Starting phenix.real_space_refine on Mon Mar 11 04:58:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l1t_0801/03_2024/6l1t_0801_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l1t_0801/03_2024/6l1t_0801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l1t_0801/03_2024/6l1t_0801.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l1t_0801/03_2024/6l1t_0801.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l1t_0801/03_2024/6l1t_0801_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l1t_0801/03_2024/6l1t_0801_updated.pdb" } resolution = 3.22 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 10 5.49 5 S 10 5.16 5 C 4360 2.51 5 N 1210 2.21 5 O 1420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7010 Number of models: 1 Model: "" Number of chains: 10 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 Time building chain proxies: 3.93, per 1000 atoms: 0.56 Number of scatterers: 7010 At special positions: 0 Unit cell: (194.743, 91.49, 50.973, 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 10 16.00 P 10 15.00 O 1420 8.00 N 1210 7.00 C 4360 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: 2.10 Conformation dependent library (CDL) restraints added in 1.3 seconds 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1720 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: 0.79 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: 2.34 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: 2320 1.33 - 1.45: 517 1.45 - 1.57: 4173 1.57 - 1.68: 10 1.68 - 1.80: 20 Bond restraints: 7040 Sorted by residual: bond pdb=" OH PTR G 39 " pdb=" P PTR G 39 " ideal model delta sigma weight residual 1.769 1.604 0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" OH PTR J 39 " pdb=" P PTR J 39 " ideal model delta sigma weight residual 1.769 1.604 0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" OH PTR B 39 " pdb=" P PTR B 39 " ideal model delta sigma weight residual 1.769 1.605 0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" OH PTR E 39 " pdb=" P PTR E 39 " ideal model delta sigma weight residual 1.769 1.605 0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" OH PTR D 39 " pdb=" P PTR D 39 " ideal model delta sigma weight residual 1.769 1.605 0.164 2.00e-02 2.50e+03 6.76e+01 ... (remaining 7035 not shown) Histogram of bond angle deviations from ideal: 101.03 - 107.12: 110 107.12 - 113.20: 4322 113.20 - 119.29: 1626 119.29 - 125.37: 3402 125.37 - 131.46: 10 Bond angle restraints: 9470 Sorted by residual: angle pdb=" OH PTR G 39 " pdb=" P PTR G 39 " pdb=" O2P PTR G 39 " ideal model delta sigma weight residual 99.92 109.71 -9.79 3.00e+00 1.11e-01 1.07e+01 angle pdb=" OH PTR F 39 " pdb=" P PTR F 39 " pdb=" O2P PTR F 39 " ideal model delta sigma weight residual 99.92 109.71 -9.79 3.00e+00 1.11e-01 1.06e+01 angle pdb=" OH PTR A 39 " pdb=" P PTR A 39 " pdb=" O2P PTR A 39 " ideal model delta sigma weight residual 99.92 109.71 -9.79 3.00e+00 1.11e-01 1.06e+01 angle pdb=" OH PTR D 39 " pdb=" P PTR D 39 " pdb=" O2P PTR D 39 " ideal model delta sigma weight residual 99.92 109.71 -9.79 3.00e+00 1.11e-01 1.06e+01 angle pdb=" OH PTR C 39 " pdb=" P PTR C 39 " pdb=" O2P PTR C 39 " ideal model delta sigma weight residual 99.92 109.69 -9.77 3.00e+00 1.11e-01 1.06e+01 ... (remaining 9465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.61: 3630 12.61 - 25.22: 390 25.22 - 37.83: 100 37.83 - 50.44: 40 50.44 - 63.05: 30 Dihedral angle restraints: 4190 sinusoidal: 1480 harmonic: 2710 Sorted by residual: dihedral pdb=" CA VAL B 49 " pdb=" C VAL B 49 " pdb=" N HIS B 50 " pdb=" CA HIS B 50 " ideal model delta harmonic sigma weight residual -180.00 -161.15 -18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA VAL G 49 " pdb=" C VAL G 49 " pdb=" N HIS G 50 " pdb=" CA HIS G 50 " ideal model delta harmonic sigma weight residual -180.00 -161.16 -18.84 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA VAL F 49 " pdb=" C VAL F 49 " pdb=" N HIS F 50 " pdb=" CA HIS F 50 " ideal model delta harmonic sigma weight residual -180.00 -161.17 -18.83 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 4187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 578 0.035 - 0.071: 358 0.071 - 0.106: 132 0.106 - 0.142: 90 0.142 - 0.177: 22 Chirality restraints: 1180 Sorted by residual: chirality pdb=" CB VAL B 55 " pdb=" CA VAL B 55 " pdb=" CG1 VAL B 55 " pdb=" CG2 VAL B 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CB VAL J 55 " pdb=" CA VAL J 55 " pdb=" CG1 VAL J 55 " pdb=" CG2 VAL J 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.84e-01 chirality pdb=" CB VAL A 55 " pdb=" CA VAL A 55 " pdb=" CG1 VAL A 55 " pdb=" CG2 VAL A 