Starting phenix.real_space_refine on Tue Feb 13 10:18:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sax_24958/02_2024/7sax_24958.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sax_24958/02_2024/7sax_24958.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sax_24958/02_2024/7sax_24958.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sax_24958/02_2024/7sax_24958.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sax_24958/02_2024/7sax_24958.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sax_24958/02_2024/7sax_24958.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= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 3431 2.51 5 N 882 2.21 5 O 964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "B ASP 114": "OD1" <-> "OD2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 47": "OE1" <-> "OE2" 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: 5305 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1627 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 6, 'TRANS': 206} Chain: "B" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1614 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain: "C" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 473 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "D" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 430 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "E" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} Chain: "F" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} Chain: "G" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} Time building chain proxies: 3.49, per 1000 atoms: 0.66 Number of scatterers: 5305 At special positions: 0 Unit cell: (66.56, 58.24, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 964 8.00 N 882 7.00 C 3431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 965.8 milliseconds 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1232 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 7 through 25 removed outlier: 3.823A pdb=" N ALA A 25 " --> pdb=" O LEU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 69 removed outlier: 5.074A pdb=" N LEU A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU A 68 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 104 Proline residue: A 75 - end of helix removed outlier: 3.592A pdb=" N VAL A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 88 " --> pdb=" O GLN A 84 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 132 through 153 removed outlier: 3.690A pdb=" N GLU A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 185 through 215 removed outlier: 4.253A pdb=" N MET A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 28 removed outlier: 5.295A pdb=" N LEU B 18 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 63 Processing helix chain 'B' and resid 69 through 104 Proline residue: B 75 - end of helix removed outlier: 3.716A pdb=" N LEU B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 128 Processing helix chain 'B' and resid 132 through 153 removed outlier: 3.519A pdb=" N LEU B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 180 Processing helix chain 'B' and resid 185 through 214 Processing helix chain 'C' and resid 10 through 31 removed outlier: 4.013A pdb=" N LEU C 14 " --> pdb=" O GLY C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 58 removed outlier: 3.869A pdb=" N ILE C 40 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLY C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 31 removed outlier: 3.804A pdb=" N LEU D 14 " --> pdb=" O GLY D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 55 removed outlier: 4.277A pdb=" N MET D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY D 55 " --> pdb=" O PHE D 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 31 removed outlier: 3.750A pdb=" N LEU E 14 " --> pdb=" O GLY E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 54 removed outlier: 3.899A pdb=" N GLY E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'F' and resid 10 through 31 removed outlier: 4.125A pdb=" N LEU F 14 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE F 15 " --> pdb=" O ILE F 11 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 55 Processing helix chain 'G' and resid 10 through 31 removed outlier: 4.011A pdb=" N LEU G 14 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 55 removed outlier: 4.193A pdb=" N MET G 39 " --> pdb=" O GLY G 35 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY G 41 " --> pdb=" O GLU G 