Starting phenix.real_space_refine on Wed Aug 5 00:34:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rvy_54292/08_2026/9rvy_54292.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rvy_54292/08_2026/9rvy_54292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rvy_54292/08_2026/9rvy_54292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rvy_54292/08_2026/9rvy_54292.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rvy_54292/08_2026/9rvy_54292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rvy_54292/08_2026/9rvy_54292.map" } resolution = 3.0 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= -0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 88 5.49 5 S 33 5.16 5 C 4487 2.51 5 N 1311 2.21 5 O 1710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7629 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 426 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 433 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3700 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 450} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1220 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 147} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 925 Classifications: {'RNA': 44} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 21, 'rna3p_pyr': 22} Link IDs: {'rna2p': 1, 'rna3p': 42} Chain: "F" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 925 Classifications: {'RNA': 44} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 21, 'rna3p_pyr': 22} Link IDs: {'rna2p': 1, 'rna3p': 42} Time building chain proxies: 1.23, per 1000 atoms: 0.16 Number of scatterers: 7629 At special positions: 0 Unit cell: (78.366, 97.428, 152.496, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 88 15.00 O 1710 8.00 N 1311 7.00 C 4487 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: 0.40 Conformation dependent library (CDL) restraints added in 269.5 milliseconds 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1374 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 5 sheets defined 70.0% alpha, 6.1% beta 34 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 695 through 747 removed outlier: 3.658A pdb=" N VAL A 699 " --> pdb=" O CYS A 695 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 747 Processing helix chain 'D' and resid 3 through 25 removed outlier: 3.786A pdb=" N LYS D 24 " --> pdb=" O ARG D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 36 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 43 through 51 Processing helix chain 'D' and resid 53 through 62 Processing helix chain 'D' and resid 95 through 110 Processing helix chain 'D' and resid 119 through 125 removed outlier: 3.846A pdb=" N HIS D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 129 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 140 through 151 Processing helix chain 'D' and resid 521 through 530 Processing helix chain 'D' and resid 535 through 554 Processing helix chain 'D' and resid 594 through 600 removed outlier: 3.845A pdb=" N THR D 598 " --> pdb=" O PRO D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 608 Processing helix chain 'D' and resid 617 through 628 removed outlier: 4.795A pdb=" N ASP D 621 " --> pdb=" O ASP D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 652 Processing helix chain 'D' and resid 654 through 658 Processing helix chain 'D' and resid 662 through 670 removed outlier: 3.613A pdb=" N TYR D 670 " --> pdb=" O LEU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 680 Processing helix chain 'D' and resid 681 through 688 removed outlier: 3.983A pdb=" N TYR D 685 " --> pdb=" O LEU D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 714 removed outlier: 4.166A pdb=" N ASP D 708 " --> pdb=" O TYR D 704 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL D 709 " --> pdb=" O ALA D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 725 Processing helix chain 'D' and resid 729 through 743 Processing helix chain 'D' and resid 746 through 773 removed outlier: 4.011A pdb=" N THR D 773 " --> pdb=" O LYS D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 780 through 787 Processing helix chain 'D' and resid 788 through 790 No H-bonds generated for 'chain 'D' and resid 788 through 790' Processing helix chain 'D' and resid 793 through 802 removed outlier: 4.245A pdb=" N GLY D 802 " --> pdb=" O GLU D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 