Starting phenix.real_space_refine on Thu Feb 15 07:08:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfi_33173/02_2024/7xfi_33173_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfi_33173/02_2024/7xfi_33173.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfi_33173/02_2024/7xfi_33173_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfi_33173/02_2024/7xfi_33173_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfi_33173/02_2024/7xfi_33173_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfi_33173/02_2024/7xfi_33173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfi_33173/02_2024/7xfi_33173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfi_33173/02_2024/7xfi_33173_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfi_33173/02_2024/7xfi_33173_updated.pdb" } resolution = 2.9 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= 0.007 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 271 5.49 5 S 12 5.16 5 C 6391 2.51 5 N 2167 2.21 5 O 2683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11524 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2801 Classifications: {'DNA': 136} Link IDs: {'rna3p': 135} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "J" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2771 Classifications: {'DNA': 136} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 135} Time building chain proxies: 6.14, per 1000 atoms: 0.53 Number of scatterers: 11524 At special positions: 0 Unit cell: (120.98, 114.668, 84.16, 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 12 16.00 P 271 15.00 O 2683 8.00 N 2167 7.00 C 6391 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.67 Conformation dependent library (CDL) restraints added in 1.2 seconds 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1402 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 0 sheets defined 63.8% alpha, 0.0% beta 126 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 6.48 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.913A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.846A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.364A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 88 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.010A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 20 No H-bonds generated for 'chain 'G' and resid 17 through 20' Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.289A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 removed outlier: 3.559A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 37 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 338 hydrogen bonds defined for protein. 1014 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for ID residue Warning, Cannot make NA restraints for ID residue Restraints generated for nucleic acids: 324 hydrogen bonds 648 hydrogen bond angles 0 basepair planarities 126 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 5.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2013 1.33 - 1.45: 4121 1.45 - 1.57: 5584 1.57 - 1.69: 541 1.69 - 1.81: 22 Bond restraints: 12281 Sorted by residual: bond pdb=" C4' DI I -50 " pdb=" O4' DI I -50 " ideal model delta sigma weight residual 1.640 1.430 0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C3' DI I -50 " pdb=" C4' DI I -50 " ideal model delta sigma weight residual 1.315 1.520 -0.205 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C4 DI I -50 " pdb=" N3 DI I -50 " ideal model delta sigma weight residual 1.507 1.353 0.154 2.00e-02 2.50e+03 5.97e+01 bond pdb=" C2 DI I -50 " pdb=" N3 DI I -50 " ideal model delta sigma weight residual 1.482 1.343 0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" C1' DI I -50 " pdb=" O4' DI I -50 " ideal model delta sigma weight residual 1.311 1.427 -0.116 2.00e-02 2.50e+03 3.36e+01 ... (remaining 12276 not shown) Histogram of bond angle deviations from ideal: 97.66 - 105.51: 1316 105.51 - 113.35: 7006 113.35 - 121.20: 6218 121.20 - 129.05: 3052 129.05 - 136.89: 