Starting phenix.real_space_refine on Fri Mar 15 04:06:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l1u_0803/03_2024/6l1u_0803_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l1u_0803/03_2024/6l1u_0803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l1u_0803/03_2024/6l1u_0803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l1u_0803/03_2024/6l1u_0803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l1u_0803/03_2024/6l1u_0803_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l1u_0803/03_2024/6l1u_0803_updated.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 15 5.49 5 S 15 5.16 5 C 6540 2.51 5 N 1815 2.21 5 O 2130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "F GLU 35": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "I GLU 35": "OE1" <-> "OE2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "J GLU 35": "OE1" <-> "OE2" Residue "J GLU 57": "OE1" <-> "OE2" Residue "K GLU 35": "OE1" <-> "OE2" Residue "K GLU 57": "OE1" <-> "OE2" Residue "L GLU 35": "OE1" <-> "OE2" Residue "L GLU 57": "OE1" <-> "OE2" Residue "M GLU 35": "OE1" <-> "OE2" Residue "M GLU 57": "OE1" <-> "OE2" Residue "N GLU 35": "OE1" <-> "OE2" Residue "N GLU 57": "OE1" <-> "OE2" Residue "O GLU 35": "OE1" <-> "OE2" Residue "O GLU 57": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10515 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.90, per 1000 atoms: 0.56 Number of scatterers: 10515 At special positions: 0 Unit cell: (197.357, 159.454, 56.201, 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 15 16.00 P 15 15.00 O 2130 8.00 N 1815 7.00 C 6540 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 - 3.50 Amino acid : False - 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: 4.15 Conformation dependent library (CDL) restraints added in 2.0 seconds 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3465 1.33 - 1.45: 810 1.45 - 1.57: 6240 1.57 - 1.68: 15 1.68 - 1.80: 30 Bond restraints: 10560 Sorted by residual: bond pdb=" OH PTR G 39 " pdb=" P PTR G 39 " ideal model delta sigma weight residual 1.769 1.602 0.167 2.00e-02 2.50e+03 6.96e+01 bond pdb=" OH PTR N 39 " pdb=" P PTR N 39 " ideal model delta sigma weight residual 1.769 1.602 0.167 2.00e-02 2.50e+03 6.96e+01 bond pdb=" OH PTR D 39 " pdb=" P PTR D 39 " ideal model delta sigma weight residual 1.769 1.602 0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" OH PTR M 39 " pdb=" P PTR M 39 " ideal model delta sigma weight residual 1.769 1.602 0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" OH PTR C 39 " pdb=" P PTR C 39 " ideal model delta sigma weight residual 1.769 1.602 0.167 2.00e-02 2.50e+03 6.93e+01 ... (remaining 10555 not shown) Histogram of bond angle deviations from ideal: 100.35 - 106.52: 105 106.52 - 112.68: 6266 112.68 - 118.85: 2675 118.85 - 125.01: 5144 125.01 - 131.18: 15 Bond angle restraints: 14205 Sorted by residual: angle pdb=" OH PTR K 39 " pdb=" P PTR K 39 " pdb=" O2P PTR K 39 " ideal model delta sigma weight residual 99.92 109.42 -9.50 3.00e+00 1.11e-01 1.00e+01 angle pdb=" OH PTR M 39 " pdb=" P PTR M 39 " pdb=" O2P PTR M 39 " ideal model delta sigma weight residual 99.92 109.40 -9.48 3.00e+00 1.11e-01 9.98e+00 angle pdb=" OH PTR J 39 " pdb=" P PTR J 39 " pdb=" O2P PTR J 39 " ideal model delta sigma weight residual 99.92 109.40 -9.48 3.00e+00 1.11e-01 9.98e+00 angle pdb=" OH PTR L 39 " pdb=" P PTR L 39 " pdb=" O2P PTR L 39 " ideal model delta sigma weight residual 99.92 109.39 -9.47 3.00e+00 1.11e-01 9.96e+00 angle pdb=" OH PTR C 39 " pdb=" P PTR C 39 " pdb=" O2P PTR C 39 " ideal model delta sigma weight residual 99.92 109.39 -9.47 3.00e+00 1.11e-01 9.96e+00 ... (remaining 14200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 5715 17.25 - 34.50: 405 34.50 - 51.75: 120 51.75 - 69.00: 15 69.00 - 86.25: 30 Dihedral angle restraints: 6285 sinusoidal: 2220 harmonic: 4065 Sorted by residual: dihedral pdb=" CA ALA G 29 " pdb=" C ALA G 29 " pdb=" N ALA G 30 " pdb=" CA ALA G 30 " ideal model delta harmonic sigma weight residual 180.00 161.32 18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ALA J 29 " pdb=" C ALA J 29 " pdb=" N ALA J 30 " pdb=" CA ALA J 30 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ALA E 29 " pdb=" C ALA E 29 " pdb=" N ALA E 30 " pdb=" CA ALA E 30 " ideal model delta harmonic sigma weight residual 180.00 161.37 18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 