Starting phenix.real_space_refine on Fri Sep 11 18:57:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pii_13437/09_2026/7pii_13437_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pii_13437/09_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_13437/09_2026/7pii_13437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pii_13437/09_2026/7pii_13437.map" model { file = "/net/cci-nas-00/data/ceres_data/7pii_13437/09_2026/7pii_13437_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pii_13437/09_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-2.2.1-6174/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: 2.32, per 1000 atoms: 0.21 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: 0.95 Conformation dependent library (CDL) restraints added in 258.6 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: 1.65 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: 2.15 Time building geometry restraints manager: 1.27 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: 15650 1.63 - 3.27: 1349 3.27 - 4.90: 107 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: 4.180 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.460 Find NCS groups from input model: 0.130 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:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.300 ------------------------------------------------------------------------------- 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= 0.785 Angle : 0.902 8.174 17116 Z= 0.765 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 / 0.79 (11895) covalent geometry : angle 0.90239 / 0.77 (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 : 0.305 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: 0.4618 (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: 0.9801 time to fit residues: 177.6530 Evaluate side-chains 120 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.162633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.116005 restraints weight = 13015.980| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 0.96 r_work: 0.3117 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1386 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= 0.161 Angle : 0.717 8.309 17116 Z= 0.408 Chirality : 0.047 0.379 1948 Planarity : 0.005 0.045 1307 Dihedral : 31.484 171.507 3648 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.05 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: 0.85 (0.28), residues: 759 helix: 1.47 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -1.85 (0.34), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 92 TYR 0.012 0.002 TYR B 51 PHE 0.011 0.002 PHE A 67 TRP 0.004 0.001 TRP E 47 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (11895) covalent geometry : angle 0.71739 / 0.41 (17116) hydrogen bonds : bond 0.05641 / 3.79 ( 690) hydrogen bonds : angle 3.41681 / 2.50 ( 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 145 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.297 Fit side-chains REVERT: A 133 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8015 (mtp180) REVERT: A 137 GLU cc_start: 0.7559 (tt0) cc_final: 0.7123 (tt0) REVERT: B 44 LYS cc_start: 0.8151 (mtmt) cc_final: 0.7917 (tttt) REVERT: C 77 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.5233 (ttt-90) REVERT: D 46 LYS cc_start: 0.8345 (mmpt) cc_final: 0.7940 (mppt) REVERT: F 44 LYS cc_start: 0.8810 (tttt) cc_final: 0.7891 (mttt) REVERT: F 49 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8101 (mp) REVERT: G 73 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7838 (t0) REVERT: H 68 ASP cc_start: 0.9139 (t0) cc_final: 0.8890 (t70) REVERT: L 525 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7358 (mtt-85) outliers start: 18 outliers final: 2 residues processed: 135 average time/residue: 0.9232 time to fit residues: 130.9031 Evaluate side-chains 125 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 62 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.0070 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.163726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.117207 restraints weight = 13121.962| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 0.96 r_work: 0.3133 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11895 Z= 0.146 Angle : 0.671 7.663 17116 Z= 0.384 Chirality : 0.045 0.393 1948 Planarity : 0.004 0.039 1307 Dihedral : 31.283 173.385 3647 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.11 % Allowed : 18.97 % Favored : 77.92 % 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: 1.68 (0.29), residues: 759 helix: 2.02 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -1.31 (0.36), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 92 TYR 0.011 0.001 TYR F 51 PHE 0.011 0.002 PHE A 67 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 0.00259 / 0.15 (11895) covalent geometry : angle 0.67079 / 0.38 (17116) hydrogen bonds : bond 0.05074 / 3.42 ( 690) hydrogen bonds : angle 3.23018 / 2.35 ( 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 148 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.313 