803 through 816 Processing helix chain 'C' and resid 6 through 25 Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 36 through 39 Processing helix chain 'C' and resid 42 through 50 removed outlier: 3.995A pdb=" N MET C 46 " --> pdb=" O PHE C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 64 removed outlier: 4.091A pdb=" N TYR C 64 " --> pdb=" O PHE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 110 removed outlier: 3.719A pdb=" N GLN C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 127 removed outlier: 4.015A pdb=" N LEU C 122 " --> pdb=" O PRO C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 138 Processing helix chain 'C' and resid 140 through 151 Processing sheet with id=AA1, first strand: chain 'D' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'D' and resid 117 through 118 Processing sheet with id=AA3, first strand: chain 'D' and resid 531 through 533 removed outlier: 3.587A pdb=" N LEU D 587 " --> pdb=" O THR D 531 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 576 " --> pdb=" O PHE D 588 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS D 613 " --> pdb=" O PHE D 637 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 28 through 29 Processing sheet with id=AA5, first strand: chain 'C' and resid 155 through 158 372 hydrogen bonds defined for protein. 1071 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.25: 1088 1.25 - 1.39: 1983 1.39 - 1.53: 4499 1.53 - 1.67: 304 1.67 - 1.81: 54 Bond restraints: 7928 Sorted by residual: bond pdb=" C ASP C 32 " pdb=" O ASP C 32 " ideal model delta sigma weight residual 1.236 1.115 0.121 1.26e-02 6.30e+03 9.20e+01 bond pdb=" C SER C 34 " pdb=" O SER C 34 " ideal model delta sigma weight residual 1.236 1.115 0.121 1.32e-02 5.74e+03 8.35e+01 bond pdb=" C MET C 8 " pdb=" O MET C 8 " ideal model delta sigma weight residual 1.237 1.139 0.097 1.19e-02 7.06e+03 6.71e+01 bond pdb=" CA GLU D 45 " pdb=" C GLU D 45 " ideal model delta sigma weight residual 1.524 1.426 0.098 1.26e-02 6.30e+03 6.02e+01 bond pdb=" CA SER C 34 " pdb=" C SER C 34 " ideal model delta sigma weight residual 1.522 1.417 0.105 1.39e-02 5.18e+03 5.70e+01 ... (remaining 7923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 10868 2.52 - 5.05: 203 5.05 - 7.57: 13 7.57 - 10.09: 0 10.09 - 12.62: 2 Bond angle restraints: 11086 Sorted by residual: angle pdb=" O3' C E 33 " pdb=" C3' C E 33 " pdb=" C2' C E 33 " ideal model delta sigma weight residual 113.70 126.32 -12.62 1.60e+00 3.91e-01 6.22e+01 angle pdb=" N6 A F 31 " pdb=" C6 A F 31 " pdb=" N1 A F 31 " ideal model delta sigma weight residual 118.60 114.88 3.72 6.00e-01 2.78e+00 3.85e+01 angle pdb=" N6 A F 30 " pdb=" C6 A F 30 " pdb=" N1 A F 30 " ideal model delta sigma weight residual 118.60 115.08 3.52 6.00e-01 2.78e+00 3.44e+01 angle pdb=" N6 A F 37 " pdb=" C6 A F 37 " pdb=" N1 A F 37 " ideal model delta sigma weight residual 118.60 115.12 3.48 6.00e-01 2.78e+00 3.37e+01 angle pdb=" N6 A F 21 " pdb=" C6 A F 21 " pdb=" N1 A F 21 " ideal model delta sigma weight residual 118.60 115.42 3.18 6.00e-01 2.78e+00 2.82e+01 ... (remaining 11081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 4619 35.79 - 71.59: 240 71.59 - 107.38: 21 107.38 - 143.18: 0 143.18 - 178.97: 2 Dihedral angle restraints: 4882 sinusoidal: 2766 harmonic: 2116 Sorted by residual: dihedral pdb=" C4' C F 33 " pdb=" C3' C F 33 " pdb=" O3' C F 33 " pdb=" P U F 34 " ideal model delta sinusoidal sigma weight residual -140.00 38.97 -178.97 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C5' C E 33 " pdb=" C4' C E 33 " pdb=" C3' C E 33 " pdb=" O3' C E 33 " ideal model delta sinusoidal sigma weight residual 82.00 55.93 26.07 1 8.00e+00 1.56e-02 1.53e+01 dihedral pdb=" C4' C E 33 " pdb=" C3' C E 33 " pdb=" O3' C E 33 " pdb=" P U E 34 " ideal model delta sinusoidal sigma weight residual 220.00 61.43 158.57 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 4879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1273 0.118 - 0.236: 44 0.236 - 0.354: 3 0.354 - 0.472: 2 0.472 - 0.590: 1 Chirality restraints: 1323 Sorted by residual: chirality pdb=" C3' C E 33 " pdb=" C4' C E 33 " pdb=" O3' C E 33 " pdb=" C2' C E 33 " both_signs ideal model delta sigma weight residual False -2.48 -1.89 -0.59 2.00e-01 2.50e+01 8.70e+00 chirality pdb=" CA SER C 34 " pdb=" N SER C 34 " pdb=" C SER C 34 " pdb=" CB SER C 34 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CA