6282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1210 0.056 - 0.113: 456 0.113 - 0.169: 89 0.169 - 0.225: 0 0.225 - 0.281: 15 Chirality restraints: 1770 Sorted by residual: chirality pdb=" CB VAL F 77 " pdb=" CA VAL F 77 " pdb=" CG1 VAL F 77 " pdb=" CG2 VAL F 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB VAL L 77 " pdb=" CA VAL L 77 " pdb=" CG1 VAL L 77 " pdb=" CG2 VAL L 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB VAL N 77 " pdb=" CA VAL N 77 " pdb=" CG1 VAL N 77 " pdb=" CG2 VAL N 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1767 not shown) Planarity restraints: 1770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 13 " -0.005 2.00e-02 2.50e+03 1.02e-02 1.04e+00 pdb=" CD GLU D 13 " 0.018 2.00e-02 2.50e+03 pdb=" OE1 GLU D 13 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU D 13 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU L 13 " -0.005 2.00e-02 2.50e+03 1.02e-02 1.04e+00 pdb=" CD GLU L 13 " 0.018 2.00e-02 2.50e+03 pdb=" OE1 GLU L 13 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU L 13 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU M 13 " -0.005 2.00e-02 2.50e+03 1.01e-02 1.03e+00 pdb=" CD GLU M 13 " 0.018 2.00e-02 2.50e+03 pdb=" OE1 GLU M 13 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU M 13 " -0.006 2.00e-02 2.50e+03 ... (remaining 1767 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 414 2.69 - 3.24: 10255 3.24 - 3.79: 15559 3.79 - 4.35: 18959 4.35 - 4.90: 37441 Nonbonded interactions: 82628 Sorted by model distance: nonbonded pdb=" O SER D 9 " pdb=" OG SER D 9 " model vdw 2.138 2.440 nonbonded pdb=" O SER A 9 " pdb=" OG SER A 9 " model vdw 2.138 2.440 nonbonded pdb=" O SER N 9 " pdb=" OG SER N 9 " model vdw 2.138 2.440 nonbonded pdb=" O SER J 9 " pdb=" OG SER J 9 " model vdw 2.138 2.440 nonbonded pdb=" O SER G 9 " pdb=" OG SER G 9 " model vdw 2.138 2.440 ... (remaining 82623 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 7.160 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 28.070 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 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 : 0.011 0.167 10560 Z= 0.515 Angle : 0.901 9.499 14205 Z= 0.449 Chirality : 0.063 0.281 1770 Planarity : 0.002 0.010 1770 Dihedral : 15.318 86.255 3705 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 0.00 % Allowed : 17.65 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.06 (0.10), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.61 (0.08), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 50 PHE 0.015 0.003 PHE F 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 THR cc_start: 0.8952 (m) cc_final: 0.8744 (t) REVERT: E 61 GLU cc_start: 0.8368 (tt0) cc_final: 0.7795 (pm20) REVERT: F 4 PHE cc_start: 0.7955 (t80) cc_final: 0.7609 (t80) REVERT: G 60 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7499 (ttmm) REVERT: H 2 ASP cc_start: 0.7968 (p0) cc_final: 0.7749 (p0) REVERT: H 6 LYS cc_start: 0.8954 (ptmm) cc_final: 0.8750 (ptmt) REVERT: H 57 GLU cc_start: 0.8114 (tp30) cc_final: 0.7880 (tp30) REVERT: I 2 ASP cc_start: 0.8147 (p0) cc_final: 0.7866 (p0) REVERT: J 2 ASP cc_start: 0.7756 (p0) cc_final: 0.7482 (p0) REVERT: J 60 LYS cc_start: 0.7329 (mmtt) cc_final: 0.7049 (pttm) REVERT: K 2 ASP cc_start: 0.7505 (p0) cc_final: 0.6344 (m-30) REVERT: K 4 PHE cc_start: 0.7937 (t80) cc_final: 0.7634 (t80) REVERT: K 75 THR cc_start: 0.8870 (m) cc_final: 0.8593 (p) REVERT: K 97 LYS cc_start: 0.8276 (mttt) cc_final: 0.7513 (mmmt) REVERT: K 100 LEU cc_start: 0.8152 (tt) cc_final: 0.7758 (pt) REVERT: L 75 THR cc_start: 0.8635 (m) cc_final: 0.8344 (m) REVERT: L 100 LEU cc_start: 0.7930 (tt) cc_final: 0.7475 (tp) REVERT: M 21 LYS cc_start: 0.8553 (mttt) cc_final: 0.8269 (mttp) REVERT: M 24 GLN cc_start: 0.7805 (mt0) cc_final: 0.7600 (mt0) REVERT: N 12 LYS cc_start: 0.8469 (tptp) cc_final: 0.8245 (tptp) REVERT: N 92 THR cc_start: 0.8475 (m) cc_final: 0.8203 (t) REVERT: N 99 GLN cc_start: 0.8442 (mt0) cc_final: 0.8242 (tm-30) REVERT: N 100 LEU cc_start: 0.8214 (tt) cc_final: 0.7981 (tt) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.2086 time to fit residues: 95.6377 Evaluate side-chains 256 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 87 optimal weight: 0.0980 chunk 136 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN B 62 GLN B 99 GLN C 62 GLN C 99 GLN D 62 GLN D 99 GLN E 62 GLN E 99 GLN F 62 GLN F 99 GLN G 62 GLN H 62 GLN I 62 