Starting phenix.real_space_refine on Fri Jul 3 00:08:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pii_13437/07_2026/7pii_13437_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pii_13437/07_2026/7pii_13437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pii_13437/07_2026/7pii_13437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pii_13437/07_2026/7pii_13437.map" model { file = "/net/cci-nas-00/data/ceres_data/7pii_13437/07_2026/7pii_13437_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pii_13437/07_2026/7pii_13437_neut.cif" } resolution = 2.68 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 244 5.49 5 S 8 5.16 5 C 6321 2.51 5 N 2070 2.21 5 O 2549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11192 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 799 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 96} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 755 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 770 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 784 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2506 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} Chain: "J" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2514 Classifications: {'DNA': 123} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 122} Chain: "K" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 178 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "L" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 185 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Time building chain proxies: 2.41, per 1000 atoms: 0.22 Number of scatterers: 11192 At special positions: 0 Unit cell: (80.607, 114.678, 123.819, 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 8 16.00 P 244 15.00 O 2549 8.00 N 2070 7.00 C 6321 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: 0.92 Conformation dependent library (CDL) restraints added in 193.1 milliseconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1450 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 68.9% alpha, 2.6% beta 121 base pairs and 220 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.629A pdb=" N LYS A 49 " --> pdb=" O GLN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.618A pdb=" N LEU A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 138 removed outlier: 5.628A pdb=" N LEU A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N GLU A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.409A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 47 through 55 Processing helix chain 'E' and resid 63 through 78 Processing helix chain 'E' and resid 87 through 116 Processing helix chain 'E' and resid 122 through 134 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.479A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.727A pdb=" N ASN A 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.452A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.916A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.180A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'L' and resid 516 through 517 408 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 282 hydrogen bonds 564 hydrogen bond angles 0 basepair planarities 121 basepair parallelities 220 stacking parallelities Total time for adding SS restraints: 1.69 Time building geometry restraints manager: 1.16 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: 1668 1.32 - 1.45: 4128 1.45 - 1.57: 5598 1.57 - 1.69: 487 1.69 - 1.81: 14 Bond restraints: 11895 Sorted by residual: bond pdb=" C3' DA I 8 " pdb=" O3' DA I 8 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.31e+01 bond pdb=" C3' DA I -6 " pdb=" O3' DA I -6 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.30e+01 bond pdb=" C3' DG I 7 " pdb=" O3' DG I 7 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.27e+01 bond pdb=" C3' DG I -14 " pdb=" O3' DG I -14 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.22e+01 bond pdb=" C3' DC J 15 " pdb=" O3' DC J 15 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.16e+01 ... (remaining 11890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 15667 1.63 - 3.27: 1334 3.27 - 4.90: 105 4.90 - 6.54: 9 6.54 - 8.17: 1 Bond angle restraints: 17116 Sorted by residual: angle pdb=" O4' DA I 57 " pdb=" C4' DA I 57 " pdb=" C3' DA I 57 " ideal model delta sigma weight residual 106.00 103.07 2.93 6.00e-01 2.78e+00 2.39e+01 angle pdb=" O4' DT I 48 " pdb=" C4' DT I 48 " pdb=" C3' DT I 48 " ideal model delta sigma weight residual 106.00 103.16 2.84 6.00e-01 2.78e+00 2.24e+01 angle