ARG D 120 " pdb=" N ARG D 120 " pdb=" C ARG D 120 " pdb=" CB ARG D 120 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 1320 not shown) Planarity restraints: 1106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A F 17 " 0.064 2.00e-02 2.50e+03 2.58e-02 1.84e+01 pdb=" N9 A F 17 " -0.034 2.00e-02 2.50e+03 pdb=" C8 A F 17 " -0.020 2.00e-02 2.50e+03 pdb=" N7 A F 17 " -0.008 2.00e-02 2.50e+03 pdb=" C5 A F 17 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A F 17 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A F 17 " 0.033 2.00e-02 2.50e+03 pdb=" N1 A F 17 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A F 17 " -0.010 2.00e-02 2.50e+03 pdb=" N3 A F 17 " -0.014 2.00e-02 2.50e+03 pdb=" C4 A F 17 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U F 11 " -0.057 2.00e-02 2.50e+03 2.65e-02 1.58e+01 pdb=" N1 U F 11 " 0.043 2.00e-02 2.50e+03 pdb=" C2 U F 11 " 0.005 2.00e-02 2.50e+03 pdb=" O2 U F 11 " 0.016 2.00e-02 2.50e+03 pdb=" N3 U F 11 " -0.007 2.00e-02 2.50e+03 pdb=" C4 U F 11 " -0.007 2.00e-02 2.50e+03 pdb=" O4 U F 11 " -0.022 2.00e-02 2.50e+03 pdb=" C5 U F 11 " 0.009 2.00e-02 2.50e+03 pdb=" C6 U F 11 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A F 35 " 0.057 2.00e-02 2.50e+03 2.33e-02 1.49e+01 pdb=" N9 A F 35 " -0.029 2.00e-02 2.50e+03 pdb=" C8 A F 35 " -0.012 2.00e-02 2.50e+03 pdb=" N7 A F 35 " -0.008 2.00e-02 2.50e+03 pdb=" C5 A F 35 " -0.009 2.00e-02 2.50e+03 pdb=" C6 A F 35 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A F 35 " 0.033 2.00e-02 2.50e+03 pdb=" N1 A F 35 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A F 35 " -0.005 2.00e-02 2.50e+03 pdb=" N3 A F 35 " -0.015 2.00e-02 2.50e+03 pdb=" C4 A F 35 " -0.014 2.00e-02 2.50e+03 ... (remaining 1103 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 170 2.66 - 3.22: 7320 3.22 - 3.78: 12620 3.78 - 4.34: 16937 4.34 - 4.90: 26125 Nonbonded interactions: 63172 Sorted by model distance: nonbonded pdb=" O ASP C 160 " pdb=" OD1 ASP C 160 " model vdw 2.105 3.040 nonbonded pdb=" O2' C E 36 " pdb=" OP1 A E 38 " model vdw 2.126 3.040 nonbonded pdb=" O ASP D 589 " pdb=" OG SER D 592 " model vdw 2.159 3.040 nonbonded pdb=" O PHE C 42 " pdb=" OG1 THR C 43 " model vdw 2.264 3.040 nonbonded pdb=" O ASP D 160 " pdb=" OD1 ASP D 160 " model vdw 2.321 3.040 ... (remaining 63167 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' selection = (chain 'B' and (resid 695 through 740 or (resid 741 through 742 and (name N or n \ ame CA or name C or name O or name CB )) or resid 743 through 747)) } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 1.270 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.150 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.007 0.128 7928 Z= 0.538 Angle : 0.817 12.618 11086 Z= 0.719 Chirality : 0.055 0.590 1323 Planarity : 0.005 0.095 1106 Dihedral : 19.035 178.970 3508 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.32 % Allowed : 24.76 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.17 (0.32), residues: 704 helix: 1.67 (0.25), residues: 460 sheet: -0.74 (0.92), residues: 28 loop : -0.93 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 634 TYR 0.012 0.001 TYR D 6 PHE 0.013 0.001 PHE C 104 TRP 0.002 0.001 TRP D 522 HIS 0.012 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.54 ( 7928) covalent geometry : angle 0.81681 / 0.72 (11086) hydrogen bonds : bond 0.11488 / 7.85 ( 444) hydrogen bonds : angle 5.49621 / 3.73 ( 1207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: D 634 ARG cc_start: 0.7865 (mtp-110) cc_final: 0.7542 (ttm110) REVERT: D 660 TYR cc_start: 0.8227 (m-80) cc_final: 0.7978 (m-80) outliers start: 2 outliers final: 3 residues processed: 108 average time/residue: 0.5153 time to fit residues: 58.4896 Evaluate side-chains 96 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 718 PHE Chi-restraints excluded: chain D residue 800 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.0470 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 708 GLN D 714 HIS C 106 ASN C 151 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.185003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.137717 restraints weight = 10526.615| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.43 r_work: 0.3261 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7928 Z= 0.158 Angle : 0.561 7.028 11086 Z= 0.313 Chirality : 0.040 0.317 1323 Planarity : 0.004 