GLN J 62 GLN K 62 GLN L 62 GLN M 62 GLN N 62 GLN O 62 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10560 Z= 0.135 Angle : 0.541 8.006 14205 Z= 0.298 Chirality : 0.049 0.139 1770 Planarity : 0.002 0.014 1770 Dihedral : 5.960 24.447 1515 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.12 % Favored : 86.88 % Rotamer: Outliers : 4.41 % Allowed : 20.39 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.71 (0.11), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.35 (0.09), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 50 PHE 0.016 0.002 PHE N 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 311 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: C 8 LEU cc_start: 0.8779 (mm) cc_final: 0.8333 (mm) REVERT: C 57 GLU cc_start: 0.8539 (tp30) cc_final: 0.8192 (tp30) REVERT: E 61 GLU cc_start: 0.8591 (tt0) cc_final: 0.8039 (pm20) REVERT: E 98 ASP cc_start: 0.7890 (p0) cc_final: 0.7653 (p0) REVERT: F 4 PHE cc_start: 0.7942 (t80) cc_final: 0.7739 (t80) REVERT: G 57 GLU cc_start: 0.7991 (tp30) cc_final: 0.7543 (mm-30) REVERT: G 60 LYS cc_start: 0.7724 (mmtt) cc_final: 0.7494 (ttmm) REVERT: H 2 ASP cc_start: 0.7833 (p0) cc_final: 0.7619 (p0) REVERT: H 57 GLU cc_start: 0.8062 (tp30) cc_final: 0.7750 (mm-30) REVERT: I 2 ASP cc_start: 0.8338 (p0) cc_final: 0.7733 (p0) REVERT: I 57 GLU cc_start: 0.8045 (tp30) cc_final: 0.7826 (mm-30) REVERT: I 60 LYS cc_start: 0.7670 (mptt) cc_final: 0.7423 (ttpt) REVERT: J 2 ASP cc_start: 0.7752 (p0) cc_final: 0.7471 (p0) REVERT: J 60 LYS cc_start: 0.7557 (mmtt) cc_final: 0.6872 (pttm) REVERT: K 2 ASP cc_start: 0.7782 (p0) cc_final: 0.6511 (m-30) REVERT: K 4 PHE cc_start: 0.7772 (t80) cc_final: 0.7428 (t80) REVERT: K 97 LYS cc_start: 0.8239 (mttt) cc_final: 0.7514 (mmtt) REVERT: K 100 LEU cc_start: 0.8323 (tt) cc_final: 0.8120 (pt) REVERT: L 12 LYS cc_start: 0.8556 (tptt) cc_final: 0.8227 (tppt) REVERT: L 99 GLN cc_start: 0.8681 (mt0) cc_final: 0.8093 (tm-30) REVERT: M 2 ASP cc_start: 0.8055 (p0) cc_final: 0.7538 (p0) REVERT: M 12 LYS cc_start: 0.8657 (tptp) cc_final: 0.8196 (mptt) REVERT: M 21 LYS cc_start: 0.8742 (mttt) cc_final: 0.8424 (mttp) REVERT: N 99 GLN cc_start: 0.8541 (mt0) cc_final: 0.8275 (tm-30) REVERT: N 100 LEU cc_start: 0.8164 (tt) cc_final: 0.7894 (tt) outliers start: 45 outliers final: 37 residues processed: 333 average time/residue: 0.1804 time to fit residues: 88.3195 Evaluate side-chains 321 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 284 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 98 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 135 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN D 99 GLN E 99 GLN F 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.050 10560 Z= 0.375 Angle : 0.747 6.912 14205 Z= 0.401 Chirality : 0.054 0.189 1770 Planarity : 0.003 0.016 1770 Dihedral : 6.793 27.966 1515 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.67 % Favored : 81.33 % Rotamer: Outliers : 9.90 % Allowed : 19.02 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.62 (0.12), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.28 (0.09), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS O 50 PHE 0.023 0.004 PHE I 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 282 time to evaluate : 1.247 Fit side-chains REVERT: B 57 GLU cc_start: 0.8557 (tp30) cc_final: 0.8218 (tp30) REVERT: C 8 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8815 (mm) REVERT: E 61 GLU cc_start: 0.8750 (tt0) cc_final: 0.8179 (pm20) REVERT: F 83 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7781 (tm-30) REVERT: G 57 GLU cc_start: 0.8069 (tp30) cc_final: 0.7634 (mm-30) REVERT: G 60 LYS cc_start: 0.8075 (mmtt) cc_final: 0.7657 (ttmm) REVERT: G 83 GLU cc_start: 0.8247 (tt0) cc_final: 0.7950 (tt0) REVERT: H 57 GLU cc_start: 0.7948 (tp30) cc_final: 0.7668 (mm-30) REVERT: I 2 ASP cc_start: 0.8562 (p0) cc_final: 0.7979 (p0) REVERT: I 12 LYS cc_start: 0.8259 (ttmt) cc_final: 0.7827 (ttpp) REVERT: I 57 GLU cc_start: 0.7971 (tp30) cc_final: 0.7707 (mm-30) REVERT: I 60 LYS cc_start: 0.7909 (mptt) cc_final: 0.7563 (ttpt) REVERT: J 20 GLU cc_start: 0.4044 (pm20) cc_final: 0.3843 (pm20) REVERT: J 60 LYS cc_start: 0.7777 (mmtt) cc_final: 0.7082 (pttm) REVERT: J 61 GLU cc_start: 0.8330 (tt0) cc_final: 0.8104 (pm20) REVERT: K 2 ASP cc_start: 0.7637 (p0) cc_final: 0.6496 (m-30) REVERT: K 4 PHE cc_start: 0.7501 (t80) cc_final: 0.7078 (t80) REVERT: K 97 LYS cc_start: 0.8469 (mttt) cc_final: 0.7607 (mmmt) REVERT: K 100 LEU cc_start: 0.8422 (tt) cc_final: 0.8137 (pt) REVERT: L 12 LYS cc_start: 0.8791 (tptt) cc_final: 0.8414 (tppt) REVERT: L 98 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7429 (p0) REVERT: M 12 LYS cc_start: 0.8684 (tptp) cc_final: 0.8274 (mttt) REVERT: M 21 LYS cc_start: 0.8831 (mttt) cc_final: 0.8492 (mttp) REVERT: M 38 LEU cc_start: 0.9355 (tt) cc_final: 0.9115 (tt) REVERT: N 4 PHE cc_start: 0.7937 (t80) cc_final: 0.7733 (t80) outliers start: 101 outliers final: 78 residues processed: 348 average time/residue: 0.1785 time to fit residues: 92.3486 Evaluate side-chains 345 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 265 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 98 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN D 99 GLN F 99 GLN K 24 GLN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10560 Z= 0.160 Angle : 0.558 6.393 14205 Z= 0.305 Chirality : 0.049 0.138 1770 Planarity : 0.002 0.013 1770 Dihedral : 6.156 31.344 1515 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % Rotamer: Outliers : 8.82 % Allowed : 20.49 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.45 (0.12), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.15 (0.09), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS O 50 PHE 0.018 0.003 PHE M 4 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 291 time to evaluate : 1.176 Fit side-chains REVERT: C 8 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8820 (mm) REVERT: E 61 GLU cc_start: 0.8685 (tt0) cc_final: 0.8215 (pm20) REVERT: F 8 LEU cc_start: 0.9159 (tp) cc_final: 0.8866 (tp) REVERT: G 57 GLU cc_start: 0.7997 (tp30) cc_final: 0.7517 (mm-30) REVERT: G 60 LYS cc_start: 0.7986 (mmtt) cc_final: 0.7543 (ttmm) REVERT: G 83 GLU cc_start: 0.8183 (tt0) cc_final: 0.7798 (tt0) REVERT: G 98 ASP cc_start: 0.9113 (OUTLIER) cc_final: 0.8283 (p0) REVERT: H 9 SER cc_start: 0.8413 (t) cc_final: 0.8174 (p) REVERT: H 57 GLU cc_start: 0.7945 (tp30) cc_final: 0.7649 (mm-30) REVERT: I 2 ASP cc_start: 0.8439 (p0) cc_final: 0.7874 (p0) REVERT: I 60 LYS cc_start: 0.7814 (mptt) cc_final: 0.7522 (ttpt) REVERT: J 60 LYS cc_start: 0.7910 (mmtt) cc_final: 0.7133 (pttm) REVERT: K 2 ASP cc_start: 0.7647 (p0) cc_final: 0.6472 (m-30) REVERT: K 4 PHE cc_start: 0.7477 (t80) cc_final: 0.7125 (t80) REVERT: K 46 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8059 (mt-10) REVERT: K 97 LYS cc_start: 0.8393 (mttt) cc_final: 0.7534 (mmmt) REVERT: K 100 LEU cc_start: 0.8449 (tt) cc_final: 0.8165 (pt) REVERT: L 12 LYS cc_start: 0.8832 (tptt) cc_final: 0.8485 (tppt) REVERT: L 98 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7379 (p0) REVERT: M 12 LYS cc_start: 0.8717 (tptp) cc_final: 0.8345 (mptt) REVERT: M 21 LYS cc_start: 0.8822 (mttt) cc_final: 0.8447 (mttp) outliers start: 90 outliers final: 69 residues processed: 343 average time/residue: 0.1785 time to fit residues: 91.7100 Evaluate side-chains 355 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 283 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 98 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN F 99 GLN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.047 10560 Z= 0.383 Angle : 0.751 8.666 14205 Z= 0.400 Chirality : 0.054 0.172 1770 Planarity : 0.003 0.012 1770 Dihedral : 6.813 32.556 1515 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.04 % Favored : 81.96 % Rotamer: Outliers : 12.45 % Allowed : 19.02 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.43 (0.13), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.13 (0.10), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS O 50 PHE 0.023 0.004 PHE I 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 279 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: B 57 GLU cc_start: 0.8528 (tp30) cc_final: 0.8278 (tp30) REVERT: C 8 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8817 (mm) REVERT: E 61 GLU cc_start: 0.8737 (tt0) cc_final: 0.8251 (pm20) REVERT: F 8 LEU cc_start: 0.9337 (tp) cc_final: 0.9070 (tp) REVERT: G 57 GLU cc_start: 0.8034 (tp30) cc_final: 0.7612 (mm-30) REVERT: G 60 LYS cc_start: 0.8100 (mmtt) cc_final: 0.7677 (ttmm) REVERT: G 83 GLU cc_start: 0.8226 (tt0) cc_final: 0.7933 (tt0) REVERT: G 98 ASP cc_start: 0.9183 (OUTLIER) cc_final: 0.8296 (p0) REVERT: H 57 GLU cc_start: 0.7934 (tp30) cc_final: 0.7629 (mm-30) REVERT: H 98 ASP