Starting phenix.real_space_refine on Thu Feb 15 16:15:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfj_33174/02_2024/7xfj_33174_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfj_33174/02_2024/7xfj_33174.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfj_33174/02_2024/7xfj_33174_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfj_33174/02_2024/7xfj_33174_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfj_33174/02_2024/7xfj_33174_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfj_33174/02_2024/7xfj_33174.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfj_33174/02_2024/7xfj_33174.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfj_33174/02_2024/7xfj_33174_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfj_33174/02_2024/7xfj_33174_updated.pdb" } resolution = 3.0 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= 0.001 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 261 5.49 5 S 21 5.16 5 C 7227 2.51 5 N 2403 2.21 5 O 2893 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 "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 39": "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: 12805 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 780 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "D" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "E" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 750 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} 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: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2690 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "J" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2668 Classifications: {'DNA': 131} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 130} Chain breaks: 1 Chain: "K" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1566 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain breaks: 3 Time building chain proxies: 6.68, per 1000 atoms: 0.52 Number of scatterers: 12805 At special positions: 0 Unit cell: (120.98, 118.876, 111.512, 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 21 16.00 P 261 15.00 O 2893 8.00 N 2403 7.00 C 7227 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: 6.50 Conformation dependent library (CDL) restraints added in 1.4 seconds 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1748 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 4 sheets defined 53.6% alpha, 2.5% beta 115 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 7.22 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.807A 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: 3.737A 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: 4.405A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 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 56 removed outlier: 3.724A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 86 through 114 Processing helix chain 'E' and resid 121 through 130 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 41 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 27 through 35 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.256A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 35 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 Processing helix chain 'K' and resid 88 through 91 removed outlier: 3.532A pdb=" N PHE K 91 " --> pdb=" O LEU K 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 88 through 91' Processing helix chain 'K' and resid 95 through 100 Processing helix chain 'K' and resid 190 through 196 Processing helix chain 'K' and resid 218 through 224 Processing helix chain 'K' and resid 229 through 231 No H-bonds generated for 'chain 'K' and resid 229 through 231' Processing sheet with id= A, first strand: chain 'K' and resid 106 through 108 removed outlier: 3.722A pdb=" N VAL K 108 " --> pdb=" O TRP K 243 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TRP K 243 " --> pdb=" O VAL K 108 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 124 through 127 removed outlier: 4.810A pdb=" N MET K 168 " --> pdb=" O LEU K 181 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 