pdb=" O4' DT J -9 " pdb=" C4' DT J -9 " pdb=" C3' DT J -9 " ideal model delta sigma weight residual 106.00 103.18 2.82 6.00e-01 2.78e+00 2.21e+01 angle pdb=" O4' DC J -4 " pdb=" C4' DC J -4 " pdb=" C3' DC J -4 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.16e+01 angle pdb=" N3 DT I 1 " pdb=" C4 DT I 1 " pdb=" O4 DT I 1 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.04e+01 ... (remaining 17111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.25: 5305 35.25 - 70.50: 1265 70.50 - 105.75: 23 105.75 - 141.01: 1 141.01 - 176.26: 2 Dihedral angle restraints: 6596 sinusoidal: 4351 harmonic: 2245 Sorted by residual: dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual -180.00 -154.05 -25.95 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA HIS F 75 " pdb=" C HIS F 75 " pdb=" N ALA F 76 " pdb=" CA ALA F 76 " ideal model delta harmonic sigma weight residual 180.00 158.07 21.93 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ARG E 133 " pdb=" C ARG E 133 " pdb=" N GLY E 134 " pdb=" CA GLY E 134 " ideal model delta harmonic sigma weight residual 180.00 158.22 21.78 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 6593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1519 0.063 - 0.126: 383 0.126 - 0.189: 41 0.189 - 0.252: 4 0.252 - 0.315: 1 Chirality restraints: 1948 Sorted by residual: chirality pdb=" CA TYR E 110 " pdb=" N TYR E 110 " pdb=" C TYR E 110 " pdb=" CB TYR E 110 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C3' DA J -49 " pdb=" C4' DA J -49 " pdb=" O3' DA J -49 " pdb=" C2' DA J -49 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1945 not shown) Planarity restraints: 1307 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 5 " 0.029 2.00e-02 2.50e+03 1.40e-02 4.92e+00 pdb=" N1 DT I 5 " -0.031 2.00e-02 2.50e+03 pdb=" C2 DT I 5 " -0.005 2.00e-02 2.50e+03 pdb=" O2 DT I 5 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DT I 5 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 5 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 5 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DT I 5 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 5 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT I 5 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 57 " -0.029 2.00e-02 2.50e+03 1.27e-02 4.45e+00 pdb=" N9 DA I 57 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DA I 57 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DA I 57 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 57 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 57 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 57 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I 57 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 57 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 57 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA I 57 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 118 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C ARG E 118 " -0.030 2.00e-02 2.50e+03 pdb=" O ARG E 118 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL E 119 " 0.010 2.00e-02 2.50e+03 ... (remaining 1304 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2013 2.76 - 3.30: 10136 3.30 - 3.83: 22576 3.83 - 4.37: 27405 4.37 - 4.90: 37724 Nonbonded interactions: 99854 Sorted by model distance: nonbonded pdb=" OG1 THR A 113 " pdb=" OD2 ASP A 125 " model vdw 2.229 3.040 nonbonded pdb=" O SER C 16 " pdb=" OG SER C 19 " model vdw 2.255 3.040 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 78 " model vdw 2.256 3.040 nonbonded pdb=" OG1 THR L 514 " pdb=" N SER L 515 " model vdw 2.266 3.120 nonbonded pdb=" NH2 ARG E 69 " pdb=" OP2 DA I 17 " model vdw 2.277 3.120 ... (remaining 99849 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 46 through 139) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 24 through 101) } ncs_group { reference = (chain 'C' and resid 15 through 111) selection = (chain 'G' and resid 15 through 111) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = (chain 'L' and resid 515 through 535) } 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: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.560 Find NCS groups from input model: 0.120 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:5.