160 Bond angle restraints: 17752 Sorted by residual: angle pdb=" C1' DI I -50 " pdb=" N9 DI I -50 " pdb=" C4 DI I -50 " ideal model delta sigma weight residual 107.36 123.90 -16.54 3.00e+00 1.11e-01 3.04e+01 angle pdb=" N GLU H 110 " pdb=" CA GLU H 110 " pdb=" CB GLU H 110 " ideal model delta sigma weight residual 110.28 116.82 -6.54 1.55e+00 4.16e-01 1.78e+01 angle pdb=" C1' DI I -50 " pdb=" N9 DI I -50 " pdb=" C8 DI I -50 " ideal model delta sigma weight residual 138.51 127.49 11.02 3.00e+00 1.11e-01 1.35e+01 angle pdb=" OP1 DI I -50 " pdb=" P DI I -50 " pdb=" OP2 DI I -50 " ideal model delta sigma weight residual 109.44 119.85 -10.41 3.00e+00 1.11e-01 1.20e+01 angle pdb=" CA GLU H 110 " pdb=" CB GLU H 110 " pdb=" CG GLU H 110 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 ... (remaining 17747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 5364 35.40 - 70.79: 1293 70.79 - 106.19: 18 106.19 - 141.59: 2 141.59 - 176.98: 1 Dihedral angle restraints: 6678 sinusoidal: 4503 harmonic: 2175 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 36.98 -176.98 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual 180.00 -161.41 -18.59 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" C4' DT J 34 " pdb=" C3' DT J 34 " pdb=" O3' DT J 34 " pdb=" P DC J 35 " ideal model delta sinusoidal sigma weight residual 220.00 88.96 131.04 1 3.50e+01 8.16e-04 1.30e+01 ... (remaining 6675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1550 0.047 - 0.094: 385 0.094 - 0.140: 75 0.140 - 0.187: 9 0.187 - 0.234: 2 Chirality restraints: 2021 Sorted by residual: chirality pdb=" CB VAL D 45 " pdb=" CA VAL D 45 " pdb=" CG1 VAL D 45 " pdb=" CG2 VAL D 45 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA GLU H 110 " pdb=" N GLU H 110 " pdb=" C GLU H 110 " pdb=" CB GLU H 110 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" C3' DI I -50 " pdb=" C2' DI I -50 " pdb=" C4' DI I -50 " pdb=" O3' DI I -50 " both_signs ideal model delta sigma weight residual False -2.42 -2.59 0.18 2.00e-01 2.50e+01 7.83e-01 ... (remaining 2018 not shown) Planarity restraints: 1307 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.049 5.00e-02 4.00e+02 7.33e-02 8.59e+00 pdb=" N PRO C 80 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.044 5.00e-02 4.00e+02 6.60e-02 6.96e+00 pdb=" N PRO G 80 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 77 " -0.195 9.50e-02 1.11e+02 8.81e-02 6.55e+00 pdb=" NE ARG G 77 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG G 77 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG G 77 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG G 77 " 0.001 2.00e-02 2.50e+03 ... (remaining 1304 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3371 2.86 - 3.37: 9472 3.37 - 3.88: 23228 3.88 - 4.39: 26323 4.39 - 4.90: 37245 Nonbonded interactions: 99639 Sorted by model distance: nonbonded pdb=" O THR G 16 " pdb=" OG SER G 19 " model vdw 2.349 2.440 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.392 2.440 nonbonded pdb=" O THR H 112 " pdb=" OG1 THR H 116 " model vdw 2.396 2.440 nonbonded pdb=" NH2 ARG G 88 " pdb=" O VAL G 100 " model vdw 2.405 2.520 nonbonded pdb=" NH1 ARG F 35 " pdb=" OP2 DG I 8 " model vdw 2.416 2.520 ... (remaining 99634 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' and resid 39 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 0.500 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: 2.340 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 38.020 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 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:11.