Fit side-chains REVERT: A 137 GLU cc_start: 0.7590 (tt0) cc_final: 0.7365 (tt0) REVERT: B 44 LYS cc_start: 0.8183 (mttt) cc_final: 0.7918 (tttt) REVERT: C 38 ASN cc_start: 0.7726 (p0) cc_final: 0.7516 (p0) REVERT: C 73 ASN cc_start: 0.7567 (t0) cc_final: 0.7281 (t0) REVERT: C 75 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7679 (mptt) REVERT: C 77 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.5174 (ttt-90) REVERT: D 35 GLU cc_start: 0.7231 (mm-30) cc_final: 0.7025 (mm-30) REVERT: F 44 LYS cc_start: 0.8754 (tttt) cc_final: 0.7926 (mttt) REVERT: F 91 LYS cc_start: 0.8653 (ttmt) cc_final: 0.8364 (tttp) REVERT: G 73 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7800 (t0) REVERT: H 51 ASP cc_start: 0.6918 (p0) cc_final: 0.6695 (m-30) REVERT: H 68 ASP cc_start: 0.9133 (t0) cc_final: 0.8914 (t70) REVERT: K 525 ARG cc_start: 0.6993 (mtm-85) cc_final: 0.6672 (mpt180) REVERT: L 525 ARG cc_start: 0.7809 (mtm-85) cc_final: 0.7523 (mtt-85) outliers start: 20 outliers final: 5 residues processed: 138 average time/residue: 0.9021 time to fit residues: 130.7741 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 : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL 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: 9.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 chunk 40 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 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** H 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.163332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.116151 restraints weight = 13088.636| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 0.96 r_work: 0.3108 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11895 Z= 0.155 Angle : 0.680 7.921 17116 Z= 0.385 Chirality : 0.045 0.416 1948 Planarity : 0.004 0.041 1307 Dihedral : 31.272 174.786 3647 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.42 % Allowed : 18.66 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.29), residues: 759 helix: 2.10 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -1.03 (0.38), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 92 TYR 0.012 0.001 TYR B 51 PHE 0.013 0.002 PHE A 67 TRP 0.004 0.001 TRP L 530 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (11895) covalent geometry : angle 0.67993 / 0.38 (17116) hydrogen bonds : bond 0.05215 / 3.49 ( 690) hydrogen bonds : angle 3.25769 / 2.38 ( 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 142 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.318 Fit side-chains REVERT: A 133 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8049 (mtp85) REVERT: A 137 GLU cc_start: 0.7541 (tt0) cc_final: 0.7136 (tt0) REVERT: B 44 LYS cc_start: 0.8128 (mttt) cc_final: 0.7904 (tttt) REVERT: C 73 ASN cc_start: 0.7546 (t0) cc_final: 0.7324 (t0) REVERT: C 77 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.5133 (ttt-90) REVERT: D 35 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7038 (mm-30) REVERT: D 46 LYS cc_start: 0.8355 (mmpt) cc_final: 0.7996 (mppt) REVERT: E 49 LYS cc_start: 0.8215 (tttp) cc_final: 0.7998 (tmtp) REVERT: F 44 LYS cc_start: 0.8795 (tttt) cc_final: 0.7983 (mttt) REVERT: G 73 ASN cc_start: 0.8126 (OUTLIER) cc_final: 0.7871 (t0) REVERT: H 47 GLN cc_start: 0.8368 (mt0) cc_final: 0.8165 (mt0) REVERT: H 51 ASP cc_start: 0.7071 (p0) cc_final: 0.6832 (m-30) REVERT: H 68 ASP cc_start: 0.9108 (t0) cc_final: 0.8881 (t70) REVERT: K 525 ARG cc_start: 0.7100 (mtm-85) cc_final: 0.6806 (mtt180) REVERT: L 525 ARG cc_start: 0.7863 (mtm-85) cc_final: 0.7575 (mtt-85) outliers start: 22 outliers final: 10 residues processed: 129 average time/residue: 1.0062 time to fit residues: 136.0289 Evaluate side-chains 130 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 D residue 51 ASP 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 G residue 73 ASN Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 94 optimal weight: 0.0970 chunk 4 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.163873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.116862 restraints weight = 13023.410| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 0.96 r_work: 0.3117 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2105 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= 0.144 Angle : 0.661 7.520 17116 Z= 0.376 Chirality : 0.044 0.411 1948 Planarity : 0.004 0.042 1307 Dihedral : 31.222 175.144 3647 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.64 % Allowed : 20.22 % Favored : 77.14 % 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: 2.03 (0.29), residues: 759 helix: 2.19 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.90 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 52 TYR 0.011 0.001 TYR B 51 PHE 0.011 0.002 PHE A 67 TRP 0.005 0.001 TRP A 47 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 (11895) covalent geometry : angle 0.66125 / 0.38 (17116) hydrogen bonds : bond 0.04989 / 3.35 ( 690) hydrogen bonds : angle 3.22210 / 2.35 ( 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 141 