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3787 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 : 0.010 0.054 11895 Z= 0.784 Angle : 0.896 8.174 17116 Z= 0.760 Chirality : 0.055 0.315 1948 Planarity : 0.004 0.038 1307 Dihedral : 28.133 176.257 5146 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.31 % Allowed : 13.53 % Favored : 86.16 % 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: -0.89 (0.27), residues: 759 helix: 0.24 (0.20), residues: 541 sheet: None (None), residues: 0 loop : -2.63 (0.31), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 35 TYR 0.014 0.002 TYR F 51 PHE 0.011 0.002 PHE A 67 TRP 0.007 0.001 TRP K 531 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.01025 / 0.78 (11895) covalent geometry : angle 0.89612 / 0.76 (17116) hydrogen bonds : bond 0.13500 / 9.03 ( 690) hydrogen bonds : angle 4.69526 / 3.52 ( 1785) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.311 Fit side-chains REVERT: A 107 GLU cc_start: 0.4059 (mt-10) cc_final: 0.3831 (mt-10) REVERT: A 137 GLU cc_start: 0.4620 (tt0) cc_final: 0.4236 (tt0) REVERT: B 44 LYS cc_start: 0.5387 (mtmt) cc_final: 0.4830 (tttt) REVERT: B 78 ARG cc_start: 0.5414 (mtm-85) cc_final: 0.5186 (mtm110) REVERT: C 20 ARG cc_start: 0.4966 (ttm110) cc_final: 0.4624 (mtm180) REVERT: D 71 GLU cc_start: 0.4649 (tm-30) cc_final: 0.4446 (tp30) REVERT: E 57 SER cc_start: 0.5724 (t) cc_final: 0.5509 (p) REVERT: E 82 VAL cc_start: 0.4382 (OUTLIER) cc_final: 0.4164 (p) REVERT: E 83 ASP cc_start: 0.6312 (p0) cc_final: 0.6030 (t70) REVERT: F 31 LYS cc_start: 0.5009 (mttp) cc_final: 0.4705 (mtpt) REVERT: F 44 LYS cc_start: 0.5327 (tttt) cc_final: 0.4232 (mttt) REVERT: F 63 GLU cc_start: 0.5441 (mt-10) cc_final: 0.5168 (mt-10) REVERT: F 91 LYS cc_start: 0.5476 (tttm) cc_final: 0.5205 (ttpp) REVERT: G 36 LYS cc_start: 0.5899 (mptt) cc_final: 0.5657 (pttt) REVERT: G 104 GLN cc_start: 0.5425 (mm-40) cc_final: 0.5119 (mm110) REVERT: L 525 ARG cc_start: 0.5300 (mtm-85) cc_final: 0.5074 (mtt-85) outliers start: 2 outliers final: 0 residues processed: 173 average time/residue: 0.8388 time to fit residues: 152.0071 Evaluate side-chains 119 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN C 24 GLN C 94 ASN C 104 GLN D 47 GLN D 49 HIS D 84 ASN E 87 GLN E 115 HIS F 75 HIS F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.162401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.114567 restraints weight = 12998.407| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.01 r_work: 0.3104 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11895 Z= 0.169 Angle : 0.704 8.390 17116 Z= 0.404 Chirality : 0.047 0.341 1948 Planarity : 0.004 0.042 1307 Dihedral : 31.576 170.056 3648 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.80 % Allowed : 18.51 % Favored : 78.69 % 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: 0.81 (0.28), residues: 759 helix: 1.46 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -1.91 (0.34), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 133 TYR 0.012 0.002 TYR B 51 PHE 0.012 0.002 PHE A 67 TRP 0.005 0.001 TRP A 47 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 (11895) covalent geometry : angle 0.70404 / 0.40 (17116) hydrogen bonds : bond 0.05816 / 3.91 ( 690) hydrogen bonds : angle 3.44058 / 2.52 ( 1785) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.265 Fit side-chains REVERT: A 133 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8048 (mtp85) REVERT: A 137 GLU cc_start: 0.7570 (tt0) cc_final: 0.7212 (tt0) REVERT: B 44 LYS cc_start: 0.8168 (mtmt) cc_final: 0.7917 (tttt) REVERT: C 77 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.5262 (ttt-90) REVERT: D 46 LYS cc_start: 0.8339 (mmpt) cc_final: 0.7872 (mppt) REVERT: F 44 LYS cc_start: 0.8816 (tttt) cc_final: 0.7880 (mttt) REVERT: F 49 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8126 (mp) REVERT: G 73 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7821 (t0) REVERT: H 68 ASP cc_start: 0.9171 (t0) cc_final: 0.8914 (t70) REVERT: L 525 ARG cc_start: 0.7678 (mtm-85) cc_final: 0.7349 (mtt-85) outliers start: 18 outliers final: 4 residues processed: 136 average time/residue: 0.7997 time to fit residues: 114.3357 Evaluate side-chains 128 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain K residue 524 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 62 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN C 104 GLN D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.163294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.116202 restraints weight = 13092.254| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 0.96 r_work: 0.3116 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11895 Z= 0.155 Angle : 0.671 7.530 17116 Z= 0.386 Chirality : 0.045 0.365 1948 Planarity : 0.004 0.039 1307 Dihedral : 