cc_start: 0.8998 (OUTLIER) cc_final: 0.8614 (p0) REVERT: I 2 ASP cc_start: 0.8490 (p0) cc_final: 0.7969 (p0) REVERT: J 60 LYS cc_start: 0.8008 (mmtt) cc_final: 0.7264 (pttm) REVERT: K 2 ASP cc_start: 0.7505 (p0) cc_final: 0.6415 (m-30) REVERT: K 4 PHE cc_start: 0.7477 (t80) cc_final: 0.7089 (t80) REVERT: K 5 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7941 (ptm) REVERT: K 100 LEU cc_start: 0.8455 (tt) cc_final: 0.8136 (pt) REVERT: L 44 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8679 (t) REVERT: L 98 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7474 (p0) REVERT: M 12 LYS cc_start: 0.8685 (tptp) cc_final: 0.8328 (mttt) REVERT: M 21 LYS cc_start: 0.8826 (mttt) cc_final: 0.8555 (mttp) REVERT: O 12 LYS cc_start: 0.4155 (OUTLIER) cc_final: 0.3098 (pttm) outliers start: 127 outliers final: 109 residues processed: 364 average time/residue: 0.1676 time to fit residues: 91.9900 Evaluate side-chains 389 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 273 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain K residue 5 MET Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain O residue 12 LYS Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 98 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN F 99 GLN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10560 Z= 0.234 Angle : 0.624 7.418 14205 Z= 0.336 Chirality : 0.050 0.147 1770 Planarity : 0.002 0.012 1770 Dihedral : 6.478 38.358 1515 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.82 % Favored : 86.18 % Rotamer: Outliers : 11.96 % Allowed : 19.51 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.35 (0.13), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.10), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 50 PHE 0.020 0.003 PHE M 4 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 292 time to evaluate : 1.342 Fit side-chains REVERT: A 5 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8380 (ptm) REVERT: E 61 GLU cc_start: 0.8704 (tt0) cc_final: 0.8271 (pm20) REVERT: F 8 LEU cc_start: 0.9199 (tp) cc_final: 0.8913 (tp) REVERT: G 57 GLU cc_start: 0.8058 (tp30) cc_final: 0.7641 (mm-30) REVERT: G 60 LYS cc_start: 0.8024 (mmtt) cc_final: 0.7584 (ttmm) REVERT: G 83 GLU cc_start: 0.8130 (tt0) cc_final: 0.7867 (tt0) REVERT: G 98 ASP cc_start: 0.9162 (OUTLIER) cc_final: 0.8297 (p0) REVERT: H 57 GLU cc_start: 0.7861 (tp30) cc_final: 0.7551 (mm-30) REVERT: H 98 ASP cc_start: 0.9002 (OUTLIER) cc_final: 0.8669 (p0) REVERT: I 2 ASP cc_start: 0.8494 (p0) cc_final: 0.7974 (p0) REVERT: I 12 LYS cc_start: 0.8470 (ttpt) cc_final: 0.8066 (pttt) REVERT: J 60 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7269 (pttm) REVERT: K 2 ASP cc_start: 0.7527 (p0) cc_final: 0.6402 (m-30) REVERT: K 4 PHE cc_start: 0.7592 (t80) cc_final: 0.7245 (t80) REVERT: K 46 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8003 (mt-10) REVERT: K 100 LEU cc_start: 0.8448 (tt) cc_final: 0.8117 (pt) REVERT: L 12 LYS cc_start: 0.8911 (tptt) cc_final: 0.8591 (tppt) REVERT: L 44 THR cc_start: 0.8877 (t) cc_final: 0.8611 (t) REVERT: L 55 VAL cc_start: 0.9174 (OUTLIER) cc_final: 0.8948 (p) REVERT: L 98 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7571 (p0) REVERT: M 12 LYS cc_start: 0.8676 (tptp) cc_final: 0.8439 (tppt) REVERT: M 21 LYS cc_start: 0.8805 (mttt) cc_final: 0.8524 (mttp) REVERT: M 99 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7480 (tm-30) REVERT: N 59 THR cc_start: 0.8986 (t) cc_final: 0.8667 (t) REVERT: O 12 LYS cc_start: 0.4403 (OUTLIER) cc_final: 0.3215 (pttm) outliers start: 122 outliers final: 98 residues processed: 367 average time/residue: 0.1754 time to fit residues: 96.0819 Evaluate side-chains 390 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 286 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 98 ASP Chi-restraints excluded: chain O residue 12 LYS Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 98 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN F 99 GLN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 10560 Z= 0.261 Angle : 0.645 7.011 14205 Z= 0.345 Chirality : 0.051 0.146 1770 Planarity : 0.002 0.010 1770 Dihedral : 6.524 38.966 1515 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.77 % Favored : 83.23 % Rotamer: Outliers : 13.04 % Allowed : 18.73 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.28 (0.13), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.10), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS O 50 PHE 0.018 0.003 PHE I 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 292 time to evaluate : 1.254 Fit side-chains REVERT: C 13 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7668 (mm-30) REVERT: E 61 GLU cc_start: 0.8689 (tt0) cc_final: 0.8247 (pm20) REVERT: F 8 LEU cc_start: 0.9305 (tp) cc_final: 0.9033 (tp) REVERT: G 57 GLU cc_start: 0.8072 (tp30) cc_final: 0.7754 (mm-30) REVERT: G 60 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7587 (ttmm) REVERT: G 83 GLU cc_start: 0.8227 (tt0) cc_final: 0.7990 (tt0) REVERT: G 98 ASP cc_start: 0.9173 (OUTLIER) cc_final: 0.8375 (p0) REVERT: H 57 GLU cc_start: 0.7835 (tp30) cc_final: 0.7582 (mm-30) REVERT: H 98 ASP cc_start: 0.9015 (OUTLIER) cc_final: 0.8688 (p0) REVERT: I 2 ASP cc_start: 0.8503 (p0) cc_final: 0.7984 (p0) REVERT: I 12 LYS cc_start: 0.8441 (ttpt) cc_final: 0.8047 (pttt) REVERT: J 60 LYS cc_start: 0.8034 (mmtt) cc_final: 0.7274 (pttm) REVERT: K 2 ASP cc_start: 0.7533 (p0) cc_final: 0.6406 (m-30) REVERT: K 4 PHE cc_start: 0.7579 (t80) cc_final: 0.7247 (t80) REVERT: K 100 LEU cc_start: 0.8529 (tt) cc_final: 0.8182 (pt) REVERT: L 44 THR cc_start: 0.8879 (t) cc_final: 0.8597 (t) REVERT: L 55 VAL cc_start: 0.9220 (OUTLIER) cc_final: 0.9007 (p) REVERT: L 98 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7580 (p0) REVERT: M 12 LYS cc_start: 0.8666 (tptp) cc_final: 0.8320 (mttt) REVERT: M 21 LYS cc_start: 0.8777 (mttt) cc_final: 0.8531 (mttp) REVERT: M 99 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7551 (tm-30) REVERT: N 59 THR cc_start: 0.8941 (t) cc_final: 0.8599 (t) REVERT: N 99 GLN cc_start: 0.8767 (mt0) cc_final: 0.8315 (tm-30) REVERT: O 12 LYS cc_start: 0.4247 (OUTLIER) cc_final: 0.3199 (pttm) REVERT: O 99 GLN cc_start: 0.8000 (tm-30) cc_final: 0.7772 (tm-30) outliers start: 133 outliers final: 120 residues processed: 376 average time/residue: 0.1739 time to fit residues: 98.3516 Evaluate side-chains 411 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 286 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 98 ASP Chi-restraints excluded: chain O residue 12 LYS Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 98 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 8.9990 chunk 43 optimal weight: 0.0980 chunk 28 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 99 GLN C 99 GLN F 99 GLN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10560 Z= 0.138 Angle : 0.555 7.173 14205 Z= 0.298 Chirality : 0.049 0.144 1770 Planarity : 0.002 0.011 1770 Dihedral : 6.106 42.929 1515 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer: Outliers : 9.90 % Allowed : 21.96 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.17 (0.13), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.10), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 PHE 0.021 0.002 PHE N 4 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 299 time to evaluate : 1.236 Fit side-chains REVERT: A 28 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: C 13 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7489 (mm-30) REVERT: E 61 GLU cc_start: 0.8623 (tt0) cc_final: 0.8273 (pm20) REVERT: F 8 LEU cc_start: 0.9085 (tp) cc_final: 0.8792 (tp) REVERT: G 57 GLU cc_start: 0.8036 (tp30) cc_final: 0.7703 (mm-30) REVERT: G 60 LYS cc_start: 0.7950 (mmtt) cc_final: 0.7487 (ttmm) REVERT: G 83 GLU cc_start: 0.8103 (tt0) cc_final: 0.7834 (tt0) REVERT: G 98 ASP cc_start: 0.9160 (OUTLIER) cc_final: 0.8421 (p0) REVERT: H 57 GLU cc_start: 0.7798 (tp30) cc_final: 0.7586 (mm-30) REVERT: H 75 THR cc_start: 0.8792 (m) cc_final: 0.8392 (p) REVERT: H 98 ASP cc_start: 0.8990 (OUTLIER) cc_final: 0.8643 (p0) REVERT: I 2 ASP cc_start: 0.8495 (p0) cc_final: 0.7977 (p0) REVERT: I 12 LYS cc_start: 0.8476 (ttpt) cc_final: 0.8234 (ttpt) REVERT: I 60 LYS cc_start: 0.7572 (mptt) cc_final: 0.7356 (ttpt) REVERT: J 60 LYS cc_start: 0.8011 (mmtt) cc_final: 0.7233 (pttm) REVERT: K 2 ASP cc_start: 0.7473 (p0) cc_final: 0.6249 (m-30) REVERT: K 4 PHE cc_start: 0.7596 (t80) cc_final: 0.7266 (t80) REVERT: K 5 MET cc_start: 0.8528 (ptm) cc_final: 0.8017 (ttp) REVERT: K 46 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8018 (mt-10) REVERT: K 100 LEU cc_start: 0.8424 (tt) cc_final: 0.8076 (pt) REVERT: L 12 LYS cc_start: 0.8914 (tptt) cc_final: 0.8646 (tppt) REVERT: L 44 THR cc_start: 0.8733 (t) cc_final: 0.8461 (t) REVERT: L 55 VAL