256 through 259 Processing sheet with id= D, first strand: chain 'K' and resid 120 through 123 removed outlier: 6.876A pdb=" N ALA K 183 " --> pdb=" O VAL K 122 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 302 hydrogen bonds 604 hydrogen bond angles 0 basepair planarities 115 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 5.32 Time building geometry restraints manager: 6.84 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: 2855 1.33 - 1.46: 4224 1.46 - 1.58: 5925 1.58 - 1.70: 520 1.70 - 1.82: 36 Bond restraints: 13560 Sorted by residual: bond pdb=" C2' AAB I -50 " pdb=" C1' AAB I -50 " ideal model delta sigma weight residual 1.341 1.522 -0.181 2.00e-02 2.50e+03 8.20e+01 bond pdb=" O4' AAB I -50 " pdb=" C1' AAB I -50 " ideal model delta sigma weight residual 1.601 1.429 0.172 2.00e-02 2.50e+03 7.40e+01 bond pdb=" C4' AAB I -50 " pdb=" O4' AAB I -50 " ideal model delta sigma weight residual 1.293 1.430 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C3' AAB I -50 " pdb=" O3' AAB I -50 " ideal model delta sigma weight residual 1.362 1.432 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C1' AAB I -50 " pdb=" O1' AAB I -50 " ideal model delta sigma weight residual 1.374 1.431 -0.057 2.00e-02 2.50e+03 8.22e+00 ... (remaining 13555 not shown) Histogram of bond angle deviations from ideal: 98.61 - 105.67: 1395 105.67 - 112.73: 7353 112.73 - 119.79: 4685 119.79 - 126.85: 5264 126.85 - 133.90: 727 Bond angle restraints: 19424 Sorted by residual: angle pdb=" CA ARG F 55 " pdb=" CB ARG F 55 " pdb=" CG ARG F 55 " ideal model delta sigma weight residual 114.10 124.35 -10.25 2.00e+00 2.50e-01 2.63e+01 angle pdb=" N MET K 164 " pdb=" CA MET K 164 " pdb=" C MET K 164 " ideal model delta sigma weight residual 114.56 108.95 5.61 1.27e+00 6.20e-01 1.95e+01 angle pdb=" CG ARG F 92 " pdb=" CD ARG F 92 " pdb=" NE ARG F 92 " ideal model delta sigma weight residual 112.00 102.78 9.22 2.20e+00 2.07e-01 1.76e+01 angle pdb=" C ARG F 95 " pdb=" CA ARG F 95 " pdb=" CB ARG F 95 " ideal model delta sigma weight residual 111.82 116.74 -4.92 1.38e+00 5.25e-01 1.27e+01 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 113.18 121.59 -8.41 2.37e+00 1.78e-01 1.26e+01 ... (remaining 19419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.60: 5911 29.60 - 59.19: 1502 59.19 - 88.79: 58 88.79 - 118.38: 0 118.38 - 147.98: 4 Dihedral angle restraints: 7475 sinusoidal: 4761 harmonic: 2714 Sorted by residual: 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 -159.03 -20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual -180.00 -160.38 -19.62 0 5.00e+00 4.00e-02 1.54e+01 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 220.00 72.02 147.98 1 3.50e+01 8.16e-04 1.45e+01 ... (remaining 7472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1763 0.055 - 0.109: 367 0.109 - 0.164: 61 0.164 - 0.219: 9 0.219 - 0.273: 3 Chirality restraints: 2203 Sorted by residual: chirality pdb=" CB VAL K 96 " pdb=" CA VAL K 96 " pdb=" CG1 VAL K 96 " pdb=" CG2 VAL K 96 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 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 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB THR K 84 " pdb=" CA THR K 84 " pdb=" OG1 THR K 84 " pdb=" CG2 THR K 84 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2200 not shown) Planarity restraints: 1565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.048 5.00e-02 4.00e+02 7.22e-02 8.33e+00 pdb=" N PRO G 80 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.043 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO C 80 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN K 93 " 0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO K 94 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO K 94 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 94 " 0.034 5.00e-02 4.00e+02 ... (remaining 1562 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3472 2.84 - 3.35: 10289 3.35 - 3.87: 24608 3.87 - 4.38: 28232 4.38 - 4.90: 40847 Nonbonded interactions: 107448 Sorted by model distance: nonbonded pdb=" O ILE F 29 " pdb=" NH1 ARG F 55 " model vdw 2.323 2.520 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.360 2.440 nonbonded pdb=" OG1 THR A 45 " pdb=" OP1 DC I 70 " model vdw 2.382 2.440 nonbonded pdb=" NH1 ARG E 72 " pdb=" OP1 DC J -23 " model vdw 2.409 2.520 nonbonded pdb=" O HIS F 75 " pdb=" NH2 ARG H 89 " model vdw 2.409 2.520 ... (remaining 107443 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 42 through 133) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 24 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 111) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 31 through 121) } 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: 0.450 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: 2.270 Check model and map are aligned: 0.180 Set scattering table: 0.130 Process input model: 42.290 Find NCS groups from input model: 0.510 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:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 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 0.181 13560 Z= 0.376 Angle : 0.781 11.051 19424 Z= 0.443 Chirality : 0.047 0.273 2203 Planarity : 0.007 0.091 1565 Dihedral : 26.182 147.980 5727 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.13 % Allowed : 0.64 % Favored : 99.23 % 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: -1.57 (0.23), residues: 919 helix: -0.64 (0.18), residues: 562 sheet: -1.57 (0.76), residues: 45 loop : -1.45 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 243 HIS 0.003 0.001 HIS F 75 PHE 0.020 0.002 PHE C 25 TYR 0.035 0.002 TYR F 98 ARG 0.016 0.001 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7827 (mtt180) cc_final: 0.7615 (mtt180) REVERT: B 77 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7955 (mtpp) REVERT: C 77 ARG cc_start: 0.7336 (ttm-80) cc_final: 0.7005 (mmm-85) REVERT: C 99 ARG cc_start: 0.6674 (mpt90) cc_final: 0.6363 (mmp80) REVERT: D 73 GLU cc_start: 0.7403 (tp30) cc_final: 0.7113 (tp30) REVERT: E 52 ARG cc_start: 0.7756 (mtt180) cc_final: 0.6896 (mtt180) REVERT: G 20 ARG cc_start: 0.7482 (ptp-170) cc_final: 0.7055 (ptp-110) REVERT: H 40 LYS cc_start: 0.7912 (mttt) cc_final: 0.7679 (mtpt) REVERT: H 82 LYS cc_start: 0.7902 (mmtm) cc_final: 0.7513 (mmpt) REVERT: H 92 GLN cc_start: 0.8447 (tt0) cc_final: 0.8164 (tt0) REVERT: K 149 MET cc_start: 0.0616 (pmm) cc_final: -0.0117 (mmt) REVERT: K 151 MET cc_start: 0.1261 (pmm) cc_final: 0.0652 (pmm) outliers start: 1 outliers final: 1 residues processed: 183 average time/residue: 2.1354 time to fit residues: 410.3127 Evaluate side-chains 114 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 106 optimal weight: 40.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN E 93 GLN H 44 GLN K 146 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13560 Z= 0.165 Angle : 0.524 7.031 19424 Z= 0.312 Chirality : 0.034 0.133 2203 Planarity : 0.005 0.055 1565 Dihedral : 29.299 153.570 3891 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.83 % Allowed : 12.61 % Favored : 84.56 % 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: 0.15 (0.26), residues: 919 helix: 0.94 (0.21), residues: 563 sheet: -1.70 (0.71), residues: 49 loop : -1.06 (0.30), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 243 HIS 0.003 0.001 HIS G 31 PHE 0.012 0.001 PHE H 67 TYR 0.011 0.001 TYR F 98 ARG 0.008 0.000 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.8283 (mtmt) cc_final: 0.7989 (mtpp) REVERT: C 77 ARG cc_start: 0.7320 (ttm-80) cc_final: 0.6847 (mmm-85) REVERT: C 99 ARG cc_start: 0.6675 (mpt90) cc_final: 0.6139 (mmm160) REVERT: D 75 SER cc_start: 0.8410 (t) cc_final: 0.8181 (p) REVERT: D 83 ARG cc_start: 0.7247 (mmt90) cc_final: 0.6820 (mtp85) REVERT: E 52 ARG cc_start: 0.7619 (mtt180) cc_final: 0.6924 (mtt180) REVERT: G 95 LYS cc_start: 0.7824 (ttmt) cc_final: 0.7487 (mttt) REVERT: H 40 LYS cc_start: 0.7888 (mttt) cc_final: 0.7665 (mtpt) REVERT: H 82 LYS cc_start: 0.7907 (mmtm) cc_final: 0.7554 (mmpt) REVERT: H 90 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: H 92 GLN cc_start: 0.8465 (tt0) cc_final: 0.8098 (tt0) REVERT: K 149 MET cc_start: 0.0571 (pmm) cc_final: -0.0124 (mmt) REVERT: K 151 MET cc_start: 0.1324 (pmm) cc_final: 0.0701 (pmm) outliers start: 22 outliers final: 10 residues processed: 137 average time/residue: 1.9412 time to fit residues: 281.0777 Evaluate side-chains 120 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS C 73 ASN H 44 GLN H 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13560 Z= 0.335 Angle : 0.628 6.957 19424 Z= 0.362 Chirality : 0.040 0.143 2203 Planarity : 0.006 0.053 1565 Dihedral : 29.959 161.538 3889 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.73 % Allowed : 15.06 % Favored : 81.21 % 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: 0.27 (0.26), residues: 919 helix: 1.09 (0.21), residues: 560 sheet: -1.32 (0.67), residues: 57 loop : -1.18 (0.31), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 284 HIS 0.005 0.001 HIS G 31 PHE 0.016 0.002 PHE C 25 TYR 0.017 0.002 TYR F 51 ARG 0.005 0.001 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6932 (mt-10) REVERT: B 77 LYS cc_start: 0.8313 (mtmt) cc_final: 0.7928 (mtpp) REVERT: C 77 ARG cc_start: 0.7483 (ttm-80) cc_final: 0.6896 (mmm-85) REVERT: D 88 SER cc_start: 0.8795 (OUTLIER) cc_final: 0.8520 (m) REVERT: D 110 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6926 (mm-30) REVERT: E 52 ARG cc_start: 0.7615 (mtt180) cc_final: 0.7319 (mtt90) REVERT: E 129 ARG cc_start: 0.7400 (tpt90) cc_final: 0.7017 (tpt90) REVERT: F 39 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.6984 (mtt90) REVERT: G 95 LYS cc_start: 0.8032 (ttmt) cc_final: 0.7714 (mttm) REVERT: H 40 LYS cc_start: 0.8097 (mttt) cc_final: 0.7837 (mtmt) REVERT: H 82 LYS cc_start: 0.8019 (mmtm) cc_final: 0.7642 (mmpt) REVERT: K 149 MET cc_start: 0.0314 (pmm) cc_final: -0.0297 (mmt) REVERT: K 151 MET cc_start: 0.1383 (pmm) cc_final: 0.1002 (pmm) REVERT: K 164 MET cc_start: 0.3966 (ttp) cc_final: 0.3169 (pmt) outliers start: 29 outliers final: 19 residues processed: 133 average time/residue: 1.7882 time to fit residues: 253.2617 Evaluate side-chains 121 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 55 optimal weight: 0.2980 chunk 11 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13560 Z= 0.232 Angle : 0.552 7.026 19424 Z= 0.325 Chirality : 0.036 0.138 2203 Planarity : 0.005 0.048 1565 Dihedral : 29.568 159.469 3889 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.73 % Allowed : 18.15 % Favored : 78.12 % 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: 0.71 (0.27), residues: 919 helix: 1.40 (0.21), residues: 569 sheet: -1.41 (0.73), residues: 49 loop : -0.94 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 243 HIS 0.005 0.001 HIS G 31 PHE 0.011 0.002 PHE C 25 TYR 0.013 0.002 TYR G 57 ARG 0.007 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 104 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.8403 (mtmt) cc_final: 0.7858 (mtpp) REVERT: C 50 TYR cc_start: 0.9107 (t80) cc_final: 0.8897 (t80) REVERT: C 77 ARG cc_start: 0.7473 (ttm-80) cc_final: 0.7051 (mmm-85) REVERT: D 83 ARG cc_start: 0.7515 (mmt90) cc_final: 0.7061 (mtp85) REVERT: D 110 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6861 (mm-30) REVERT: E 52 ARG cc_start: 0.7551 (mtt180) cc_final: 0.7255 (mtt90) REVERT: E 129 ARG cc_start: 0.7304 (tpt90) cc_final: 0.6872 (tpt90) REVERT: F 39 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.6924 (mtt90) REVERT: G 95 LYS cc_start: 0.8009 (ttmt) cc_final: 0.7718 (mttt) REVERT: H 40 LYS cc_start: 0.8016 (mttt) cc_final: 0.7760 (mttt) REVERT: H 82 LYS cc_start: 0.8058 (mmtm) cc_final: 0.7677 (mmpt) REVERT: H 92 GLN cc_start: 0.8433 (tt0) cc_final: 0.8150 (tt0) REVERT: K 149 MET cc_start: 0.0137 (pmm) cc_final: -0.0447 (mmt) REVERT: K 151 MET cc_start: 0.1486 (pmm) cc_final: 0.1123 (pmm) REVERT: K 164 MET cc_start: 0.3533 (ttp) cc_final: 0.2912 (pmt) outliers start: 29 outliers final: 19 residues processed: 117 average time/residue: 1.9096 time to fit residues: 236.8568 Evaluate side-chains 119 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.0000 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13560 Z= 0.293 Angle : 0.598 7.000 19424 