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.77e-01 ... (remaining 1177 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 94 " -0.010 2.00e-02 2.50e+03 8.68e-03 1.32e+00 pdb=" CG PHE B 94 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE B 94 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 94 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 94 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 94 " 0.010 2.00e-02 2.50e+03 8.57e-03 1.29e+00 pdb=" CG PHE F 94 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE F 94 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE F 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE F 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE F 94 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 94 " 0.010 2.00e-02 2.50e+03 8.52e-03 1.27e+00 pdb=" CG PHE H 94 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE H 94 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE H 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE H 94 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE H 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE H 94 " 0.002 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2160 2.82 - 3.34: 5914 3.34 - 3.86: 10554 3.86 - 4.38: 11356 4.38 - 4.90: 22255 Nonbonded interactions: 52239 Sorted by model distance: nonbonded pdb=" NZ LYS D 34 " pdb=" O2P PTR E 39 " model vdw 2.296 2.520 nonbonded pdb=" NZ LYS G 34 " pdb=" O1P PTR G 39 " model vdw 2.314 2.520 nonbonded pdb=" NZ LYS D 34 " pdb=" O1P PTR D 39 " model vdw 2.314 2.520 nonbonded pdb=" NZ LYS E 34 " pdb=" O1P PTR E 39 " model vdw 2.314 2.520 nonbonded pdb=" NZ LYS F 34 " pdb=" O1P PTR F 39 " model vdw 2.314 2.520 ... (remaining 52234 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' } 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: 1.720 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: 6.780 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 18.430 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 0.165 7040 Z= 0.528 Angle : 0.919 9.793 9470 Z= 0.442 Chirality : 0.058 0.177 1180 Planarity : 0.002 0.009 1180 Dihedral : 14.062 63.051 2470 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.63 % Favored : 87.37 % Rotamer: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % 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: -5.37 (0.15), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.11), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.004 HIS I 50 PHE 0.020 0.003 PHE B 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 42 SER cc_start: 0.9172 (p) cc_final: 0.8949 (p) REVERT: E 32 LYS cc_start: 0.8528 (ttpt) cc_final: 0.8281 (mtpp) REVERT: G 32 LYS cc_start: 0.8941 (ttpt) cc_final: 0.8520 (mtpp) REVERT: G 59 THR cc_start: 0.9161 (p) cc_final: 0.8923 (p) REVERT: I 2 ASP cc_start: 0.8725 (p0) cc_final: 0.8416 (p0) REVERT: J 57 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7065 (pm20) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1400 time to fit residues: 36.9860 Evaluate side-chains 149 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7040 Z= 0.230 Angle : 0.645 7.377 9470 Z= 0.341 Chirality : 0.051 0.142 1180 Planarity : 0.002 0.015 1180 Dihedral : 6.409 28.634 1010 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 7.06 % Allowed : 17.79 % Favored : 75.15 % 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: -4.87 (0.17), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.13), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS G 50 PHE 0.017 0.003 PHE G 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 184 time to evaluate : 0.764 Fit side-chains REVERT: A 13 GLU cc_start: 0.7695 (tp30) cc_final: 0.7462 (tm-30) REVERT: A 42 SER cc_start: 0.9149 (p) cc_final: 0.8887 (p) REVERT: B 32 LYS cc_start: 0.8857 (ttpt) cc_final: 0.8655 (mtpp) REVERT: D 2 ASP cc_start: 0.8877 (p0) cc_final: 0.8560 (p0) REVERT: D 38 LEU cc_start: 0.9370 (tt) cc_final: 0.9115 (tp) REVERT: E 32 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8331 (mtpt) REVERT: G 32 LYS cc_start: 0.8851 (ttpt) cc_final: 0.8477 (mtpt) REVERT: H 2 ASP cc_start: 0.8770 (p0) cc_final: 0.8480 (p0) REVERT: I 2 ASP cc_start: 0.8681 (p0) cc_final: 0.8432 (p0) REVERT: I 32 LYS cc_start: 0.8716 (ttpt) cc_final: 0.8350 (tttt) REVERT: J 2 ASP cc_start: 0.8628 (p0) cc_final: 0.8351 (p0) outliers start: 48 outliers final: 43 residues processed: 214 average time/residue: 0.1318 time to fit residues: 41.0300 Evaluate side-chains 212 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 169 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 77 VAL 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 77 