cc_start: 0.9258 (OUTLIER) cc_final: 0.9038 (p) REVERT: L 98 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7514 (p0) REVERT: L 99 GLN cc_start: 0.7722 (tm-30) cc_final: 0.7411 (tm-30) REVERT: M 12 LYS cc_start: 0.8598 (tptp) cc_final: 0.8382 (tppt) REVERT: M 21 LYS cc_start: 0.8775 (mttt) cc_final: 0.8266 (mttp) REVERT: M 98 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7888 (p0) REVERT: M 99 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7476 (tm-30) REVERT: N 59 THR cc_start: 0.8960 (t) cc_final: 0.8626 (t) REVERT: N 99 GLN cc_start: 0.8755 (mt0) cc_final: 0.8242 (tm-30) REVERT: O 99 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7812 (tm-30) outliers start: 101 outliers final: 89 residues processed: 362 average time/residue: 0.1729 time to fit residues: 92.8423 Evaluate side-chains 389 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 294 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 98 ASP Chi-restraints excluded: chain O residue 12 LYS Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 98 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 58 optimal weight: 0.0070 chunk 105 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 127 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 142 optimal weight: 0.0170 chunk 86 optimal weight: 8.9990 overall best weight: 2.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN F 99 GLN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10560 Z= 0.186 Angle : 0.579 7.112 14205 Z= 0.310 Chirality : 0.049 0.143 1770 Planarity : 0.002 0.010 1770 Dihedral : 6.174 43.553 1515 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.30 % Favored : 84.70 % Rotamer: Outliers : 10.69 % Allowed : 21.18 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.11 (0.13), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.10), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS O 50 PHE 0.015 0.003 PHE I 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 296 time to evaluate : 0.977 Fit side-chains REVERT: C 13 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7459 (mm-30) REVERT: E 2 ASP cc_start: 0.8778 (p0) cc_final: 0.8403 (p0) REVERT: E 61 GLU cc_start: 0.8633 (tt0) cc_final: 0.8307 (pm20) REVERT: F 8 LEU cc_start: 0.9166 (tp) cc_final: 0.8860 (tp) REVERT: G 57 GLU cc_start: 0.8045 (tp30) cc_final: 0.7718 (mm-30) REVERT: G 60 LYS cc_start: 0.7981 (mmtt) cc_final: 0.7515 (ttmm) REVERT: G 83 GLU cc_start: 0.8203 (tt0) cc_final: 0.7954 (tt0) REVERT: G 98 ASP cc_start: 0.9175 (OUTLIER) cc_final: 0.8443 (p0) REVERT: H 57 GLU cc_start: 0.7800 (tp30) cc_final: 0.7599 (mm-30) REVERT: H 98 ASP cc_start: 0.9011 (OUTLIER) cc_final: 0.8677 (p0) REVERT: I 2 ASP cc_start: 0.8501 (p0) cc_final: 0.7989 (p0) REVERT: I 12 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8217 (ttpt) REVERT: I 60 LYS cc_start: 0.7594 (mptt) cc_final: 0.7381 (ttpt) REVERT: J 20 GLU cc_start: 0.3800 (pm20) cc_final: 0.2329 (tt0) REVERT: J 60 LYS cc_start: 0.7902 (mmtt) cc_final: 0.7185 (pttm) REVERT: K 2 ASP cc_start: 0.7472 (p0) cc_final: 0.6172 (m-30) REVERT: K 4 PHE cc_start: 0.7659 (t80) cc_final: 0.7361 (t80) REVERT: K 46 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8012 (mt-10) REVERT: K 100 LEU cc_start: 0.8422 (tt) cc_final: 0.8129 (pt) REVERT: L 12 LYS cc_start: 0.8889 (tptt) cc_final: 0.8613 (tppt) REVERT: L 44 THR cc_start: 0.8747 (t) cc_final: 0.8501 (t) REVERT: L 55 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.9065 (p) REVERT: L 98 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7489 (p0) REVERT: L 99 GLN cc_start: 0.7710 (tm-30) cc_final: 0.7382 (tm-30) REVERT: M 12 LYS cc_start: 0.8588 (tptp) cc_final: 0.8379 (tppt) REVERT: M 21 LYS cc_start: 0.8803 (mttt) cc_final: 0.8309 (mttp) REVERT: M 98 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7899 (p0) REVERT: M 99 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7431 (tm-30) REVERT: N 59 THR cc_start: 0.8919 (t) cc_final: 0.8571 (t) REVERT: N 99 GLN cc_start: 0.8747 (mt0) cc_final: 0.8258 (tm-30) REVERT: O 12 LYS cc_start: 0.3918 (OUTLIER) cc_final: 0.2708 (pttm) REVERT: O 99 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7745 (tm-30) outliers start: 109 outliers final: 100 residues processed: 363 average time/residue: 0.1670 time to fit residues: 90.1554 Evaluate side-chains 396 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 290 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 