31.418 171.307 3647 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.42 % Allowed : 18.51 % Favored : 78.07 % 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: 1.63 (0.29), residues: 759 helix: 1.97 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -1.31 (0.37), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 92 TYR 0.012 0.001 TYR F 51 PHE 0.013 0.002 PHE A 67 TRP 0.003 0.001 TRP K 531 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.16 (11895) covalent geometry : angle 0.67121 / 0.39 (17116) hydrogen bonds : bond 0.05203 / 3.48 ( 690) hydrogen bonds : angle 3.25177 / 2.37 ( 1785) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.224 Fit side-chains REVERT: A 133 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.7955 (mtp85) REVERT: A 137 GLU cc_start: 0.7613 (tt0) cc_final: 0.7168 (tt0) REVERT: B 44 LYS cc_start: 0.8175 (mttt) cc_final: 0.7963 (tttt) REVERT: C 75 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7717 (mptt) REVERT: C 77 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.5333 (ttt-90) REVERT: D 46 LYS cc_start: 0.8305 (mmpt) cc_final: 0.7966 (mppt) REVERT: E 49 LYS cc_start: 0.8244 (tttp) cc_final: 0.8012 (tmtp) REVERT: F 44 LYS cc_start: 0.8779 (tttt) cc_final: 0.8013 (mttt) REVERT: F 91 LYS cc_start: 0.8625 (ttmt) cc_final: 0.8367 (tttp) REVERT: G 73 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7805 (t0) REVERT: H 68 ASP cc_start: 0.9134 (t0) cc_final: 0.8911 (t70) REVERT: K 525 ARG cc_start: 0.7062 (mtm-85) cc_final: 0.6757 (mpt180) REVERT: L 525 ARG cc_start: 0.7863 (mtm-85) cc_final: 0.7572 (mtt-85) outliers start: 22 outliers final: 5 residues processed: 138 average time/residue: 0.8107 time to fit residues: 117.7542 Evaluate side-chains 125 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS C 24 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.160138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.113034 restraints weight = 12992.352| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 0.97 r_work: 0.3055 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11895 Z= 0.245 Angle : 0.780 9.752 17116 Z= 0.430 Chirality : 0.051 0.397 1948 Planarity : 0.006 0.042 1307 Dihedral : 31.646 171.426 3647 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.04 % Allowed : 19.28 % Favored : 76.67 % 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: 1.22 (0.28), residues: 759 helix: 1.57 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -1.16 (0.37), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 133 TYR 0.016 0.002 TYR B 51 PHE 0.025 0.003 PHE A 78 TRP 0.006 0.002 TRP E 47 HIS 0.006 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.25 (11895) covalent geometry : angle 0.77998 / 0.43 (17116) hydrogen bonds : bond 0.06903 / 4.63 ( 690) hydrogen bonds : angle 3.49132 / 2.55 ( 1785) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.273 Fit side-chains REVERT: A 133 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8195 (mtp85) REVERT: A 137 GLU cc_start: 0.7559 (tt0) cc_final: 0.7266 (tt0) REVERT: B 44 LYS cc_start: 0.8185 (mttt) cc_final: 0.7924 (tttt) REVERT: C 77 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.5780 (ttt-90) REVERT: E 49 LYS cc_start: 0.8183 (tttp) cc_final: 0.7961 (tmtp) REVERT: F 44 LYS cc_start: 0.8858 (tttt) cc_final: 0.7942 (mtmt) REVERT: F 91 LYS cc_start: 0.8699 (ttmt) cc_final: 0.8465 (ttpp) REVERT: G 73 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7837 (t0) REVERT: K 525 ARG cc_start: 0.7342 (mtm-85) cc_final: 0.7041 (mpt180) REVERT: L 525 ARG cc_start: 0.7815 (mtm-85) cc_final: 0.7504 (mtt-85) outliers start: 26 outliers final: 9 residues processed: 131 average time/residue: 0.8576 time to fit residues: 117.9199 Evaluate side-chains 129 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 73 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 4 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN C 104 GLN D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.161896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.113578 restraints weight = 12958.885| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 0.99 r_work: 0.3082 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11895 Z= 0.158 Angle : 0.710 8.615 17116 Z= 0.400 Chirality : 0.047 0.378 1948 Planarity : 0.005 0.070 1307 Dihedral : 31.608 172.132 3647 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.49 % Allowed : 20.84 % Favored : 76.67 % 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: 1.53 (0.29), residues: 759 helix: 1.80 