Z= 0.348 Chirality : 0.038 0.145 2203 Planarity : 0.005 0.048 1565 Dihedral : 29.823 162.214 3889 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.25 % Allowed : 18.53 % Favored : 77.22 % 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: 0.65 (0.27), residues: 919 helix: 1.32 (0.21), residues: 567 sheet: -1.30 (0.75), residues: 48 loop : -0.90 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 270 HIS 0.006 0.001 HIS G 31 PHE 0.013 0.002 PHE C 25 TYR 0.017 0.002 TYR F 51 ARG 0.005 0.001 ARG K 276 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 102 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6862 (mt-10) REVERT: A 120 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8158 (mtm) REVERT: B 77 LYS cc_start: 0.8415 (mtmt) cc_final: 0.7882 (mtpp) REVERT: C 77 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.7127 (mmm-85) REVERT: D 83 ARG cc_start: 0.7665 (mmt90) cc_final: 0.7170 (mtp85) REVERT: D 110 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6857 (mm-30) REVERT: E 52 ARG cc_start: 0.7553 (mtt180) cc_final: 0.7161 (mtt90) REVERT: E 129 ARG cc_start: 0.7444 (tpt90) cc_final: 0.7002 (tpt90) REVERT: F 39 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.6848 (mtt90) REVERT: G 95 LYS cc_start: 0.8037 (ttmt) cc_final: 0.7718 (mttm) REVERT: G 110 ASN cc_start: 0.7211 (t0) cc_final: 0.6994 (t0) REVERT: H 40 LYS cc_start: 0.8077 (mttt) cc_final: 0.7821 (mttt) REVERT: H 82 LYS cc_start: 0.7799 (mmtm) cc_final: 0.7469 (mmpt) REVERT: K 98 LEU cc_start: 0.3270 (OUTLIER) cc_final: 0.2963 (mt) REVERT: K 149 MET cc_start: -0.0236 (pmm) cc_final: -0.0725 (mmt) REVERT: K 151 MET cc_start: 0.1823 (pmm) cc_final: 0.1586 (pmm) outliers start: 33 outliers final: 22 residues processed: 119 average time/residue: 1.7338 time to fit residues: 219.8164 Evaluate side-chains 120 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 95 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 98 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 0.0570 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13560 Z= 0.221 Angle : 0.565 7.020 19424 Z= 0.334 Chirality : 0.037 0.156 2203 Planarity : 0.005 0.055 1565 Dihedral : 29.730 162.380 3889 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.25 % Allowed : 19.56 % Favored : 76.19 % 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: 0.86 (0.27), residues: 919 helix: 1.53 (0.22), residues: 567 sheet: -1.50 (0.89), residues: 37 loop : -0.90 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 270 HIS 0.005 0.001 HIS G 31 PHE 0.011 0.002 PHE A 67 TYR 0.019 0.002 TYR F 88 ARG 0.004 0.000 ARG K 276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 101 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6946 (mt-10) REVERT: A 120 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8141 (mtm) REVERT: B 77 LYS cc_start: 0.8493 (mtmt) cc_final: 0.7973 (mtpp) REVERT: C 50 TYR cc_start: 0.9107 (t80) cc_final: 0.8899 (t80) REVERT: C 77 ARG cc_start: 0.7459 (ttm-80) cc_final: 0.6950 (mmm-85) REVERT: D 83 ARG cc_start: 0.7645 (mmt90) cc_final: 0.7159 (mtp85) REVERT: E 52 ARG cc_start: 0.7505 (mtt180) cc_final: 0.6857 (mtt180) REVERT: E 129 ARG cc_start: 0.7354 (tpt90) cc_final: 0.6914 (tpt90) REVERT: F 39 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.6806 (mtt90) REVERT: G 95 LYS cc_start: 0.8042 (ttmt) cc_final: 0.7709 (mttt) REVERT: H 40 LYS cc_start: 0.8067 (mttt) cc_final: 0.7809 (mttt) REVERT: H 82 LYS cc_start: 0.7907 (mmtm) cc_final: 0.7546 (mmpt) REVERT: K 149 MET cc_start: -0.0161 (pmm) cc_final: -0.0752 (mmt) REVERT: K 151 MET cc_start: 0.1848 (pmm) cc_final: 0.1602 (pmm) outliers start: 33 outliers final: 23 residues processed: 120 average time/residue: 1.8524 time to fit residues: 235.7922 Evaluate side-chains 122 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13560 Z= 0.191 Angle : 0.550 7.062 19424 Z= 0.325 Chirality : 0.035 0.135 2203 Planarity : 0.004 0.045 1565 Dihedral : 29.612 162.508 3889 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.86 % Allowed : 20.21 % Favored : 75.93 % 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: 