TYR A 647 PHE 0.019 0.002 PHE A 627 TRP 0.008 0.001 TRP D 610 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 3898) covalent geometry : angle 0.49385 / 0.27 ( 5284) hydrogen bonds : bond 0.06391 / 4.20 ( 278) hydrogen bonds : angle 3.49895 / 2.49 ( 834) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.104 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0375 time to fit residues: 3.1339 Evaluate side-chains 55 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.162927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.119093 restraints weight = 3944.048| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.26 r_work: 0.2958 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3898 Z= 0.144 Angle : 0.472 5.324 5284 Z= 0.249 Chirality : 0.034 0.123 630 Planarity : 0.003 0.026 620 Dihedral : 13.354 83.751 678 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.60 % Allowed : 5.06 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.37), residues: 484 helix: 2.12 (0.25), residues: 378 sheet: None (None), residues: 0 loop : -2.07 (0.54), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 630 TYR 0.004 0.001 TYR A 647 PHE 0.022 0.002 PHE C 627 TRP 0.009 0.001 TRP D 610 HIS 0.001 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 3898) covalent geometry : angle 0.47172 / 0.25 ( 5284) hydrogen bonds : bond 0.05391 / 3.51 ( 278) hydrogen bonds : angle 3.11578 / 2.22 ( 834) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.129 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 56 average time/residue: 0.0421 time to fit residues: 3.3537 Evaluate side-chains 58 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain D residue 815 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 5 optimal weight: 0.0570 chunk 39 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.168357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.124712 restraints weight = 3909.298| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.26 r_work: 0.2979 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3898 Z= 0.115 Angle : 0.433 5.322 5284 Z= 0.229 Chirality : 0.033 0.119 630 Planarity : 0.003 0.025 620 Dihedral : 12.744 82.822 678 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.60 % Allowed : 5.36 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.37), residues: 484 helix: 2.61 (0.25), residues: 378 sheet: None (None), residues: 0 loop : -2.07 (0.54), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 630 TYR 0.003 0.001 TYR A 578 PHE 0.022 0.002 PHE C 627 TRP 0.008 0.001 TRP B 607 HIS 0.001 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 3898) covalent geometry : angle 0.43266 / 0.23 ( 5284) hydrogen bonds : bond 0.04410 / 2.91 ( 278) hydrogen bonds : angle 2.88136 / 2.06 ( 834) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.125 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 55 average time/residue: 0.0405 time to fit residues: 3.1886 Evaluate side-chains 55 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain D residue 815 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.164888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.120737 restraints weight = 3925.390| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.28 r_work: 0.2950 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3898 Z= 0.137 Angle : 0.458 5.363 5284 Z= 0.242 Chirality : 0.034 0.123 630 Planarity : 0.003 0.025 620 Dihedral : 12.832 82.414 678 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.19 % Allowed : 5.95 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.37), residues: 484 helix: 2.65 (0.25), residues: 378 sheet: None (None), residues: 0 loop : -2.17 (0.53), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 630 TYR 0.003 0.001 TYR C 578 PHE 0.022 0.002 PHE C 627 TRP 0.009 0.001 TRP B 607 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 3898) covalent geometry : angle 0.45842 / 0.24 ( 5284) hydrogen bonds : bond 0.04894 / 3.20 ( 278) hydrogen bonds : angle 2.94460 / 2.10 ( 834) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.109 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 58 average time/residue: 0.0384 time to fit residues: 3.2616 Evaluate side-chains 61 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain D residue 815 ILE Chi-restraints excluded: chain D residue 821 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.0770 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 12 optimal weight: 0.0570 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.169151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.124399 restraints weight = 3993.837| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.31 r_work: 0.2996 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3898 Z= 0.098 Angle : 0.415 5.318 5284 Z= 0.218 Chirality : 0.032 0.116 630 Planarity : 0.003 0.024 620 Dihedral : 12.244 81.336 678 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.19 % Allowed : 6.55 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.37), residues: 484 helix: 3.03 (0.25), residues: 378 sheet: None (None), residues: 0 loop : -2.12 (0.53), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 630 TYR 0.002 0.000 TYR A 647 PHE 0.023 0.002 PHE C 627 TRP 0.008 0.001 TRP B 607 HIS 0.001 0.001 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 ( 3898) covalent geometry : angle 0.41481 / 0.22 ( 5284) hydrogen bonds : bond 0.03813 / 2.53 ( 278) hydrogen bonds : angle 2.72075 / 1.95 ( 834) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.086 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 0.0368 time to fit residues: 2.8464 Evaluate side-chains 55 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain D residue 815 ILE Chi-restraints excluded: chain D residue 821 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 20.0000 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 42 optimal weight: 0.0070 chunk 48 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.160213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.115322 restraints weight = 3996.078| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.28 r_work: 0.2931 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3898 Z= 0.174 Angle : 0.491 5.383 5284 Z= 0.259 Chirality : 0.035 0.127 630 Planarity : 0.003 0.024 620 Dihedral : 12.950 