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.294 Fit side-chains REVERT: A 133 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.7974 (mtp85) REVERT: A 137 GLU cc_start: 0.7519 (tt0) cc_final: 0.7096 (tt0) REVERT: B 44 LYS cc_start: 0.8118 (mttt) cc_final: 0.7891 (tttt) REVERT: C 38 ASN cc_start: 0.7710 (p0) cc_final: 0.7464 (p0) REVERT: C 73 ASN cc_start: 0.7532 (t0) cc_final: 0.7319 (t0) REVERT: C 77 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.5075 (ttt-90) REVERT: D 35 GLU cc_start: 0.7300 (mm-30) cc_final: 0.7044 (mm-30) REVERT: D 46 LYS cc_start: 0.8387 (mmpt) cc_final: 0.8016 (mppt) REVERT: E 49 LYS cc_start: 0.8214 (tttp) cc_final: 0.7951 (tmtp) REVERT: F 44 LYS cc_start: 0.8802 (tttt) cc_final: 0.8000 (mttt) REVERT: G 73 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7867 (t0) REVERT: H 51 ASP cc_start: 0.7107 (p0) cc_final: 0.6870 (m-30) REVERT: H 68 ASP cc_start: 0.9097 (t0) cc_final: 0.8881 (t70) REVERT: K 525 ARG cc_start: 0.7174 (mtm-85) cc_final: 0.6861 (mtt180) REVERT: L 525 ARG cc_start: 0.7743 (mtm-85) cc_final: 0.7449 (mtt-85) outliers start: 17 outliers final: 8 residues processed: 133 average time/residue: 0.9232 time to fit residues: 128.9708 Evaluate side-chains 129 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 77 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 87 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 14 optimal weight: 0.0470 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 95 optimal weight: 0.0970 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.164272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.116621 restraints weight = 13076.270| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.09 r_work: 0.3090 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11895 Z= 0.137 Angle : 0.653 7.499 17116 Z= 0.373 Chirality : 0.044 0.411 1948 Planarity : 0.004 0.062 1307 Dihedral : 31.188 175.377 3647 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.95 % Allowed : 20.84 % Favored : 76.21 % 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: 2.14 (0.29), residues: 759 helix: 2.26 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.84 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 52 TYR 0.010 0.001 TYR B 51 PHE 0.011 0.002 PHE A 67 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 0.00243 / 0.14 (11895) covalent geometry : angle 0.65320 / 0.37 (17116) hydrogen bonds : bond 0.04872 / 3.27 ( 690) hydrogen bonds : angle 3.21236 / 2.34 ( 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 138 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.317 Fit side-chains REVERT: A 133 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8016 (mtp85) REVERT: A 137 GLU cc_start: 0.7568 (tt0) cc_final: 0.7153 (tt0) REVERT: B 44 LYS cc_start: 0.8149 (mttt) cc_final: 0.7948 (tttt) REVERT: C 38 ASN cc_start: 0.7708 (p0) cc_final: 0.7444 (p0) REVERT: C 73 ASN cc_start: 0.7565 (OUTLIER) cc_final: 0.7350 (t0) REVERT: C 77 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.5180 (ttt-90) REVERT: D 35 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7112 (mm-30) REVERT: D 46 LYS cc_start: 0.8428 (mmpt) cc_final: 0.8070 (mppt) REVERT: E 49 LYS cc_start: 0.8287 (tttp) cc_final: 0.8027 (tmtp) REVERT: F 44 LYS cc_start: 0.8816 (tttt) cc_final: 0.8055 (mttt) REVERT: H 47 GLN cc_start: 0.8424 (mt0) cc_final: 0.8161 (mt0) REVERT: H 51 ASP cc_start: 0.7145 (p0) cc_final: 0.6924 (m-30) REVERT: H 68 ASP cc_start: 0.9129 (t0) cc_final: 0.8903 (t70) REVERT: K 525 ARG cc_start: 0.7217 (mtm-85) cc_final: 0.6874 (mtt180) REVERT: L 525 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7529 (mtt-85) outliers start: 19 outliers final: 9 residues processed: 130 average time/residue: 0.9385 time to fit residues: 128.1330 Evaluate side-chains 130 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 73 ASN Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 51 ASP 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 H residue 63 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 77 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.163166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.113976 restraints weight = 12989.330| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.12 r_work: 0.3055 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2216 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= 0.159 Angle : 0.674 7.787 17116 Z= 0.381 Chirality : 0.045 0.417 1948 Planarity : 0.004 0.042 1307 Dihedral : 31.187 175.850 3647 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.80 % Allowed : 21.00 % Favored : 76.21 % 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: 2.07 (0.29), residues: 759 helix: 2.19 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -0.79 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 52 TYR 0.012 0.002 TYR B 51 PHE 0.013 0.002 PHE A 67 TRP 0.004 0.001 TRP E 47 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (11895) covalent geometry : angle 0.67428 / 0.38 (17116) hydrogen bonds : bond 0.05297 / 3.54 ( 690) hydrogen bonds : angle 3.24208 / 