37 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1709 1.34 - 1.46: 681 1.46 - 1.57: 2938 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 5384 Sorted by residual: bond pdb=" CG1 ILE D 15 " pdb=" CD1 ILE D 15 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.74e+00 bond pdb=" CB MET A 12 " pdb=" CG MET A 12 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.60e+00 bond pdb=" CB MET E 54 " pdb=" CG MET E 54 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.33e+00 bond pdb=" CG1 ILE B 15 " pdb=" CD1 ILE B 15 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.28e+00 bond pdb=" CG1 ILE D 23 " pdb=" CD1 ILE D 23 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.26e+00 ... (remaining 5379 not shown) Histogram of bond angle deviations from ideal: 96.15 - 103.72: 56 103.72 - 111.29: 2357 111.29 - 118.86: 2097 118.86 - 126.43: 2673 126.43 - 134.00: 72 Bond angle restraints: 7255 Sorted by residual: angle pdb=" CB MET D 54 " pdb=" CG MET D 54 " pdb=" SD MET D 54 " ideal model delta sigma weight residual 112.70 100.94 11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C ILE E 53 " pdb=" N MET E 54 " pdb=" CA MET E 54 " ideal model delta sigma weight residual 122.31 115.73 6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CB MET E 54 " pdb=" CG MET E 54 " pdb=" SD MET E 54 " ideal model delta sigma weight residual 112.70 103.40 9.30 3.00e+00 1.11e-01 9.62e+00 angle pdb=" C ARG A 11 " pdb=" N MET A 12 " pdb=" CA MET A 12 " ideal model delta sigma weight residual 122.06 116.31 5.75 1.86e+00 2.89e-01 9.55e+00 angle pdb=" CA ARG A 9 " pdb=" CB ARG A 9 " pdb=" CG ARG A 9 " ideal model delta sigma weight residual 114.10 118.91 -4.81 2.00e+00 2.50e-01 5.79e+00 ... (remaining 7250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 2882 17.57 - 35.14: 267 35.14 - 52.71: 38 52.71 - 70.28: 8 70.28 - 87.85: 2 Dihedral angle restraints: 3197 sinusoidal: 1279 harmonic: 1918 Sorted by residual: dihedral pdb=" CA MET E 54 " pdb=" C MET E 54 " pdb=" N GLY E 55 " pdb=" CA GLY E 55 " ideal model delta harmonic sigma weight residual 180.00 157.94 22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA VAL A 115 " pdb=" C VAL A 115 " pdb=" N LYS A 116 " pdb=" CA LYS A 116 " 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=" CA MET A 12 " pdb=" C MET A 12 " pdb=" N ILE A 13 " pdb=" CA ILE A 13 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 3194 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 589 0.043 - 0.086: 234 0.086 - 0.130: 24 0.130 - 0.173: 5 0.173 - 0.216: 2 Chirality restraints: 854 Sorted by residual: chirality pdb=" CB VAL F 22 " pdb=" CA VAL F 22 " pdb=" CG1 VAL F 22 " pdb=" CG2 VAL F 22 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE B 156 " pdb=" CA ILE B 156 " pdb=" CG1 ILE B 156 " pdb=" CG2 ILE B 156 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CA MET E 54 " pdb=" N MET E 54 " pdb=" C MET E 54 " pdb=" CB MET E 54 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 851 not shown) Planarity restraints: 908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 52 " 0.011 2.00e-02 2.50e+03 1.13e-02 2.24e+00 pdb=" CG PHE C 52 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE C 52 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C 52 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE C 52 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 52 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 52 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 12 " 0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C MET A 12 " -0.021 2.00e-02 2.50e+03 pdb=" O MET A 12 " 0.008 2.00e-02 2.50e+03 pdb=" N ILE A 13 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 9 " 0.005 2.00e-02 2.50e+03 1.04e-02 1.09e+00 pdb=" C ARG A 9 " -0.018 2.00e-02 2.50e+03 pdb=" O ARG A 9 " 0.007 2.00e-02 2.50e+03 pdb=" N GLN A 10 " 0.006 2.00e-02 2.50e+03 ... (remaining 905 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 234 2.72 - 3.26: 5640 3.26 - 3.81: 8814 3.81 - 4.35: 10573 4.35 - 4.90: 18257 Nonbonded interactions: 43518 Sorted by model distance: nonbonded pdb=" NH1 ARG B 9 " pdb=" OE2 GLU C 47 " model vdw 2.174 2.520 nonbonded pdb=" O ALA B 60 " pdb=" OG1 THR B 64 " model vdw 2.232 2.440 nonbonded pdb=" NE2 GLN A 51 " pdb=" OD1 ASP A 55 " model vdw 2.240 2.520 nonbonded pdb=" OG1 THR A 112 " pdb=" OD1 ASP A 114 " model vdw 2.262 2.440 nonbonded pdb=" OE1 GLU A 131 " pdb=" NH1 ARG A 133 " model vdw 2.283 2.520 ... (remaining 43513 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 5 through 215) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 9 through 60) selection = (chain 'D' and resid 9 through 60) } ncs_group { reference = (chain 'E' and resid 9 through 57) selection = (chain 'F' and resid 9 through 57) selection = (chain 'G' and resid 9 through 57) } 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: 0.010 Normalize map: mean=0, sd=1: 0.830 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: 0.000 Extract box with map and model: 3.910 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.620 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:11.