82.151 678 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.19 % Allowed : 6.85 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.37), residues: 484 helix: 2.77 (0.25), residues: 378 sheet: None (None), residues: 0 loop : -2.31 (0.51), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 630 TYR 0.003 0.001 TYR A 578 PHE 0.024 0.002 PHE C 627 TRP 0.010 0.001 TRP B 607 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.17 ( 3898) covalent geometry : angle 0.49123 / 0.26 ( 5284) hydrogen bonds : bond 0.05337 / 3.48 ( 278) hydrogen bonds : angle 3.00644 / 2.16 ( 834) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.127 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 60 average time/residue: 0.0380 time to fit residues: 3.3087 Evaluate side-chains 64 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain D residue 815 ILE Chi-restraints excluded: chain D residue 821 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.161412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.117315 restraints weight = 3962.464| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.25 r_work: 0.2935 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3898 Z= 0.161 Angle : 0.489 5.384 5284 Z= 0.256 Chirality : 0.035 0.124 630 Planarity : 0.003 0.024 620 Dihedral : 12.965 83.412 678 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.19 % Allowed : 5.95 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.37), residues: 484 helix: 2.71 (0.25), residues: 378 sheet: None (None), residues: 0 loop : -2.33 (0.52), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 630 TYR 0.002 0.001 TYR A 578 PHE 0.025 0.002 PHE C 627 TRP 0.009 0.001 TRP D 607 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.16 ( 3898) covalent geometry : angle 0.48877 / 0.26 ( 5284) hydrogen bonds : bond 0.05181 / 3.37 ( 278) hydrogen bonds : angle 2.98338 / 2.13 ( 834) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.125 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 60 average time/residue: 0.0409 time to fit residues: 3.4966 Evaluate side-chains 61 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain D residue 815 ILE Chi-restraints excluded: chain D residue 821 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.161778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.117641 restraints weight = 4013.844| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.24 r_work: 0.2925 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3898 Z= 0.153 Angle : 0.483 5.402 5284 Z= 0.252 Chirality : 0.034 0.123 630 Planarity : 0.003 0.024 620 Dihedral : 12.948 83.384 678 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.19 % Allowed : 6.25 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.37), residues: 484 helix: 2.74 (0.25), residues: 378 sheet: None (None), residues: 0 loop : -2.43 (0.50), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 630 TYR 0.003 0.001 TYR C 578 PHE 0.025 0.002 PHE C 627 TRP 0.009 0.001 TRP D 607 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.15 ( 3898) covalent geometry : angle 0.48253 / 0.25 ( 5284) hydrogen bonds : bond 0.05039 / 3.29 ( 278) hydrogen bonds : angle 2.95690 / 2.12 ( 834) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.094 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 60 average time/residue: 0.0342 time to fit residues: 2.9235 Evaluate side-chains 62 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain D residue 815 ILE Chi-restraints excluded: chain D residue 821 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 0.0980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.165217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.120653 restraints weight = 3956.292| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.29 r_work: 0.2958 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3898 Z= 0.114 Angle : 0.449 5.438 5284 Z= 0.233 Chirality : 0.033 0.116 630 Planarity : 0.003 0.025 620 Dihedral : 12.552 82.519 678 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.19 % Allowed : 6.55 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.37), residues: 484 helix: 2.96 (0.25), residues: 378 sheet: None (None), residues: 0 loop : -2.35 (0.51), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 630 TYR 0.002 0.000 TYR C 578 PHE 0.025 0.002 PHE C 627 TRP 0.008 0.001 TRP D 607 HIS 0.001 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 3898) covalent geometry : angle 0.44873 / 0.23 ( 5284) hydrogen bonds : bond 0.04271 / 2.81 ( 278) hydrogen bonds : angle 2.80701 / 2.01 ( 834) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 968 Ramachandran restraints generated. 484 Oldfield, 0 Emsley, 484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.132 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 60 average time/residue: 0.0389 time to fit residues: 3.3527 Evaluate side-chains 60 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain D residue 815 ILE Chi-restraints excluded: chain D residue 821 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.0770 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.0040 chunk 20 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.3950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.167884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.123669 restraints weight = 3929.267| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.28 r_work: 0.2982 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3898 Z= 0.104 Angle : 0.452 6.585 5284 Z= 0.227 Chirality : 0.033 0.116 630 Planarity : 0.003 0.024 620 Dihedral : 12.248 80.495 678 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.89 % Allowed : 6.85 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.10 (0.37), residues: 484 helix: 3.14 (0.24), residues: 378 sheet: None (None), residues: 0 loop : -2.38 (0.51), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 630 TYR 0.002 0.000 TYR A 578 PHE 0.025 0.002 PHE C 627 TRP 0.008 0.001 TRP B 607 HIS 0.002 0.001 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 3898) covalent geometry : angle 0.45234 / 0.23 ( 5284) hydrogen bonds : bond 0.03853 / 2.54 ( 278) hydrogen bonds : angle 2.71183 / 1.95 ( 834) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1051.48 seconds wall clock time: 18 minutes 45.28 seconds (1125.28 seconds total)