2.36 ( 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 139 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.312 Fit side-chains REVERT: A 133 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8052 (mtp85) REVERT: A 137 GLU cc_start: 0.7660 (tt0) cc_final: 0.7338 (tt0) REVERT: B 44 LYS cc_start: 0.8191 (mttt) cc_final: 0.7965 (tttt) REVERT: C 73 ASN cc_start: 0.7586 (t0) cc_final: 0.7371 (t0) REVERT: C 77 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.5395 (ttt-90) REVERT: D 35 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7157 (mm-30) REVERT: D 46 LYS cc_start: 0.8445 (mmpt) cc_final: 0.8066 (mppt) REVERT: E 49 LYS cc_start: 0.8253 (tttp) cc_final: 0.7984 (tmtp) REVERT: F 44 LYS cc_start: 0.8837 (tttt) cc_final: 0.8041 (mttt) REVERT: G 73 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7949 (t0) REVERT: H 51 ASP cc_start: 0.7251 (p0) cc_final: 0.7003 (m-30) REVERT: K 525 ARG cc_start: 0.7301 (mtm-85) cc_final: 0.6993 (mtt180) REVERT: L 525 ARG cc_start: 0.7772 (mtm-85) cc_final: 0.7445 (mtt-85) outliers start: 18 outliers final: 7 residues processed: 131 average time/residue: 0.9556 time to fit residues: 131.5012 Evaluate side-chains 126 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 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 F residue 92 ARG Chi-restraints excluded: chain G residue 73 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 2 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.163683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.116386 restraints weight = 12971.190| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 0.96 r_work: 0.3115 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11895 Z= 0.145 Angle : 0.668 7.602 17116 Z= 0.379 Chirality : 0.045 0.414 1948 Planarity : 0.005 0.070 1307 Dihedral : 31.180 175.906 3647 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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: 2.12 (0.29), residues: 759 helix: 2.22 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.78 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 52 TYR 0.011 0.001 TYR B 51 PHE 0.012 0.002 PHE A 67 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 0.00264 / 0.14 (11895) covalent geometry : angle 0.66813 / 0.38 (17116) hydrogen bonds : bond 0.05097 / 3.42 ( 690) hydrogen bonds : angle 3.24245 / 2.36 ( 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 133 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.341 Fit side-chains REVERT: A 133 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8023 (mtp85) REVERT: A 137 GLU cc_start: 0.7592 (tt0) cc_final: 0.7259 (tt0) REVERT: B 44 LYS cc_start: 0.8146 (mttt) cc_final: 0.7915 (tttt) REVERT: C 38 ASN cc_start: 0.7579 (p0) cc_final: 0.7345 (p0) REVERT: C 77 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.5241 (ttt-90) REVERT: D 35 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7043 (mm-30) REVERT: D 46 LYS cc_start: 0.8422 (mmpt) cc_final: 0.8036 (mppt) REVERT: E 49 LYS cc_start: 0.8209 (tttp) cc_final: 0.7926 (tmtp) REVERT: E 77 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7725 (mtpt) REVERT: F 44 LYS cc_start: 0.8817 (tttt) cc_final: 0.7987 (mttt) REVERT: G 73 ASN cc_start: 0.8146 (OUTLIER) cc_final: 0.7876 (t0) REVERT: H 51 ASP cc_start: 0.7124 (p0) cc_final: 0.6909 (m-30) REVERT: K 525 ARG cc_start: 0.7185 (mtm-85) cc_final: 0.6871 (mtt180) REVERT: L 525 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7396 (mtt-85) outliers start: 17 outliers final: 8 residues processed: 125 average time/residue: 0.9277 time to fit residues: 121.8098 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 : 0.344 ------------------------------------------------------------------------------- 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 77 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 88 THR 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 F residue 79 LYS Chi-restraints excluded: chain G residue 73 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 15 optimal weight: 0.5980 chunk 84 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.163579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.116279 restraints weight = 12867.740| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 0.95 r_work: 0.3116 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11895 Z= 0.152 Angle : 0.669 7.558 17116 Z= 0.379 Chirality : 0.045 0.413 1948 Planarity : 0.005 0.082 1307 Dihedral : 31.174 175.847 3647 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.87 % Allowed : 22.08 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.29), residues: 759 helix: 2.19 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.76 (0.39), residues: 215 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 0.011 0.002 PHE A 67 TRP 0.003 0.001 TRP E 47 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 (11895) covalent geometry : angle 0.66923 / 0.38 (17116) hydrogen bonds : bond 0.05122 / 3.43 ( 690) hydrogen bonds : angle 3.23723 / 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 130 