VAL Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 5 MET Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 77 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.059 7040 Z= 0.448 Angle : 0.828 7.317 9470 Z= 0.440 Chirality : 0.058 0.202 1180 Planarity : 0.003 0.018 1180 Dihedral : 7.219 30.571 1010 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.11 % Favored : 85.89 % Rotamer: Outliers : 12.79 % Allowed : 15.15 % Favored : 72.06 % 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: -4.94 (0.16), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.13), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.005 HIS C 50 PHE 0.025 0.004 PHE G 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 159 time to evaluate : 0.795 Fit side-chains REVERT: A 42 SER cc_start: 0.9199 (p) cc_final: 0.8965 (p) REVERT: B 32 LYS cc_start: 0.8865 (ttpt) cc_final: 0.8659 (mtpp) REVERT: D 2 ASP cc_start: 0.8881 (p0) cc_final: 0.8513 (p0) REVERT: E 26 VAL cc_start: 0.9218 (m) cc_final: 0.8989 (t) REVERT: E 32 LYS cc_start: 0.8702 (ttpt) cc_final: 0.8454 (mtpt) REVERT: G 32 LYS cc_start: 0.8870 (ttpt) cc_final: 0.8548 (mtpt) REVERT: I 2 ASP cc_start: 0.8638 (p0) cc_final: 0.8399 (p0) REVERT: J 2 ASP cc_start: 0.8869 (p0) cc_final: 0.8586 (p0) outliers start: 87 outliers final: 80 residues processed: 223 average time/residue: 0.1232 time to fit residues: 40.6162 Evaluate side-chains 233 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 153 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 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 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR 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 22 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 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 D residue 74 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 59 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 74 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain I residue 5 MET Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 54 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 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 98 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7040 Z= 0.100 Angle : 0.540 6.945 9470 Z= 0.284 Chirality : 0.047 0.136 1180 Planarity : 0.002 0.013 1180 Dihedral : 5.853 28.842 1010 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 10.29 % Allowed : 17.65 % Favored : 72.06 % 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: -4.41 (0.18), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.14), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 50 PHE 0.011 0.002 PHE E 4 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 190 time to evaluate : 0.716 Fit side-chains REVERT: B 32 LYS cc_start: 0.8813 (ttpt) cc_final: 0.8581 (mtpp) REVERT: B 83 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: D 2 ASP cc_start: 0.8819 (p0) cc_final: 0.8421 (p0) REVERT: D 8 LEU cc_start: 0.9108 (mm) cc_final: 0.8734 (mm) REVERT: E 32 LYS cc_start: 0.8643 (ttpt) cc_final: 0.8435 (mtpt) REVERT: F 57 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: G 32 LYS cc_start: 0.8830 (ttpt) cc_final: 0.8477 (mtpt) REVERT: I 2 ASP cc_start: 0.8762 (p0) cc_final: 0.8452 (p0) REVERT: J 2 ASP cc_start: 0.8838 (p0) cc_final: 0.8567 (p0) outliers start: 70 outliers final: 55 residues processed: 234 average time/residue: 0.1201 time to fit residues: 42.0114 Evaluate side-chains 238 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 181 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 98 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.066 7040 Z= 0.541 Angle : 0.892 7.737 9470 Z= 0.473 Chirality : 0.061 0.211 1180 Planarity : 0.003 0.014 1180 Dihedral : 7.326 30.652 1010 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.26 % Favored : 84.74 % Rotamer: Outliers : 13.82 % Allowed : 17.35 % Favored : 68.82 % 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: -4.82 (0.17), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.13), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.005 HIS C 50 PHE 0.029 0.005 PHE G 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 158 time to evaluate : 0.830 Fit side-chains REVERT: B 32 LYS cc_start: 0.8867 (ttpt) cc_final: 0.8660 (mtpp) REVERT: B 83 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: D 2 ASP cc_start: 0.8803 (p0) cc_final: 0.8411 (p0) REVERT: F 57 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: G 32 LYS cc_start: 0.8799 (ttpt) cc_final: 0.8478 (mtpt) REVERT: I 2 ASP cc_start: 0.8765 (p0) cc_final: 0.8557 (p0) REVERT: J 2 ASP cc_start: 0.8783 (p0) cc_final: 0.8508 (p0) REVERT: J 59 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8847 (p) outliers start: 94 outliers final: 87 residues processed: 230 average time/residue: 0.1231 time to fit residues: 42.1132 Evaluate side-chains 244 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 154 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 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 22 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 59 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 74 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain I residue 5 MET Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 98 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7040 Z= 0.103 Angle : 0.581 8.106 9470 Z= 0.299 Chirality : 0.047 0.139 1180 Planarity : 0.002 0.011 1180 Dihedral : 5.967 30.134 1010 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 12.65 % Allowed : 18.97 % Favored : 68.38 % 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: -4.38 (0.18), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.14), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.012 0.002 PHE C 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 179 time to evaluate : 0.825 Fit side-chains REVERT: A 13 GLU cc_start: 0.7634 (tp30) cc_final: 0.7412 (tm-30) REVERT: B 32 LYS cc_start: 0.8806 (ttpt) cc_final: 0.8561 (mtpp) REVERT: B 83 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: D 2 ASP cc_start: 0.8716 (p0) cc_final: 0.8247 (p0) REVERT: D 54 THR cc_start: 0.8985 (p) cc_final: 0.8670 (t) REVERT: F 57 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: G 32 LYS cc_start: 0.8806 (ttpt) cc_final: 0.8416 (mtpt) REVERT: I 2 ASP cc_start: 0.8841 (p0) cc_final: 0.8534 (p0) REVERT: J 2 ASP cc_start: 0.8871 (p0) cc_final: 0.8595 (p0) outliers start: 86 outliers final: 71 residues processed: 235 average time/residue: 0.1184 time to fit residues: 41.6519 Evaluate side-chains 251 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 178 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 22 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain I residue 5 MET Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 98 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 0.0980 chunk 96 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 99 GLN B 24 GLN I 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 7040 Z= 0.339 Angle : 0.731 7.998 9470 Z= 0.382 Chirality : 0.053 0.153 1180 Planarity : 0.002 0.018 1180 Dihedral : 6.794 30.944 1010 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.47 % Favored : 86.53 % Rotamer: Outliers : 13.38 % Allowed : 18.97 % Favored : 67.65 % 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: -4.53 (0.18), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.14), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS B 50 PHE 0.021 0.003 PHE G 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 166 time to evaluate : 0.728 Fit side-chains REVERT: A 13 GLU cc_start: 0.7822 (tp30) cc_final: 0.7491 (tm-30) REVERT: B 32 LYS cc_start: 0.8801 (ttpt) cc_final: 0.8584 (mtpp) REVERT: B 83 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: D 2 ASP cc_start: 0.8639 (p0) cc_final: 0.8159 (p0) REVERT: F 57 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: G 32 LYS cc_start: 0.8836 (ttpt) cc_final: 0.8496 (mtpt) REVERT: I 2 ASP cc_start: 0.8823 (p0) cc_final: 0.8518 (p0) REVERT: J 2 ASP cc_start: 0.8861 (p0) cc_final: 0.8569 (p0) outliers start: 91 outliers final: 84 residues processed: 229 average time/residue: 0.1129 time to fit residues: 38.6267 Evaluate side-chains 249 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 163 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain I residue 5 MET Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 98 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 99 GLN B 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 7040 Z= 0.272 Angle : 0.703 8.695 9470 Z= 0.366 Chirality : 0.051 0.139 1180 Planarity : 0.002 0.017 1180 Dihedral : 6.698 32.389 1010 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 13.09 % Allowed : 19.71 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.48 (0.18), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.14), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS C 50 PHE 0.018 0.003 PHE C 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 166 time to evaluate : 0.734 Fit side-chains REVERT: A 13 GLU cc_start: 0.7751 (tp30) cc_final: 0.7480 (tm-30) REVERT: B 32 LYS cc_start: 0.8857 (ttpt) cc_final: 0.8652 (mtpp) REVERT: B 83 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: D 2 ASP cc_start: 0.8618 (p0) cc_final: 0.8153 (p0) REVERT: F 57 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: G 32 LYS cc_start: 0.8859 (ttpt) cc_final: 0.8536 (mtpt) REVERT: I 2 ASP cc_start: 0.8830 (p0) cc_final: 0.8525 (p0) REVERT: J 2 ASP cc_start: 0.8864 (p0) cc_final: 0.8579 (p0) REVERT: J 28 GLU cc_start: 0.7826 (tt0) cc_final: 0.7487 (mt-10) outliers start: 89 outliers final: 85 residues processed: 229 average time/residue: 0.1226 time to fit residues: 41.9982 Evaluate side-chains 253 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 166 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 59 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 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain I residue 5 MET Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 98 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 99 GLN B 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 7040 Z= 0.273 Angle : 0.696 8.655 9470 Z= 0.364 Chirality : 0.051 0.137 1180 Planarity : 0.002 0.015 1180 Dihedral : 6.713 33.254 1010 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.53 % Favored : 87.47 % Rotamer: Outliers : 13.24 % Allowed : 19.26 % Favored : 67.50 % 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: -4.45 (0.18), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.14), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS C 50 PHE 0.018 0.003 PHE G 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 166 time to evaluate : 0.840 Fit side-chains REVERT: B 32 LYS cc_start: 0.8862 (ttpt) cc_final: 0.8654 (mtpp) REVERT: B 83 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: D 2 ASP cc_start: 0.8623 (p0) cc_final: 0.8151 (p0) REVERT: F 57 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: G 32 LYS cc_start: 0.8822 (ttpt) cc_final: 0.8435 (mtpt) REVERT: I 2 ASP cc_start: 0.8834 (p0) cc_final: 0.8524 (p0) REVERT: J 2 ASP cc_start: 0.8858 (p0) cc_final: 0.8579 (p0) outliers start: 90 outliers final: 88 residues processed: 231 average time/residue: 0.1166 time to fit residues: 40.2591 Evaluate side-chains 256 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 166 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 59 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 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain I residue 5 MET Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 98 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 7040 Z= 0.305 Angle : 0.735 9.485 9470 Z= 0.383 Chirality : 0.052 0.139 1180 Planarity : 0.002 0.014 1180 Dihedral : 6.812 32.913 1010 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % Rotamer: Outliers : 13.68 % Allowed : 18.97 % Favored : 67.35 % 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: -4.47 (0.18), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.14), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS G 50 PHE 0.021 0.003 PHE G 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 165 time to evaluate : 0.803 Fit side-chains REVERT: B 32 LYS cc_start: 0.8859 (ttpt) cc_final: 0.8653 (mtpp) REVERT: B 83 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: D 2 ASP cc_start: 0.8606 (p0) cc_final: 0.8138 (p0) REVERT: F 57 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: G 32 LYS cc_start: 0.8833 (ttpt) cc_final: 0.8476 (mtpt) REVERT: I 2 ASP cc_start: 0.8832 (p0) cc_final: 0.8514 (p0) REVERT: J 2 ASP cc_start: 0.8857 (p0) cc_final: 0.8579 (p0) outliers start: 93 outliers final: 90 residues processed: 232 average time/residue: 0.1174 time to fit residues: 41.1175 Evaluate side-chains 256 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 164 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 59 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 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain I residue 5 MET Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 98 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.121646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.108153 restraints weight = 10540.745| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.69 r_work: 0.3563 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7040 Z= 0.105 Angle : 0.582 8.692 9470 Z= 0.302 Chirality : 0.047 0.140 1180 Planarity : 0.002 0.030 1180 Dihedral : 5.930 33.739 1010 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 10.74 % Allowed : 21.91 % Favored : 67.35 % 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: -4.19 (0.19), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.15), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.011 0.002 PHE C 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1762.26 seconds wall clock time: 32 minutes 51.69 seconds (1971.69 seconds total)