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -1.04 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 52 TYR 0.012 0.002 TYR B 51 PHE 0.011 0.002 PHE A 67 TRP 0.008 0.001 TRP A 47 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (11895) covalent geometry : angle 0.70969 / 0.40 (17116) hydrogen bonds : bond 0.05635 / 3.78 ( 690) hydrogen bonds : angle 3.42472 / 2.50 ( 1785) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.214 Fit side-chains REVERT: A 133 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8076 (mtp85) REVERT: B 44 LYS cc_start: 0.8121 (mttt) cc_final: 0.7852 (tttt) REVERT: C 77 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.5556 (ttt-90) REVERT: D 35 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6892 (mm-30) REVERT: D 46 LYS cc_start: 0.8406 (mmpt) cc_final: 0.7965 (mppt) REVERT: D 76 GLU cc_start: 0.8590 (tp30) cc_final: 0.8381 (tp30) REVERT: E 49 LYS cc_start: 0.8165 (tttp) cc_final: 0.7874 (tmtp) REVERT: F 44 LYS cc_start: 0.8848 (tttt) cc_final: 0.7897 (mttt) REVERT: F 91 LYS cc_start: 0.8680 (ttmt) cc_final: 0.8456 (ttpp) REVERT: G 73 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7821 (t0) REVERT: H 57 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.7989 (mtpt) REVERT: H 68 ASP cc_start: 0.9132 (t0) cc_final: 0.8906 (t70) REVERT: K 525 ARG cc_start: 0.7237 (mtm-85) cc_final: 0.6897 (mpt180) REVERT: L 525 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7468 (mtt-85) outliers start: 16 outliers final: 8 residues processed: 125 average time/residue: 0.8097 time to fit residues: 106.2941 Evaluate side-chains 128 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 87 optimal weight: 9.9990 chunk 1 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 14 optimal weight: 0.0270 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 95 optimal weight: 0.0470 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN C 104 GLN D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.163101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.115931 restraints weight = 13010.677| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 0.96 r_work: 0.3111 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11895 Z= 0.143 Angle : 0.667 7.785 17116 Z= 0.381 Chirality : 0.045 0.376 1948 Planarity : 0.004 0.042 1307 Dihedral : 31.502 172.242 3647 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.49 % Allowed : 21.15 % Favored : 76.36 % 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: 1.87 (0.29), residues: 759 helix: 2.05 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -0.87 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 52 TYR 0.011 0.001 TYR B 51 PHE 0.011 0.002 PHE E 67 TRP 0.007 0.001 TRP A 47 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (11895) covalent geometry : angle 0.66749 / 0.38 (17116) hydrogen bonds : bond 0.05130 / 3.43 ( 690) hydrogen bonds : angle 3.32135 / 2.42 ( 1785) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.311 Fit side-chains REVERT: B 44 LYS cc_start: 0.8095 (mttt) cc_final: 0.7858 (tttt) REVERT: C 38 ASN cc_start: 0.7499 (p0) cc_final: 0.7289 (p0) REVERT: C 77 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.5400 (ttt-90) REVERT: D 35 GLU cc_start: 0.7246 (mm-30) cc_final: 0.7037 (mm-30) REVERT: D 46 LYS cc_start: 0.8416 (mmpt) cc_final: 0.7980 (mppt) REVERT: E 49 LYS cc_start: 0.8188 (tttp) cc_final: 0.7903 (tmtp) REVERT: F 44 LYS cc_start: 0.8835 (tttt) cc_final: 0.7952 (mttt) REVERT: G 73 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7842 (t0) REVERT: H 68 ASP cc_start: 0.9091 (t0) cc_final: 0.8843 (t70) REVERT: K 525 ARG cc_start: 0.7230 (mtm-85) cc_final: 0.6888 (mpt180) REVERT: L 525 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.7430 (mtt-85) outliers start: 16 outliers final: 8 residues processed: 128 average time/residue: 0.8692 time to fit residues: 116.7211 Evaluate side-chains 125 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 77 optimal weight: 9.9990 chunk 11 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.163485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.116157 restraints weight = 12985.417| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 0.96 r_work: 0.3113 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11895 Z= 0.147 Angle : 0.654 7.394 17116 Z= 0.375 Chirality : 0.044 0.385 1948 Planarity : 0.004 0.044 1307 Dihedral : 31.324 172.766 3647 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.18 % Allowed : 21.15 % Favored : 76.67 % 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: 