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 : 0.007 0.085 5384 Z= 0.469 Angle : 0.660 11.764 7255 Z= 0.344 Chirality : 0.044 0.216 854 Planarity : 0.003 0.018 908 Dihedral : 13.544 87.846 1965 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.33), residues: 675 helix: 1.69 (0.23), residues: 507 sheet: None (None), residues: 0 loop : -2.01 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 38 HIS 0.002 0.001 HIS D 32 PHE 0.026 0.002 PHE C 52 TYR 0.017 0.003 TYR A 117 ARG 0.014 0.001 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.590 Fit side-chains REVERT: A 6 GLU cc_start: 0.7621 (pt0) cc_final: 0.7325 (pt0) REVERT: A 10 GLN cc_start: 0.7704 (mt0) cc_final: 0.7308 (mt0) REVERT: A 88 GLN cc_start: 0.7893 (tp40) cc_final: 0.7247 (tm-30) REVERT: A 96 GLU cc_start: 0.7158 (pt0) cc_final: 0.6717 (mt-10) REVERT: B 34 ASP cc_start: 0.7712 (m-30) cc_final: 0.7494 (m-30) REVERT: B 62 ARG cc_start: 0.7276 (ttm-80) cc_final: 0.7042 (mmt-90) REVERT: B 147 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6974 (mt-10) REVERT: B 194 GLU cc_start: 0.7372 (tp30) cc_final: 0.6803 (tp30) REVERT: B 205 SER cc_start: 0.8607 (p) cc_final: 0.8398 (p) REVERT: C 37 GLU cc_start: 0.7341 (mp0) cc_final: 0.7128 (mp0) REVERT: C 54 MET cc_start: 0.7212 (mmm) cc_final: 0.6882 (mmm) REVERT: D 6 LYS cc_start: 0.5783 (ptpp) cc_final: 0.5258 (ptmt) REVERT: F 34 LYS cc_start: 0.8063 (ttpt) cc_final: 0.7592 (tppt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 1.1216 time to fit residues: 170.7599 Evaluate side-chains 122 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 0.0970 chunk 53 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5384 Z= 0.144 Angle : 0.452 5.733 7255 Z= 0.240 Chirality : 0.036 0.152 854 Planarity : 0.003 0.017 908 Dihedral : 3.922 15.485 705 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.13 % Allowed : 12.93 % Favored : 82.94 % 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: 2.32 (0.33), residues: 675 helix: 2.46 (0.23), residues: 513 sheet: None (None), residues: 0 loop : -1.65 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 38 HIS 0.011 0.001 HIS A 210 PHE 0.018 0.001 PHE A 61 TYR 0.009 0.002 TYR A 117 ARG 0.003 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 0.553 Fit side-chains REVERT: A 6 GLU cc_start: 0.7694 (pt0) cc_final: 0.7437 (pt0) REVERT: A 88 GLN cc_start: 0.7835 (tp40) cc_final: 0.7281 (tm-30) REVERT: A 139 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6940 (pt0) REVERT: A 163 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6720 (mm-30) REVERT: B 147 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6711 (mt-10) REVERT: B 194 GLU cc_start: 0.7311 (tp30) cc_final: 0.6758 (tp30) REVERT: B 205 SER cc_start: 0.8562 (p) cc_final: 0.8354 (p) REVERT: B 209 LYS cc_start: 0.8255 (tttp) cc_final: 0.7969 (ttpm) REVERT: C 37 GLU cc_start: 0.7217 (mp0) cc_final: 0.7013 (mp0) REVERT: C 54 MET cc_start: 0.7275 (mmm) cc_final: 0.6938 (mmm) REVERT: D 6 LYS cc_start: 0.5521 (ptpp) cc_final: 0.4940 (ptmt) REVERT: F 34 LYS cc_start: 0.7809 (ttpt) cc_final: 0.7391 (tppt) outliers start: 23 outliers final: 5 residues processed: 134 average time/residue: 1.0684 time to fit residues: 149.8643 Evaluate side-chains 127 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain F residue 27 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 55 optimal weight: 0.0570 chunk 21 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN B 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5384 Z= 0.127 Angle : 0.435 6.575 7255 Z= 0.230 Chirality : 0.036 0.158 854 Planarity : 0.002 0.018 908 Dihedral : 3.689 13.389 705 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.49 % Allowed : 15.26 % Favored : 80.25 % 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: 2.64 (0.33), residues: 675 helix: 2.76 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.84 