1.06 (0.27), residues: 919 helix: 1.69 (0.22), residues: 567 sheet: -0.99 (1.12), residues: 25 loop : -0.91 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 270 HIS 0.004 0.001 HIS G 31 PHE 0.010 0.001 PHE H 67 TYR 0.016 0.002 TYR C 57 ARG 0.013 0.001 ARG K 109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 101 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7312 (mt-10) cc_final: 0.6930 (mt-10) REVERT: B 77 LYS cc_start: 0.8471 (mtmt) cc_final: 0.8019 (mtpp) REVERT: C 77 ARG cc_start: 0.7437 (ttm-80) cc_final: 0.6924 (mmm-85) REVERT: D 83 ARG cc_start: 0.7571 (mmt90) cc_final: 0.7073 (mtp85) REVERT: E 52 ARG cc_start: 0.7491 (mtt180) cc_final: 0.6857 (mtt180) REVERT: E 129 ARG cc_start: 0.7338 (tpt90) cc_final: 0.6893 (tpt90) REVERT: F 39 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.6844 (mtt90) REVERT: F 92 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6696 (ttp80) REVERT: G 95 LYS cc_start: 0.7988 (ttmt) cc_final: 0.7678 (mttt) REVERT: H 40 LYS cc_start: 0.8031 (mttt) cc_final: 0.7782 (mttt) REVERT: H 82 LYS cc_start: 0.7912 (mmtm) cc_final: 0.7541 (mmpt) REVERT: K 149 MET cc_start: -0.0175 (pmm) cc_final: -0.0763 (mmt) REVERT: K 151 MET cc_start: 0.1877 (pmm) cc_final: 0.1626 (pmm) outliers start: 30 outliers final: 21 residues processed: 115 average time/residue: 1.9343 time to fit residues: 235.4846 Evaluate side-chains 120 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.0370 chunk 33 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 108 optimal weight: 0.7980 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13560 Z= 0.185 Angle : 0.538 7.070 19424 Z= 0.318 Chirality : 0.035 0.138 2203 Planarity : 0.004 0.045 1565 Dihedral : 29.413 162.591 3889 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.47 % Allowed : 21.11 % Favored : 75.42 % 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: 1.22 (0.27), residues: 919 helix: 1.81 (0.22), residues: 569 sheet: -1.12 (0.95), residues: 31 loop : -0.81 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 270 HIS 0.004 0.001 HIS G 31 PHE 0.009 0.001 PHE H 67 TYR 0.019 0.001 TYR C 57 ARG 0.006 0.000 ARG K 109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7001 (mt-10) REVERT: B 77 LYS cc_start: 0.8382 (mtmt) cc_final: 0.7912 (mtpp) REVERT: C 72 ASP cc_start: 0.6385 (OUTLIER) cc_final: 0.5952 (t0) REVERT: C 77 ARG cc_start: 0.7439 (ttm-80) cc_final: 0.6917 (mmm-85) REVERT: D 83 ARG cc_start: 0.7517 (mmt90) cc_final: 0.7045 (mtp85) REVERT: E 52 ARG cc_start: 0.7414 (mtt180) cc_final: 0.6753 (mtt180) REVERT: E 129 ARG cc_start: 0.7364 (tpt90) cc_final: 0.6914 (tpt90) REVERT: F 39 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.6840 (mtt90) REVERT: G 95 LYS cc_start: 0.7968 (ttmt) cc_final: 0.7676 (mttt) REVERT: H 40 LYS cc_start: 0.8014 (mttt) cc_final: 0.7758 (mttt) REVERT: H 82 LYS cc_start: 0.7964 (mmtm) cc_final: 0.7639 (mmpt) REVERT: K 149 MET cc_start: 0.0175 (pmm) cc_final: -0.0448 (mmt) outliers start: 27 outliers final: 21 residues processed: 113 average time/residue: 2.1978 time to fit residues: 263.9043 Evaluate side-chains 120 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 20.0000 chunk 105 optimal weight: 0.2980 chunk 108 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13560 Z= 0.193 Angle : 0.539 7.118 19424 Z= 0.318 Chirality : 0.035 0.156 2203 Planarity : 0.004 0.045 1565 Dihedral : 29.354 163.475 3889 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.35 % Allowed : 21.49 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.27 (0.27), residues: 919 helix: 1.82 (0.22), residues: 569 sheet: -0.96 (0.99), residues: 31 loop : -0.75 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 243 HIS 0.004 0.001 HIS G 31 PHE 0.010 0.001 PHE H 67 TYR 0.023 0.002 TYR C 57 ARG 0.007 0.000 ARG K 109 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7038 (mtp-110) cc_final: 0.6829 (mtp180) REVERT: A 105 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6985 (mt-10) REVERT: B 77 LYS cc_start: 0.8379 (mtmt) cc_final: 0.7909 (mtpp) REVERT: C 72 ASP cc_start: 0.6469 (OUTLIER) cc_final: 