2.00 (0.29), residues: 759 helix: 2.14 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -0.83 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 52 TYR 0.012 0.001 TYR B 51 PHE 0.017 0.002 PHE A 78 TRP 0.005 0.001 TRP A 47 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (11895) covalent geometry : angle 0.65423 / 0.38 (17116) hydrogen bonds : bond 0.05142 / 3.43 ( 690) hydrogen bonds : angle 3.24686 / 2.37 ( 1785) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.267 Fit side-chains REVERT: B 44 LYS cc_start: 0.8135 (mttt) cc_final: 0.7906 (tttt) REVERT: C 38 ASN cc_start: 0.7548 (p0) cc_final: 0.7317 (p0) REVERT: C 77 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.5286 (ttt-90) REVERT: D 35 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6976 (mm-30) REVERT: D 46 LYS cc_start: 0.8435 (mmpt) cc_final: 0.7993 (mppt) REVERT: E 49 LYS cc_start: 0.8173 (tttp) cc_final: 0.7885 (tmtp) REVERT: F 44 LYS cc_start: 0.8831 (tttt) cc_final: 0.7992 (mttt) REVERT: H 68 ASP cc_start: 0.9097 (t0) cc_final: 0.8881 (t70) REVERT: L 525 ARG cc_start: 0.7778 (mtm-85) cc_final: 0.7451 (mtt-85) outliers start: 14 outliers final: 7 residues processed: 133 average time/residue: 0.8378 time to fit residues: 117.2455 Evaluate side-chains 128 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 2 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN C 104 GLN D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.163496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.116019 restraints weight = 12928.742| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 0.97 r_work: 0.3110 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11895 Z= 0.154 Angle : 0.657 7.601 17116 Z= 0.375 Chirality : 0.044 0.381 1948 Planarity : 0.004 0.043 1307 Dihedral : 31.327 173.245 3647 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.33 % Allowed : 21.77 % Favored : 75.89 % 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: 2.02 (0.29), residues: 759 helix: 2.15 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.79 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 52 TYR 0.012 0.002 TYR B 51 PHE 0.017 0.002 PHE A 78 TRP 0.004 0.001 TRP K 531 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (11895) covalent geometry : angle 0.65657 / 0.38 (17116) hydrogen bonds : bond 0.05185 / 3.46 ( 690) hydrogen bonds : angle 3.26306 / 2.37 ( 1785) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.403 Fit side-chains REVERT: B 44 LYS cc_start: 0.8164 (mttt) cc_final: 0.7926 (tttt) REVERT: C 38 ASN cc_start: 0.7607 (p0) cc_final: 0.7364 (p0) REVERT: C 77 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.5277 (ttt-90) REVERT: C 111 ILE cc_start: 0.5479 (pt) cc_final: 0.4847 (pp) REVERT: E 49 LYS cc_start: 0.8197 (tttp) cc_final: 0.7909 (tmtp) REVERT: E 77 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7673 (mtpt) REVERT: F 44 LYS cc_start: 0.8834 (tttt) cc_final: 0.7990 (mttt) REVERT: G 73 ASN cc_start: 0.8112 (OUTLIER) cc_final: 0.7845 (t0) REVERT: H 68 ASP cc_start: 0.9100 (t0) cc_final: 0.8849 (t70) REVERT: K 525 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.7126 (mpt180) REVERT: L 525 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7504 (mtt-85) outliers start: 15 outliers final: 8 residues processed: 132 average time/residue: 0.8865 time to fit residues: 123.0177 Evaluate side-chains 126 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 15 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN C 104 GLN D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.163705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.116323 restraints weight = 12843.570| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 0.96 r_work: 0.3114 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11895 Z= 0.152 Angle : 0.656 7.766 17116 Z= 0.375 Chirality : 0.044 0.381 1948 Planarity : 0.004 0.051 1307 Dihedral : 31.278 173.470 3647 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.64 % Allowed : 21.46 % Favored : 75.89 % 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: 2.06 (0.29), residues: 759 helix: 2.19 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.78 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 525 TYR 0.012 0.002 TYR B 51 PHE 0.015 0.002 PHE A 78 TRP 0.003 0.001 TRP K 531 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (11895) covalent geometry : angle 0.65572 / 0.37 (17116) hydrogen bonds : bond 0.05148 / 3.44 ( 690) hydrogen bonds : angle 3.24713 / 2.36 ( 1785) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.308 