0.045 1106 Dihedral : 16.316 175.939 2055 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.22 % Allowed : 22.67 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.53 (0.32), residues: 704 helix: 1.91 (0.24), residues: 462 sheet: -0.96 (0.97), residues: 25 loop : -0.70 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 730 TYR 0.012 0.001 TYR C 6 PHE 0.021 0.002 PHE C 104 TRP 0.003 0.001 TRP D 692 HIS 0.005 0.001 HIS D 714 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 ( 7928) covalent geometry : angle 0.56104 / 0.31 (11086) hydrogen bonds : bond 0.05313 / 3.52 ( 444) hydrogen bonds : angle 4.51809 / 3.09 ( 1207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.157 Fit side-chains REVERT: D 621 ASP cc_start: 0.6856 (OUTLIER) cc_final: 0.6439 (p0) REVERT: D 634 ARG cc_start: 0.7901 (mtp-110) cc_final: 0.7500 (ttm110) REVERT: D 743 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7834 (ttp) REVERT: D 798 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7803 (tm-30) REVERT: D 801 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7580 (mptt) REVERT: C 29 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8396 (m) REVERT: C 99 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7241 (mt-10) REVERT: C 110 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7616 (pp30) REVERT: C 149 MET cc_start: 0.6612 (tmm) cc_final: 0.6109 (mmt) outliers start: 20 outliers final: 8 residues processed: 107 average time/residue: 0.4906 time to fit residues: 55.1402 Evaluate side-chains 104 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain B residue 735 GLN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 718 PHE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 801 LYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 78 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 706 ASN A 708 GLN ** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.185812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.139457 restraints weight = 10561.916| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.68 r_work: 0.3261 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7928 Z= 0.126 Angle : 0.510 7.212 11086 Z= 0.283 Chirality : 0.037 0.262 1323 Planarity : 0.004 0.037 1106 Dihedral : 16.314 178.737 2053 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.55 % Favored : 96.31 % Rotamer: Outliers : 4.02 % Allowed : 22.35 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.73 (0.32), residues: 704 helix: 2.04 (0.24), residues: 461 sheet: -0.67 (0.93), residues: 28 loop : -0.54 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 730 TYR 0.012 0.001 TYR D 660 PHE 0.025 0.002 PHE D 588 TRP 0.005 0.001 TRP D 692 HIS 0.003 0.001 HIS C 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 7928) covalent geometry : angle 0.50955 / 0.28 (11086) hydrogen bonds : bond 0.04746 / 3.15 ( 444) hydrogen bonds : angle 4.32413 / 2.97 ( 1207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 745 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6421 (mp0) REVERT: D 621 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.6204 (p0) REVERT: D 634 ARG cc_start: 0.7980 (mtp-110) cc_final: 0.7550 (ttm110) REVERT: D 743 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7886 (ttp) REVERT: D 798 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7793 (tm-30) REVERT: D 801 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7600 (mptt) REVERT: C 29 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8321 (m) REVERT: C 110 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7617 (pp30) REVERT: C 134 ARG cc_start: 0.8220 (ttp-170) cc_final: 0.8014 (ttp-170) REVERT: C 149 MET cc_start: 0.6585 (tmm) cc_final: 0.6087 (mmt) outliers start: 25 outliers final: 10 residues processed: 107 average time/residue: 0.5310 time to fit residues: 59.6638 Evaluate side-chains 110 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain B residue 735 GLN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 801 LYS Chi-restraints excluded: chain D residue 811 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 77 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 708 GLN ** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.184925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.139481 restraints weight = 10639.168| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.68 r_work: 0.3238 