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 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 : 0.006 0.210 12281 Z= 0.365 Angle : 0.756 16.544 17752 Z= 0.433 Chirality : 0.043 0.234 2021 Planarity : 0.007 0.088 1307 Dihedral : 27.572 176.982 5276 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -0.78 (0.26), residues: 735 helix: -0.38 (0.19), residues: 541 sheet: None (None), residues: 0 loop : -0.43 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.007 0.002 PHE H 62 TYR 0.015 0.002 TYR C 50 ARG 0.024 0.001 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.833 Fit side-chains REVERT: A 56 LYS cc_start: 0.7785 (ttmm) cc_final: 0.7354 (mtpt) REVERT: C 19 SER cc_start: 0.8426 (p) cc_final: 0.8224 (t) REVERT: C 74 LYS cc_start: 0.7746 (mtmm) cc_final: 0.7486 (mptt) REVERT: C 77 ARG cc_start: 0.8058 (ttm-80) cc_final: 0.7791 (ttp-170) REVERT: C 99 ARG cc_start: 0.7395 (mmm160) cc_final: 0.7092 (mmp-170) REVERT: D 96 ARG cc_start: 0.7905 (mtt-85) cc_final: 0.7467 (mtm180) REVERT: D 105 LYS cc_start: 0.7622 (mttt) cc_final: 0.7325 (mttp) REVERT: D 117 LYS cc_start: 0.7747 (tttm) cc_final: 0.7538 (ttpp) REVERT: E 49 ARG cc_start: 0.7433 (mtm110) cc_final: 0.7166 (mtp180) REVERT: E 52 ARG cc_start: 0.7265 (mtm-85) cc_final: 0.6686 (mtm110) REVERT: E 122 LYS cc_start: 0.7852 (pttt) cc_final: 0.7547 (ptpt) REVERT: F 78 ARG cc_start: 0.8623 (mtm-85) cc_final: 0.8255 (mtm110) REVERT: G 74 LYS cc_start: 0.7564 (mppt) cc_final: 0.7236 (mmtt) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 2.1621 time to fit residues: 354.8219 Evaluate side-chains 101 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN C 31 HIS C 104 GLN D 81 ASN E 55 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12281 Z= 0.266 Angle : 0.581 5.783 17752 Z= 0.345 Chirality : 0.036 0.145 2021 Planarity : 0.005 0.057 1307 Dihedral : 30.776 176.922 3800 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.57 % Allowed : 12.36 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.77 (0.29), residues: 735 helix: 0.89 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.33 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.011 0.002 PHE H 67 TYR 0.015 0.002 TYR A 54 ARG 0.007 0.001 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 0.870 Fit side-chains REVERT: A 56 LYS cc_start: 0.7833 (ttmm) cc_final: 0.7413 (mtpt) REVERT: A 125 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7535 (mt0) REVERT: A 128 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8347 (mtp180) REVERT: C 74 LYS cc_start: 0.7876 (mtmm) cc_final: 0.7446 (mptt) REVERT: C 75 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.6397 (mtpp) REVERT: C 77 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.8002 (ttp-170) REVERT: C 99 ARG cc_start: 0.7421 (mmm160) cc_final: 0.7180 (mmp-170) REVERT: D 96 ARG cc_start: 0.7800 (mtt-85) cc_final: 0.7357 (mtm180) REVERT: D 105 LYS cc_start: 0.7738 (mttt) cc_final: 0.7469 (tmtp) REVERT: E 49 ARG cc_start: 0.7533 (mtm110) cc_final: 0.7191 (mtp180) REVERT: E 76 GLN cc_start: 0.7613 (tt0) cc_final: 0.7055 (pt0) REVERT: E 122 LYS cc_start: 0.7926 (pttt) cc_final: 0.7714 (ptpt) REVERT: F 59 LYS cc_start: 0.8154 (tttp) cc_final: 0.7661 (ttpp) REVERT: G 99 ARG cc_start: 0.7753 (mmm-85) cc_final: 0.7195 (mmm160) outliers start: 16 outliers final: 8 residues processed: 138 average time/residue: 2.0390 time to fit residues: 295.2052 Evaluate side-chains 122 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN F 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12281 Z= 0.201 Angle : 0.543 6.275 17752 Z= 0.328 Chirality : 0.034 0.139 2021 Planarity : 0.004 0.049 1307 Dihedral : 30.737 176.219 3800 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.09 % Allowed : 17.98 % Favored : 79.94 % 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: 1.47 (0.29), residues: 735 helix: 1.46 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.31 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 31 PHE 0.007 0.001 PHE A 67 TYR 0.012 0.001 TYR D 37 ARG 0.009 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 0.824 Fit side-chains REVERT: A 56 LYS cc_start: 0.7862 (ttmm) cc_final: 0.7423 (mtpt) REVERT: A 125 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7498 (mt0) REVERT: C 74 LYS cc_start: 0.7889 (mtmm) cc_final: 0.7393 (mptt) REVERT: C 75 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.6354 (mtpp) REVERT: C 77 ARG cc_start: 0.8231 (ttm-80) cc_final: 0.8022 (ttp-170) REVERT: C 99 ARG cc_start: 0.7419 (mmm160) cc_final: 0.7176 (mmp-170) REVERT: D 96 ARG cc_start: 0.7785 (mtt-85) cc_final: 0.7335 (mtm180) REVERT: D 105 LYS cc_start: 0.7881 (mttt) cc_final: 0.7470 (tttt) REVERT: E 76 GLN cc_start: 0.7630 (tt0) cc_final: 0.7048 (pt0) REVERT: E 122 LYS cc_start: 0.7958 (pttt) cc_final: 0.7702 (ptpt) REVERT: F 59 LYS cc_start: 0.8195 (tttp) cc_final: 0.7670 (ttpp) outliers start: 13 outliers final: 8 residues processed: 121 average time/residue: 2.0189 time to fit residues: 256.5465 Evaluate side-chains 119 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 59 optimal weight: 0.0980 chunk 89 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 104 GLN F 25 ASN H 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12281 Z= 0.313 Angle : 0.601 6.351 17752 Z= 0.354 Chirality : 0.037 0.140 2021 Planarity : 0.005 0.057 1307 Dihedral : 31.024 174.928 3800 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.53 % Allowed : 17.66 % Favored : 78.81 % 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: 1.42 (0.29), residues: 735 helix: 1.47 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -0.49 (0.38), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 31 PHE 0.012 0.002 PHE F 100 TYR 0.014 0.002 TYR A 54 ARG 0.008 0.001 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 0.984 Fit side-chains REVERT: A 56 LYS cc_start: 0.7916 (ttmm) cc_final: 0.7390 (mtmt) REVERT: A 128 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8393 (mtp180) REVERT: B 92 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8059 (mtp85) REVERT: B 95 ARG cc_start: 0.8147 (mtt180) cc_final: 0.7770 (mtt-85) REVERT: C 56 GLU cc_start: 0.8480 (tt0) cc_final: 0.8214 (tt0) REVERT: C 74 LYS cc_start: 0.7866 (mtmm) cc_final: 0.7376 (mptt) REVERT: C 75 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.6724 (mtpp) REVERT: C 99 ARG cc_start: 0.7475 (mmm160) cc_final: 0.7244 (mmm160) REVERT: D 96 ARG cc_start: 0.7872 (mtt-85) cc_final: 0.7607 (mtt-85) REVERT: D 105 LYS cc_start: 0.7937 (mttt) cc_final: 0.7590 (tmtm) REVERT: E 76 GLN cc_start: 0.7650 (tt0) cc_final: 0.6924 (pt0) REVERT: E 83 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.6828 (mpt-90) REVERT: F 59 LYS cc_start: 0.8254 (tttp) cc_final: 0.7726 (ttpp) REVERT: G 92 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7055 (mt-10) REVERT: G 99 ARG cc_start: 0.7910 (mmm-85) cc_final: 0.7288 (mmm160) REVERT: H 54 LYS cc_start: 0.7668 (tptt) cc_final: 0.7435 (mmmt) REVERT: H 117 LYS cc_start: 0.7905 (tttp) cc_final: 0.7686 (tttp) outliers start: 22 outliers final: 9 residues processed: 132 average time/residue: 1.9606 time to fit residues: 272.2352 Evaluate side-chains 124 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.1980 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 104 GLN F 25 ASN H 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12281 Z= 0.221 Angle : 0.561 6.448 17752 Z= 0.337 Chirality : 0.035 0.138 2021 Planarity : 0.004 0.044 1307 Dihedral : 30.976 174.342 3800 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.21 % Allowed : 19.26 % Favored : 77.53 % 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: 1.72 (0.29), residues: 735 helix: 1.73 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.51 (0.38), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 31 PHE 0.009 0.002 PHE A 67 TYR 0.011 0.002 TYR F 51 ARG 0.006 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 0.837 Fit side-chains REVERT: A 56 LYS cc_start: 0.7925 (ttmm) cc_final: 0.7433 (mtpt) REVERT: A 128 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8388 (mtp180) REVERT: B 92 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7953 (mtp85) REVERT: B 95 ARG cc_start: 0.8158 (mtt180) cc_final: 0.7773 (mtt-85) REVERT: C 56 GLU cc_start: 0.8447 (tt0) cc_final: 0.8188 (tt0) REVERT: C 74 LYS cc_start: 0.7860 (mtmm) cc_final: 0.7381 (mptt) REVERT: C 75 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.6711 (mtpp) REVERT: C 99 ARG cc_start: 0.7388 (mmm160) cc_final: 0.7152 (mmm160) REVERT: D 96 ARG cc_start: 0.7868 (mtt-85) cc_final: 0.7608 (mtt-85) REVERT: D 105 LYS cc_start: 0.7954 (mttt) cc_final: 0.7568 (tttm) REVERT: E 76 GLN cc_start: 0.7651 (tt0) cc_final: 0.6919 (pt0) REVERT: F 59 LYS cc_start: 0.8197 (tttp) cc_final: 0.7680 (ttpp) REVERT: G 92 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7043 (mt-10) REVERT: G 99 ARG cc_start: 0.7934 (mmm-85) cc_final: 0.7289 (mmm160) REVERT: H 54 LYS cc_start: 0.7671 (tptt) cc_final: 0.7427 (mmmt) outliers start: 20 outliers final: 12 residues processed: 126 average time/residue: 1.9727 time to fit residues: 261.2578 Evaluate side-chains 126 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 0.0170 chunk 94 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 104 GLN F 25 ASN H 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12281 Z= 0.171 Angle : 0.546 5.779 17752 Z= 0.330 Chirality : 0.034 0.135 2021 Planarity : 0.004 0.043 1307 Dihedral : 30.943 174.330 3800 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.41 % Allowed : 20.22 % Favored : 77.37 % 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: 2.02 (0.30), residues: 735 helix: 1.97 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.46 (0.38), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.009 0.001 PHE A 67 TYR 0.011 0.001 TYR G 57 ARG 0.007 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 0.903 Fit side-chains REVERT: A 56 LYS cc_start: 0.7944 (ttmm) cc_final: 0.7438 (mtpt) REVERT: A 128 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8390 (mtp180) REVERT: B 92 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7912 (mtp85) REVERT: B 95 ARG cc_start: 0.8153 (mtt180) cc_final: 0.7794 (mtt-85) REVERT: C 56 GLU cc_start: 0.8442 (tt0) cc_final: 0.8171 (tt0) REVERT: C 74 LYS cc_start: 0.7854 (mtmm) cc_final: 0.7371 (mptt) REVERT: C 75 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.6700 (mtpp) REVERT: C 99 ARG cc_start: 0.7394 (mmm160) cc_final: 0.7161 (mmm160) REVERT: D 96 ARG cc_start: 0.7845 (mtt-85) cc_final: 0.7595 (mtt-85) REVERT: D 105 LYS cc_start: 0.7971 (mttt) cc_final: 0.7601 (tttm) REVERT: E 76 GLN cc_start: 0.7647 (tt0) cc_final: 0.6916 (pt0) REVERT: F 59 LYS cc_start: 0.8180 (tttp) cc_final: 0.7662 (ttpp) REVERT: G 74 LYS cc_start: 0.8223 (mtmm) cc_final: 0.7785 (mptt) REVERT: G 92 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7044 (mt-10) REVERT: G 99 ARG cc_start: 0.7928 (mmm-85) cc_final: 0.7287 (mmm160) REVERT: H 54 LYS cc_start: 0.7753 (tptt) cc_final: 0.7518 (mmmt) outliers start: 15 outliers final: 12 residues processed: 122 average time/residue: 1.9492 time to fit residues: 250.1366 Evaluate side-chains 125 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 0.0370 chunk 94 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN F 25 ASN H 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12281 Z= 0.178 Angle : 0.542 5.882 17752 Z= 0.328 Chirality : 0.033 0.133 2021 Planarity : 0.005 0.090 1307 Dihedral : 30.876 173.929 3800 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.57 % Allowed : 21.03 % Favored : 76.40 % 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: 2.15 (0.30), residues: 735 helix: 2.07 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -0.42 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.009 0.001 PHE A 67 TYR 0.010 0.001 TYR G 57 ARG 0.024 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 0.790 Fit side-chains REVERT: A 56 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7430 (mtpt) REVERT: A 125 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7480 (mt0) REVERT: A 128 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8341 (mtp180) REVERT: B 95 ARG cc_start: 0.8140 (mtt180) cc_final: 0.7798 (mtt-85) REVERT: C 56 GLU cc_start: 0.8448 (tt0) cc_final: 0.8176 (tt0) REVERT: C 74 LYS cc_start: 0.7865 (mtmm) cc_final: 0.7388 (mptt) REVERT: C 75 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.6717 (mtpp) REVERT: C 99 ARG cc_start: 0.7398 (mmm160) cc_final: 0.7164 (mmm160) REVERT: D 96 ARG cc_start: 0.7840 (mtt-85) cc_final: 0.7591 (mtt-85) REVERT: D 105 LYS cc_start: 0.7949 (mttt) cc_final: 0.7586 (tttm) REVERT: E 76 GLN cc_start: 0.7639 (tt0) cc_final: 0.6918 (pt0) REVERT: E 83 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.6765 (mpt-90) REVERT: F 59 LYS cc_start: 0.8200 (tttp) cc_final: 0.7620 (ttpp) REVERT: G 74 LYS cc_start: 0.8212 (mtmm) cc_final: 0.7770 (mptt) REVERT: G 99 ARG cc_start: 0.7931 (mmm-85) cc_final: 0.7298 (mmm160) REVERT: H 53 SER cc_start: 0.8602 (t) cc_final: 0.8298 (m) REVERT: H 54 LYS cc_start: 0.7796 (tptt) cc_final: 0.7514 (mmmt) REVERT: H 82 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.7807 (mttt) outliers start: 16 outliers final: 8 residues processed: 124 average time/residue: 1.9692 time to fit residues: 256.6393 Evaluate side-chains 124 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 82 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12281 Z= 0.180 Angle : 0.533 5.469 17752 Z= 0.322 Chirality : 0.033 0.134 2021 Planarity : 0.005 0.098 1307 Dihedral : 30.751 173.912 3800 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.77 % Allowed : 21.67 % Favored : 76.57 % 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: 2.39 (0.30), residues: 735 helix: 2.25 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -0.36 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.008 0.001 PHE A 67 TYR 0.010 0.001 TYR G 57 ARG 0.008 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 0.817 Fit side-chains REVERT: A 56 LYS cc_start: 0.7956 (ttmm) cc_final: 0.7450 (mtpt) REVERT: A 128 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8306 (mtp180) REVERT: B 95 ARG cc_start: 0.8125 (mtt180) cc_final: 0.7786 (mtt-85) REVERT: C 56 GLU cc_start: 0.8467 (tt0) cc_final: 0.8196 (tt0) REVERT: C 74 LYS cc_start: 0.7843 (mtmm) cc_final: 0.7351 (mptt) REVERT: C 75 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.6705 (mtpp) REVERT: C 99 ARG cc_start: 0.7439 (mmm160) cc_final: 0.7202 (mmm160) REVERT: D 105 LYS cc_start: 0.8015 (mttt) cc_final: 0.7669 (tttm) REVERT: E 76 GLN cc_start: 0.7655 (tt0) cc_final: 0.6918 (pt0) REVERT: E 83 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.6799 (mpt-90) REVERT: F 59 LYS cc_start: 0.8210 (tttp) cc_final: 0.7617 (ttpp) REVERT: G 99 ARG cc_start: 0.7937 (mmm-85) cc_final: 0.7294 (mmm160) REVERT: H 53 SER cc_start: 0.8561 (t) cc_final: 0.8251 (m) REVERT: H 54 LYS cc_start: 0.7773 (tptt) cc_final: 0.7516 (mmmt) outliers start: 11 outliers final: 7 residues processed: 123 average time/residue: 1.9615 time to fit residues: 253.4733 Evaluate side-chains 122 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 76 GLN F 25 ASN G 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12281 Z= 0.249 Angle : 0.560 5.701 17752 Z= 0.334 Chirality : 0.035 0.136 2021 Planarity : 0.004 0.042 1307 Dihedral : 30.763 175.104 3800 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.89 % Allowed : 20.39 % Favored : 76.73 % 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: 2.16 (0.30), residues: 735 helix: 2.06 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.41 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 31 PHE 0.009 0.002 PHE F 100 TYR 0.012 0.002 TYR G 57 ARG 0.010 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 0.967 Fit side-chains REVERT: A 56 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7435 (mtpt) REVERT: A 128 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8377 (mtp180) REVERT: B 92 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7987 (mtp85) REVERT: B 95 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7754 (mtt-85) REVERT: C 56 GLU cc_start: 0.8477 (tt0) cc_final: 0.8211 (tt0) REVERT: C 74 LYS cc_start: 0.7854 (mtmm) cc_final: 0.7356 (mptt) REVERT: C 75 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.6769 (mtpp) REVERT: C 99 ARG cc_start: 0.7400 (mmm160) cc_final: 0.7178 (mmm160) REVERT: D 96 ARG cc_start: 0.7857 (mtt-85) cc_final: 0.7606 (mtt-85) REVERT: D 105 LYS cc_start: 0.7951 (mttt) cc_final: 0.7584 (tttm) REVERT: E 76 GLN cc_start: 0.7535 (tt0) cc_final: 0.6911 (pt0) REVERT: E 83 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.6816 (mpt-90) REVERT: F 59 LYS cc_start: 0.8235 (tttp) cc_final: 0.7682 (ttpp) REVERT: G 99 ARG cc_start: 0.7936 (mmm-85) cc_final: 0.7302 (mmm160) REVERT: H 54 LYS cc_start: 0.7791 (tptt) cc_final: 0.7549 (mmmt) REVERT: H 82 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.7811 (mttt) outliers start: 18 outliers final: 9 residues processed: 125 average time/residue: 2.0039 time to fit residues: 263.2483 Evaluate side-chains 126 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 82 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN F 25 ASN G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12281 Z= 0.257 Angle : 0.563 5.752 17752 Z= 0.335 Chirality : 0.035 0.135 2021 Planarity : 0.004 0.042 1307 Dihedral : 30.766 175.013 3800 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.73 % Allowed : 20.22 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.10 (0.30), residues: 735 helix: 2.01 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.42 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 46 PHE 0.009 0.002 PHE F 100 TYR 0.011 0.002 TYR G 57 ARG 0.008 0.000 ARG A 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 0.923 Fit side-chains REVERT: A 56 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7416 (mtmt) REVERT: A 128 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8354 (mtp180) REVERT: B 92 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8000 (mtp85) REVERT: B 95 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7754 (mtt-85) REVERT: C 56 GLU cc_start: 0.8475 (tt0) cc_final: 0.8211 (tt0) REVERT: C 74 LYS cc_start: 0.7851 (mtmm) cc_final: 0.7352 (mptt) REVERT: C 75 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.6772 (mtpp) REVERT: C 99 ARG cc_start: 0.7402 (mmm160) cc_final: 0.7178 (mmm160) REVERT: D 96 ARG cc_start: 0.7856 (mtt-85) cc_final: 0.7607 (mtt-85) REVERT: D 105 LYS cc_start: 0.7952 (mttt) cc_final: 0.7583 (tttm) REVERT: E 76 GLN cc_start: 0.7540 (tt0) cc_final: 0.6911 (pt0) REVERT: E 83 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.6817 (mpt-90) REVERT: F 59 LYS cc_start: 0.8235 (tttp) cc_final: 0.7683 (ttpp) REVERT: G 99 ARG cc_start: 0.7940 (mmm-85) cc_final: 0.7305 (mmm160) REVERT: H 54 LYS cc_start: 0.7798 (tptt) cc_final: 0.7551 (mmmt) REVERT: H 82 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.7814 (mttt) outliers start: 17 outliers final: 11 residues processed: 123 average time/residue: 1.9614 time to fit residues: 253.5901 Evaluate side-chains 128 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 82 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 9 optimal weight: 0.0070 chunk 14 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN F 25 ASN G 73 ASN H 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.170043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.124796 restraints weight = 12654.964| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 0.85 r_work: 0.3188 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 12281 Z= 0.329 Angle : 0.610 6.197 17752 Z= 0.358 Chirality : 0.038 0.140 2021 Planarity : 0.005 0.041 1307 Dihedral : 31.029 174.539 3800 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.73 % Allowed : 20.06 % Favored : 77.21 % 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: 1.69 (0.29), residues: 735 helix: 1.72 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -0.62 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 46 PHE 0.012 0.002 PHE F 100 TYR 0.015 0.002 TYR A 54 ARG 0.006 0.001 ARG A 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4330.10 seconds wall clock time: 77 minutes 17.27 seconds (4637.27 seconds total)