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.342 Fit side-chains REVERT: A 133 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.7987 (mtp85) REVERT: A 137 GLU cc_start: 0.7602 (tt0) cc_final: 0.7252 (tt0) REVERT: B 44 LYS cc_start: 0.8146 (mttt) cc_final: 0.7914 (tttt) REVERT: C 38 ASN cc_start: 0.7559 (p0) cc_final: 0.7326 (p0) REVERT: C 77 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.5237 (ttt-90) REVERT: D 35 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7033 (mm-30) REVERT: D 46 LYS cc_start: 0.8426 (mmpt) cc_final: 0.8038 (mppt) REVERT: E 49 LYS cc_start: 0.8187 (tttp) cc_final: 0.7909 (tmtp) REVERT: E 77 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7718 (mtpt) REVERT: F 44 LYS cc_start: 0.8817 (tttt) cc_final: 0.7981 (mttt) REVERT: G 73 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7889 (t0) REVERT: H 51 ASP cc_start: 0.7158 (p0) cc_final: 0.6919 (m-30) REVERT: K 525 ARG cc_start: 0.7203 (mtm-85) cc_final: 0.6885 (mtt180) REVERT: L 525 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.7393 (mtt-85) outliers start: 12 outliers final: 7 residues processed: 125 average time/residue: 0.9723 time to fit residues: 127.4543 Evaluate side-chains 128 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 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 F residue 79 LYS Chi-restraints excluded: chain G residue 73 ASN 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: 0.9980 chunk 51 optimal weight: 0.0870 chunk 9 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.163739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115459 restraints weight = 13029.912| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.00 r_work: 0.3115 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11895 Z= 0.145 Angle : 0.664 7.519 17116 Z= 0.377 Chirality : 0.044 0.413 1948 Planarity : 0.005 0.082 1307 Dihedral : 31.167 175.918 3647 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.02 % Allowed : 22.08 % 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: 2.12 (0.29), residues: 759 helix: 2.22 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.75 (0.39), residues: 215 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 0.011 0.002 PHE A 67 TRP 0.003 0.001 TRP E 47 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (11895) covalent geometry : angle 0.66408 / 0.38 (17116) hydrogen bonds : bond 0.05045 / 3.38 ( 690) hydrogen bonds : angle 3.23886 / 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 130 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.337 Fit side-chains REVERT: A 133 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.7978 (mtp85) REVERT: A 137 GLU cc_start: 0.7586 (tt0) cc_final: 0.7227 (tt0) REVERT: B 44 LYS cc_start: 0.8148 (mttt) cc_final: 0.7883 (tttt) REVERT: C 38 ASN cc_start: 0.7554 (p0) cc_final: 0.7313 (p0) REVERT: C 77 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.5198 (ttt-90) REVERT: D 35 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7010 (mm-30) REVERT: D 46 LYS cc_start: 0.8433 (mmpt) cc_final: 0.7999 (mppt) REVERT: E 49 LYS cc_start: 0.8151 (tttp) cc_final: 0.7850 (tmtp) REVERT: E 77 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7675 (mtpt) REVERT: F 44 LYS cc_start: 0.8817 (tttt) cc_final: 0.7931 (mttt) REVERT: G 73 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7866 (t0) REVERT: H 51 ASP cc_start: 0.7135 (p0) cc_final: 0.6882 (m-30) REVERT: K 525 ARG cc_start: 0.7189 (mtm-85) cc_final: 0.6851 (mtt180) REVERT: L 525 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.7366 (mtt-85) outliers start: 13 outliers final: 7 residues processed: 125 average time/residue: 0.9631 time to fit residues: 126.3997 Evaluate side-chains 128 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 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 F residue 79 LYS Chi-restraints excluded: chain G residue 73 ASN 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: 10.0000 chunk 94 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.163702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.116228 restraints weight = 13055.464| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 0.96 r_work: 0.3118 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11895 Z= 0.151 Angle : 0.666 7.493 17116 Z= 0.377 Chirality : 0.044 0.412 1948 Planarity : 0.005 0.088 1307 Dihedral : 31.145 175.960 3647 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.49 % Allowed : 21.93 % 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: 2.13 (0.29), residues: 759 helix: 2.23 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -0.75 (0.40), residues: 216 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 0.011 0.002 PHE A 67 TRP 0.004 0.001 TRP A 47 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (11895) covalent geometry : angle 0.66629 / 0.38 (17116) hydrogen bonds : bond 0.05091 / 3.40 ( 690) hydrogen bonds : angle 3.23066 / 2.35 ( 1785) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4649.07 seconds wall clock time: 79 minutes 44.60 seconds (4784.60 seconds total)