0.6021 (t0) REVERT: C 77 ARG cc_start: 0.7441 (ttm-80) cc_final: 0.6926 (mmm-85) REVERT: D 83 ARG cc_start: 0.7483 (mmt90) cc_final: 0.7045 (mtp85) REVERT: E 52 ARG cc_start: 0.7421 (mtt180) cc_final: 0.6830 (mtt180) REVERT: E 129 ARG cc_start: 0.7384 (tpt90) cc_final: 0.6931 (tpt90) REVERT: F 39 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.6787 (mtt90) REVERT: F 74 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7221 (mt-10) REVERT: F 92 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.6833 (ttp80) REVERT: G 95 LYS cc_start: 0.7924 (ttmt) cc_final: 0.7626 (mttt) REVERT: H 40 LYS cc_start: 0.8024 (mttt) cc_final: 0.7763 (mttt) REVERT: H 82 LYS cc_start: 0.7872 (mmtm) cc_final: 0.7564 (mmpt) REVERT: K 149 MET cc_start: 0.0261 (pmm) cc_final: -0.0349 (mmt) outliers start: 26 outliers final: 19 residues processed: 114 average time/residue: 1.8742 time to fit residues: 226.5280 Evaluate side-chains 120 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 52 optimal weight: 0.0070 chunk 77 optimal weight: 6.9990 chunk 116 optimal weight: 30.0000 chunk 107 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 9 optimal weight: 0.0970 chunk 71 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13560 Z= 0.236 Angle : 0.564 7.037 19424 Z= 0.330 Chirality : 0.036 0.158 2203 Planarity : 0.005 0.048 1565 Dihedral : 29.485 166.992 3889 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.22 % Allowed : 21.49 % Favored : 75.29 % 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: 1.12 (0.27), residues: 919 helix: 1.70 (0.22), residues: 568 sheet: -1.04 (1.00), residues: 31 loop : -0.81 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 243 HIS 0.006 0.001 HIS G 31 PHE 0.010 0.002 PHE H 67 TYR 0.022 0.002 TYR C 57 ARG 0.012 0.001 ARG K 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 101 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7182 (mtp-110) cc_final: 0.6897 (mtp180) REVERT: A 105 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6961 (mt-10) REVERT: A 120 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8250 (mtm) REVERT: B 77 LYS cc_start: 0.8476 (mtmt) cc_final: 0.8033 (mtpp) REVERT: C 72 ASP cc_start: 0.6348 (OUTLIER) cc_final: 0.5918 (t0) REVERT: C 77 ARG cc_start: 0.7459 (ttm-80) cc_final: 0.6936 (mmm-85) REVERT: D 83 ARG cc_start: 0.7538 (mmt90) cc_final: 0.7094 (mtp85) REVERT: E 52 ARG cc_start: 0.7463 (mtt180) cc_final: 0.7188 (mtt90) REVERT: E 129 ARG cc_start: 0.7408 (tpt90) cc_final: 0.6942 (tpt90) REVERT: F 39 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.6835 (mtt90) REVERT: F 92 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.6789 (ttp80) REVERT: G 95 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7664 (mttm) REVERT: H 40 LYS cc_start: 0.8033 (mttt) cc_final: 0.7775 (mttt) REVERT: H 82 LYS cc_start: 0.7773 (mmtm) cc_final: 0.7364 (mmpt) REVERT: K 149 MET cc_start: 0.0031 (pmm) cc_final: -0.0296 (mmt) outliers start: 25 outliers final: 19 residues processed: 112 average time/residue: 1.9958 time to fit residues: 236.6440 Evaluate side-chains 119 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 81 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.200799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.157669 restraints weight = 14644.894| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.15 r_work: 0.3321 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13560 Z= 0.230 Angle : 0.558 7.051 19424 Z= 0.328 Chirality : 0.036 0.157 2203 Planarity : 0.004 0.045 1565 Dihedral : 29.432 167.513 3889 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.22 % Allowed : 21.75 % Favored : 75.03 % 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: 1.11 (0.27), residues: 919 helix: 1.70 (0.22), residues: 569 sheet: -1.17 (0.99), residues: 31 loop : -0.81 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 243 HIS 0.005 0.001 HIS G 31 PHE 0.010 0.002 PHE A 67 TYR 0.024 0.002 TYR C 57 ARG 0.009 0.001 ARG F 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4435.12 seconds wall clock time: 79 minutes 24.82 seconds (4764.82 seconds total)