Fit side-chains REVERT: B 44 LYS cc_start: 0.8131 (mttt) cc_final: 0.7908 (tttt) REVERT: C 38 ASN cc_start: 0.7587 (p0) cc_final: 0.7350 (p0) REVERT: C 77 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.5233 (ttt-90) REVERT: C 111 ILE cc_start: 0.5526 (pt) cc_final: 0.4916 (pp) REVERT: D 46 LYS cc_start: 0.8352 (mmpt) cc_final: 0.7970 (mppt) REVERT: E 49 LYS cc_start: 0.8177 (tttp) cc_final: 0.7884 (tmtp) REVERT: E 77 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7686 (mtpt) REVERT: F 44 LYS cc_start: 0.8834 (tttt) cc_final: 0.7997 (mttt) REVERT: G 73 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7824 (t0) REVERT: H 68 ASP cc_start: 0.9092 (t0) cc_final: 0.8834 (t70) REVERT: K 525 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7047 (mtt180) REVERT: L 525 ARG cc_start: 0.7790 (mtm-85) cc_final: 0.7461 (mtt-85) outliers start: 17 outliers final: 8 residues processed: 128 average time/residue: 0.9176 time to fit residues: 123.5074 Evaluate side-chains 126 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 78 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.0370 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN C 104 GLN D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.163980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.116661 restraints weight = 12991.167| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 0.96 r_work: 0.3124 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11895 Z= 0.142 Angle : 0.651 7.431 17116 Z= 0.373 Chirality : 0.043 0.380 1948 Planarity : 0.005 0.076 1307 Dihedral : 31.271 173.638 3647 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.02 % Allowed : 22.40 % Favored : 75.58 % 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: 2.11 (0.29), residues: 759 helix: 2.23 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.77 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 52 TYR 0.011 0.001 TYR B 51 PHE 0.013 0.002 PHE A 78 TRP 0.004 0.001 TRP A 47 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (11895) covalent geometry : angle 0.65111 / 0.37 (17116) hydrogen bonds : bond 0.05046 / 3.37 ( 690) hydrogen bonds : angle 3.25138 / 2.36 ( 1785) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.349 Fit side-chains REVERT: B 44 LYS cc_start: 0.8120 (mttt) cc_final: 0.7904 (tttt) REVERT: C 38 ASN cc_start: 0.7555 (p0) cc_final: 0.7314 (p0) REVERT: C 77 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.5202 (ttt-90) REVERT: C 111 ILE cc_start: 0.5518 (pt) cc_final: 0.4920 (pp) REVERT: D 46 LYS cc_start: 0.8391 (mmpt) cc_final: 0.7959 (mppt) REVERT: E 49 LYS cc_start: 0.8175 (tttp) cc_final: 0.7909 (tmtp) REVERT: E 77 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7652 (mtpt) REVERT: F 44 LYS cc_start: 0.8840 (tttt) cc_final: 0.8003 (mttt) REVERT: G 73 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7822 (t0) REVERT: H 68 ASP cc_start: 0.9095 (t0) cc_final: 0.8835 (t70) REVERT: K 525 ARG cc_start: 0.7680 (mtm-85) cc_final: 0.7053 (mtt180) REVERT: L 525 ARG cc_start: 0.7755 (mtm-85) cc_final: 0.7445 (mtt-85) outliers start: 13 outliers final: 8 residues processed: 123 average time/residue: 0.8812 time to fit residues: 113.8881 Evaluate side-chains 126 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 30.0000 chunk 85 optimal weight: 9.9990 chunk 94 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN C 104 GLN D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.164019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.116695 restraints weight = 13051.776| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 0.96 r_work: 0.3122 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11895 Z= 0.144 Angle : 0.648 7.401 17116 Z= 0.372 Chirality : 0.043 0.379 1948 Planarity : 0.005 0.079 1307 Dihedral : 31.257 173.709 3647 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.87 % Allowed : 22.55 % Favored : 75.58 % 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: 2.11 (0.29), residues: 759 helix: 2.22 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.76 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 52 TYR 0.011 0.001 TYR B 51 PHE 0.013 0.002 PHE A 78 TRP 0.004 0.001 TRP A 47 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (11895) covalent geometry : angle 0.64839 / 0.37 (17116) hydrogen bonds : bond 0.05028 / 3.36 ( 690) hydrogen bonds : angle 3.24457 / 2.36 ( 1785) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4304.23 seconds wall clock time: 73 minutes 47.60 seconds (4427.60 seconds total)