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7928 Z= 0.150 Angle : 0.514 7.535 11086 Z= 0.281 Chirality : 0.038 0.234 1323 Planarity : 0.004 0.036 1106 Dihedral : 16.325 178.075 2051 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.12 % Favored : 96.73 % Rotamer: Outliers : 3.86 % Allowed : 22.67 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.84 (0.32), residues: 704 helix: 2.08 (0.24), residues: 459 sheet: -0.71 (0.91), residues: 28 loop : -0.37 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 788 TYR 0.014 0.001 TYR D 660 PHE 0.018 0.002 PHE D 718 TRP 0.008 0.001 TRP D 692 HIS 0.003 0.001 HIS C 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 7928) covalent geometry : angle 0.51426 / 0.28 (11086) hydrogen bonds : bond 0.04803 / 3.17 ( 444) hydrogen bonds : angle 4.29664 / 2.95 ( 1207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 621 ASP cc_start: 0.6875 (OUTLIER) cc_final: 0.6228 (p0) REVERT: D 633 LEU cc_start: 0.8709 (mt) cc_final: 0.8474 (mp) REVERT: D 634 ARG cc_start: 0.7986 (mtp-110) cc_final: 0.7565 (ttm110) REVERT: D 668 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7739 (tm-30) REVERT: D 743 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7857 (ttp) REVERT: D 798 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7880 (tm-30) REVERT: D 801 LYS cc_start: 0.7908 (mptm) cc_final: 0.7501 (mptt) REVERT: C 29 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8331 (m) REVERT: C 46 MET cc_start: 0.8872 (mtp) cc_final: 0.8534 (ptp) REVERT: C 108 MET cc_start: 0.5157 (OUTLIER) cc_final: 0.4343 (tmm) REVERT: C 110 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7632 (pp30) REVERT: C 149 MET cc_start: 0.6622 (tmm) cc_final: 0.6093 (mmt) outliers start: 24 outliers final: 14 residues processed: 110 average time/residue: 0.5076 time to fit residues: 58.7261 Evaluate side-chains 108 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 735 GLN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 718 PHE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 811 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 708 GLN B 706 ASN ** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.186210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.139300 restraints weight = 10534.944| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.50 r_work: 0.3271 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7928 Z= 0.127 Angle : 0.504 7.941 11086 Z= 0.276 Chirality : 0.036 0.213 1323 Planarity : 0.004 0.046 1106 Dihedral : 16.359 176.837 2051 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.12 % Favored : 96.73 % Rotamer: Outliers : 3.86 % Allowed : 24.76 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 704 helix: 2.09 (0.24), residues: 459 sheet: -0.89 (0.89), residues: 28 loop : -0.26 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 730 TYR 0.014 0.001 TYR C 161 PHE 0.022 0.002 PHE D 718 TRP 0.010 0.002 TRP D 692 HIS 0.003 0.001 HIS C 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 7928) covalent geometry : angle 0.50378 / 0.28 (11086) hydrogen bonds : bond 0.04505 / 2.99 ( 444) hydrogen bonds : angle 4.21417 / 2.91 ( 1207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.232 Fit side-chains REVERT: D 621 ASP cc_start: 0.6862 (OUTLIER) cc_final: 0.6300 (p0) REVERT: D 633 LEU cc_start: 0.8678 (mt) cc_final: 0.8432 (mp) REVERT: D 634 ARG cc_start: 0.7970 (mtp-110) cc_final: 0.7520 (ttm110) REVERT: D 668 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7720 (tm-30) REVERT: D 743 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7805 (ttp) REVERT: D 790 MET cc_start: 0.8358 (mtp) cc_final: 0.8141 (mtp) REVERT: D 798 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7834 (tm-30) REVERT: D 801 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7452 (mptt) REVERT: C 29 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8284 (m) REVERT: C 108 MET cc_start: 0.5124 (OUTLIER) cc_final: 0.4243 (tmm) REVERT: C 110 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7572 (pp30) REVERT: C 149 MET cc_start: 0.6536 (tmm) cc_final: 0.5994 (mmt) outliers start: 24 outliers final: 9 residues processed: 107 average time/residue: 0.4757 time to fit residues: 53.7173 Evaluate side-chains 107 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 735 GLN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 801 LYS Chi-restraints excluded: chain D residue 811 