98 ASP Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 98 ASP Chi-restraints excluded: chain O residue 12 LYS Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 98 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 94 optimal weight: 0.0670 chunk 126 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN F 99 GLN K 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10560 Z= 0.113 Angle : 0.528 7.598 14205 Z= 0.284 Chirality : 0.048 0.139 1770 Planarity : 0.002 0.009 1770 Dihedral : 5.859 46.466 1515 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 7.75 % Allowed : 24.22 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.01 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.10), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 50 PHE 0.022 0.002 PHE N 4 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 303 time to evaluate : 1.253 Fit side-chains REVERT: C 13 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7390 (mm-30) REVERT: E 2 ASP cc_start: 0.8710 (p0) cc_final: 0.8366 (p0) REVERT: E 61 GLU cc_start: 0.8598 (tt0) cc_final: 0.8291 (pm20) REVERT: F 8 LEU cc_start: 0.8798 (tp) cc_final: 0.8469 (tp) REVERT: G 57 GLU cc_start: 0.8013 (tp30) cc_final: 0.7619 (mm-30) REVERT: G 60 LYS cc_start: 0.7885 (mmtt) cc_final: 0.7416 (ttmm) REVERT: G 83 GLU cc_start: 0.8084 (tt0) cc_final: 0.7840 (tt0) REVERT: G 98 ASP cc_start: 0.9126 (OUTLIER) cc_final: 0.8550 (p0) REVERT: H 57 GLU cc_start: 0.7779 (tp30) cc_final: 0.7574 (mm-30) REVERT: H 75 THR cc_start: 0.8795 (m) cc_final: 0.8404 (p) REVERT: H 98 ASP cc_start: 0.8992 (OUTLIER) cc_final: 0.8625 (p0) REVERT: I 2 ASP cc_start: 0.8063 (p0) cc_final: 0.7512 (p0) REVERT: I 12 LYS cc_start: 0.8466 (ttpt) cc_final: 0.8228 (ttpt) REVERT: J 60 LYS cc_start: 0.7870 (mmtt) cc_final: 0.7161 (pttm) REVERT: K 2 ASP cc_start: 0.7730 (p0) cc_final: 0.6420 (m-30) REVERT: K 4 PHE cc_start: 0.7922 (t80) cc_final: 0.7521 (t80) REVERT: K 5 MET cc_start: 0.8504 (ptm) cc_final: 0.8065 (ttp) REVERT: K 46 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8026 (mt-10) REVERT: K 100 LEU cc_start: 0.8322 (tt) cc_final: 0.7732 (pt) REVERT: L 12 LYS cc_start: 0.8863 (tptt) cc_final: 0.8600 (tppt) REVERT: L 44 THR cc_start: 0.8666 (t) cc_final: 0.8404 (t) REVERT: L 99 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7356 (tm-30) REVERT: M 21 LYS cc_start: 0.8776 (mttt) cc_final: 0.8262 (mttp) REVERT: M 98 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7831 (p0) REVERT: M 99 GLN cc_start: 0.8063 (tm-30) cc_final: 0.7405 (tm-30) REVERT: N 59 THR cc_start: 0.8936 (t) cc_final: 0.8608 (t) REVERT: N 79 GLN cc_start: 0.9169 (pt0) cc_final: 0.8969 (pt0) REVERT: N 99 GLN cc_start: 0.8842 (mt0) cc_final: 0.8247 (tm-30) REVERT: O 99 GLN cc_start: 0.7945 (tm-30) cc_final: 0.7708 (tm-30) outliers start: 79 outliers final: 72 residues processed: 351 average time/residue: 0.1757 time to fit residues: 91.8605 Evaluate side-chains 370 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 295 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 99 GLN Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 92 THR Chi-restraints excluded: chain M residue 98 ASP Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 98 ASP Chi-restraints excluded: chain O residue 12 LYS Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 98 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 6 optimal weight: 0.0000 chunk 86 optimal weight: 9.9990 overall best weight: 3.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN E 99 GLN F 99 GLN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.117375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.100769 restraints weight = 18770.928| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.72 r_work: 0.3546 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10560 Z= 0.222 Angle : 0.621 9.729 14205 Z= 0.328 Chirality : 0.050 0.141 1770 Planarity : 0.002 0.009 1770 Dihedral : 6.221 44.950 1515 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 8.82 % Allowed : 23.24 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.02 (0.14), residues: 1425 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.10), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS O 50 PHE 0.017 0.003 PHE C 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2671.88 seconds wall clock time: 48 minutes 52.65 seconds (2932.65 seconds total)