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 708 GLN ** D 714 HIS ** 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 = 0.4303 r_free = 0.4303 target = 0.186038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.138357 restraints weight = 10622.841| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.69 r_work: 0.3251 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7928 Z= 0.129 Angle : 0.509 8.421 11086 Z= 0.274 Chirality : 0.036 0.199 1323 Planarity : 0.004 0.056 1106 Dihedral : 16.352 175.466 2051 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.70 % Favored : 97.16 % Rotamer: Outliers : 4.50 % Allowed : 24.28 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.85 (0.32), residues: 704 helix: 2.09 (0.24), residues: 459 sheet: -0.83 (0.90), residues: 28 loop : -0.33 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 730 TYR 0.029 0.001 TYR D 393 PHE 0.014 0.002 PHE D 586 TRP 0.012 0.001 TRP D 692 HIS 0.003 0.001 HIS C 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 7928) covalent geometry : angle 0.50876 / 0.27 (11086) hydrogen bonds : bond 0.04444 / 2.93 ( 444) hydrogen bonds : angle 4.17252 / 2.87 ( 1207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 745 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6222 (mp0) REVERT: D 621 ASP cc_start: 0.6857 (OUTLIER) cc_final: 0.6302 (p0) REVERT: D 633 LEU cc_start: 0.8646 (mt) cc_final: 0.8395 (mp) REVERT: D 634 ARG cc_start: 0.7960 (mtp-110) cc_final: 0.7509 (ttm110) REVERT: D 668 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7751 (tm-30) REVERT: D 730 ARG cc_start: 0.7430 (mmt90) cc_final: 0.7030 (mmt90) REVERT: D 743 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7812 (ttp) REVERT: D 798 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7798 (tm-30) REVERT: D 801 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7446 (mptt) REVERT: C 29 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8292 (m) REVERT: C 108 MET cc_start: 0.5060 (OUTLIER) cc_final: 0.4180 (tmm) REVERT: C 110 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7538 (pp30) REVERT: C 149 MET cc_start: 0.6607 (tmm) cc_final: 0.6033 (mmt) outliers start: 28 outliers final: 12 residues processed: 113 average time/residue: 0.4921 time to fit residues: 58.5091 Evaluate side-chains 107 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain B residue 735 GLN Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 801 LYS Chi-restraints excluded: chain D residue 811 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 74 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 56 optimal weight: 0.3980 chunk 40 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.185911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.137872 restraints weight = 10486.862| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.54 r_work: 0.3262 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7928 Z= 0.134 Angle : 0.512 8.720 11086 Z= 0.276 Chirality : 0.036 0.190 1323 Planarity : 0.004 0.070 1106 Dihedral : 16.362 174.306 2051 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.84 % Favored : 97.02 % Rotamer: Outliers : 4.34 % Allowed : 25.56 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.86 (0.32), residues: 704 helix: 2.11 (0.24), residues: 459 sheet: -0.97 (0.88), residues: 28 loop : -0.33 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG D 47 TYR 0.021 0.001 TYR D 393 PHE 0.013 0.002 PHE D 718 TRP 0.012 0.002 TRP D 692 HIS 0.003 0.001 HIS C 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 7928) covalent geometry : angle 0.51245 / 0.28 (11086) hydrogen bonds : bond 0.04434 / 2.93 ( 444) hydrogen bonds : angle 4.12627 / 2.85 ( 1207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: D 44 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8087 (mtmt) REVERT: D 621 ASP cc_start: 0.6862 (OUTLIER) cc_final: 0.6317 (p0) REVERT: D 633 LEU cc_start: 0.8667 (mt) cc_final: 0.8443 (mp) REVERT: D 634 ARG cc_start: 0.7965 (mtp-110) cc_final: 0.7506 (ttm110) REVERT: D 668 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7751 (tm-30) REVERT: D 743 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7802 (ttp) REVERT: C 29 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8286 (m) REVERT: C 108 MET cc_start: 0.5050 (OUTLIER) cc_final: 0.4247 (tmm) REVERT: C 110 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7616 (pp30) REVERT: C 149 MET cc_start: 0.6611 (tmm) cc_final: 0.6075 (mmt) outliers start: 27 outliers final: 12 residues processed: 106 average time/residue: 0.5001 time to fit residues: 55.8030 Evaluate side-chains 106 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain B residue 735 GLN Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 811 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 75 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 30.0000 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.183882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.136351 restraints weight = 10530.725| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.67 r_work: 0.3218 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7928 Z= 0.206 Angle : 0.576 8.980 11086 Z= 0.303 Chirality : 0.039 0.195 1323 Planarity : 0.005 0.087 1106 Dihedral : 16.377 172.326 2051 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.84 % Favored : 97.02 % Rotamer: Outliers : 4.18 % Allowed : 26.05 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.54 (0.32), residues: 704 helix: 1.89 (0.24), residues: 459 sheet: -1.19 (0.86), residues: 28 loop : -0.51 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 47 TYR 0.028 0.002 TYR D 393 PHE 0.024 0.003 PHE D 718 TRP 0.008 0.001 TRP D 692 HIS 0.004 0.001 HIS D 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 ( 7928) covalent geometry : angle 0.57575 / 0.30 (11086) hydrogen bonds : bond 0.05037 / 3.32 ( 444) hydrogen bonds : angle 4.30655 / 2.97 ( 1207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 44 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8214 (mtmt) REVERT: D 633 LEU cc_start: 0.8709 (mt) cc_final: 0.8502 (mp) REVERT: D 634 ARG cc_start: 0.7941 (mtp-110) cc_final: 0.7595 (ttm110) REVERT: D 668 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7741 (tm-30) REVERT: D 743 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7771 (ttp) REVERT: C 29 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8368 (m) REVERT: C 108 MET cc_start: 0.5089 (OUTLIER) cc_final: 0.4192 (tmm) REVERT: C 110 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7617 (pp30) REVERT: C 149 MET cc_start: 0.6706 (tmm) cc_final: 0.6139 (mmt) outliers start: 26 outliers final: 14 residues processed: 105 average time/residue: 0.4949 time to fit residues: 54.8309 Evaluate side-chains 108 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 735 GLN Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 730 ARG Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 780 SER Chi-restraints excluded: chain D residue 811 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 67 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 728 GLN ** D 714 HIS ** 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 = 0.4286 r_free = 0.4286 target = 0.184453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.136821 restraints weight = 10504.395| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.71 r_work: 0.3227 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7928 Z= 0.163 Angle : 0.546 9.065 11086 Z= 0.290 Chirality : 0.037 0.193 1323 Planarity : 0.004 0.064 1106 Dihedral : 16.435 172.670 2051 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.84 % Favored : 97.02 % Rotamer: Outliers : 3.54 % Allowed : 27.01 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.58 (0.32), residues: 704 helix: 1.91 (0.24), residues: 458 sheet: -1.12 (0.87), residues: 28 loop : -0.48 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 47 TYR 0.020 0.001 TYR D 393 PHE 0.017 0.002 PHE C 104 TRP 0.010 0.001 TRP D 692 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 7928) covalent geometry : angle 0.54603 / 0.29 (11086) hydrogen bonds : bond 0.04672 / 3.08 ( 444) hydrogen bonds : angle 4.26091 / 2.94 ( 1207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 44 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8173 (mtmt) REVERT: D 633 LEU cc_start: 0.8708 (mt) cc_final: 0.8472 (mp) REVERT: D 634 ARG cc_start: 0.7927 (mtp-110) cc_final: 0.7558 (ttm110) REVERT: D 668 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7778 (tm-30) REVERT: D 743 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7803 (ttp) REVERT: C 29 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8344 (m) REVERT: C 46 MET cc_start: 0.8901 (mtp) cc_final: 0.8455 (ptp) REVERT: C 108 MET cc_start: 0.5233 (OUTLIER) cc_final: 0.4322 (tmm) REVERT: C 110 GLN cc_start: 0.7944 (tm-30) cc_final: 0.7674 (pp30) REVERT: C 149 MET cc_start: 0.6704 (tmm) cc_final: 0.6126 (mmt) outliers start: 22 outliers final: 14 residues processed: 101 average time/residue: 0.4871 time to fit residues: 51.8128 Evaluate side-chains 108 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 728 GLN Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 735 GLN Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 730 ARG Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 780 SER Chi-restraints excluded: chain D residue 811 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 0.0570 chunk 18 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 728 GLN ** D 714 HIS ** 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 = 0.4293 r_free = 0.4293 target = 0.185170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.138075 restraints weight = 10500.198| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.74 r_work: 0.3235 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7928 Z= 0.145 Angle : 0.540 9.115 11086 Z= 0.286 Chirality : 0.037 0.214 1323 Planarity : 0.004 0.062 1106 Dihedral : 16.444 172.697 2051 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.70 % Favored : 97.16 % Rotamer: Outliers : 2.57 % Allowed : 28.14 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.58 (0.32), residues: 704 helix: 1.92 (0.24), residues: 458 sheet: -1.12 (0.87), residues: 28 loop : -0.50 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 47 TYR 0.019 0.001 TYR D 393 PHE 0.031 0.002 PHE D 718 TRP 0.010 0.001 TRP D 692 HIS 0.003 0.001 HIS D 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 7928) covalent geometry : angle 0.53973 / 0.29 (11086) hydrogen bonds : bond 0.04543 / 2.99 ( 444) hydrogen bonds : angle 4.23187 / 2.92 ( 1207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8133 (tmm) cc_final: 0.7919 (ptp) REVERT: B 710 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7172 (mp0) REVERT: D 44 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8162 (mtmt) REVERT: D 633 LEU cc_start: 0.8762 (mt) cc_final: 0.8510 (mp) REVERT: D 634 ARG cc_start: 0.7971 (mtp-110) cc_final: 0.7613 (ttm110) REVERT: D 668 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7767 (tm-30) REVERT: D 743 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7820 (ttp) REVERT: D 801 LYS cc_start: 0.7752 (mptm) cc_final: 0.7534 (mmtp) REVERT: C 29 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8340 (m) REVERT: C 46 MET cc_start: 0.8886 (mtp) cc_final: 0.8528 (ptp) REVERT: C 108 MET cc_start: 0.5296 (OUTLIER) cc_final: 0.4469 (tmm) REVERT: C 110 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7683 (pp30) REVERT: C 149 MET cc_start: 0.6684 (tmm) cc_final: 0.6072 (mmt) outliers start: 16 outliers final: 11 residues processed: 99 average time/residue: 0.5311 time to fit residues: 55.2577 Evaluate side-chains 106 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain B residue 735 GLN Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 730 ARG Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 780 SER Chi-restraints excluded: chain D residue 811 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 728 GLN D 76 GLN ** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.182442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.134251 restraints weight = 10435.709| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.68 r_work: 0.3190 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 7928 Z= 0.236 Angle : 0.621 9.403 11086 Z= 0.323 Chirality : 0.041 0.243 1323 Planarity : 0.005 0.069 1106 Dihedral : 16.477 171.269 2051 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.98 % Favored : 96.88 % Rotamer: Outliers : 2.73 % Allowed : 28.14 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.18 (0.31), residues: 704 helix: 1.64 (0.24), residues: 458 sheet: -1.43 (0.87), residues: 28 loop : -0.70 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 47 TYR 0.020 0.002 TYR D 393 PHE 0.018 0.003 PHE D 17 TRP 0.006 0.001 TRP D 692 HIS 0.005 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.24 ( 7928) covalent geometry : angle 0.62141 / 0.32 (11086) hydrogen bonds : bond 0.05387 / 3.55 ( 444) hydrogen bonds : angle 4.41933 / 3.08 ( 1207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2111.70 seconds wall clock time: 36 minutes 41.97 seconds (2201.97 seconds total)