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 38 HIS 0.007 0.001 HIS A 210 PHE 0.027 0.001 PHE C 52 TYR 0.010 0.002 TYR B 17 ARG 0.006 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 0.569 Fit side-chains REVERT: A 6 GLU cc_start: 0.7682 (pt0) cc_final: 0.7421 (pt0) REVERT: A 88 GLN cc_start: 0.7775 (tp40) cc_final: 0.7134 (tm-30) REVERT: A 163 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6781 (mm-30) REVERT: B 48 GLN cc_start: 0.8265 (mt0) cc_final: 0.8041 (mt0) REVERT: B 63 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6526 (pm20) REVERT: B 194 GLU cc_start: 0.7349 (tp30) cc_final: 0.6787 (tp30) REVERT: B 205 SER cc_start: 0.8563 (p) cc_final: 0.8361 (p) REVERT: B 209 LYS cc_start: 0.8282 (tttp) cc_final: 0.7973 (ttpm) REVERT: C 54 MET cc_start: 0.7178 (mmm) cc_final: 0.6814 (mmm) REVERT: D 6 LYS cc_start: 0.5449 (ptpp) cc_final: 0.4914 (ptmt) REVERT: E 47 GLU cc_start: 0.7342 (tp30) cc_final: 0.6837 (tp30) outliers start: 25 outliers final: 7 residues processed: 132 average time/residue: 1.1153 time to fit residues: 153.5129 Evaluate side-chains 129 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain F residue 27 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 0.0170 chunk 29 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 58 optimal weight: 0.0980 chunk 17 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5384 Z= 0.124 Angle : 0.437 7.683 7255 Z= 0.228 Chirality : 0.036 0.142 854 Planarity : 0.002 0.021 908 Dihedral : 3.571 13.636 705 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 5.39 % Allowed : 16.34 % Favored : 78.28 % 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: 2.84 (0.33), residues: 675 helix: 2.90 (0.22), residues: 514 sheet: None (None), residues: 0 loop : -1.77 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 38 HIS 0.006 0.001 HIS A 210 PHE 0.026 0.001 PHE C 52 TYR 0.009 0.002 TYR B 17 ARG 0.006 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 129 time to evaluate : 1.146 Fit side-chains REVERT: A 6 GLU cc_start: 0.7647 (pt0) cc_final: 0.7379 (pt0) REVERT: A 10 GLN cc_start: 0.7315 (mt0) cc_final: 0.7025 (mt0) REVERT: A 88 GLN cc_start: 0.7757 (tp40) cc_final: 0.7089 (tm-30) REVERT: A 163 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6795 (mm-30) REVERT: B 48 GLN cc_start: 0.8308 (mt0) cc_final: 0.8084 (mt0) REVERT: B 63 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6272 (pm20) REVERT: B 99 THR cc_start: 0.8121 (t) cc_final: 0.7816 (p) REVERT: B 194 GLU cc_start: 0.7338 (tp30) cc_final: 0.6787 (tp30) REVERT: B 205 SER cc_start: 0.8566 (p) cc_final: 0.8357 (p) REVERT: B 209 LYS cc_start: 0.8307 (tttp) cc_final: 0.8010 (ttpm) REVERT: D 6 LYS cc_start: 0.5426 (ptpp) cc_final: 0.4877 (ptmt) REVERT: E 47 GLU cc_start: 0.7387 (tp30) cc_final: 0.6768 (tp30) outliers start: 30 outliers final: 10 residues processed: 136 average time/residue: 1.1647 time to fit residues: 165.9770 Evaluate side-chains 138 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain F residue 27 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5384 Z= 0.154 Angle : 0.455 6.314 7255 Z= 0.239 Chirality : 0.037 0.139 854 Planarity : 0.002 0.023 908 Dihedral : 3.624 14.433 705 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.31 % Allowed : 19.03 % Favored : 76.66 % 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: 2.85 (0.33), residues: 675 helix: 2.92 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.76 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 38 HIS 0.011 0.001 HIS A 210 PHE 0.023 0.001 PHE C 52 TYR 0.011 0.002 TYR B 17 ARG 0.006 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 0.573 Fit side-chains REVERT: A 6 GLU cc_start: 0.7618 (pt0) cc_final: 0.7366 (pt0) REVERT: A 10 GLN cc_start: 0.7317 (mt0) cc_final: 0.7096 (mt0) REVERT: A 88 GLN cc_start: 0.7779 (tp40) cc_final: 0.7102 (tm-30) REVERT: A 163 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6850 (mm-30) REVERT: B 48 GLN cc_start: 0.8304 (mt0) cc_final: 0.8075 (mt0) REVERT: B 63 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6360 (pm20) REVERT: B 102 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6777 (mt-10) REVERT: B 194 GLU cc_start: 0.7362 (tp30) cc_final: 0.6806 (tp30) REVERT: B 205 SER cc_start: 0.8578 (p) cc_final: 0.8351 (p) REVERT: B 209 LYS cc_start: 0.8376 (tttp) cc_final: 0.8031 (ttpm) REVERT: D 6 LYS cc_start: 0.5340 (ptpp) cc_final: 0.4790 (ptmt) REVERT: E 47 GLU cc_start: 0.7379 (tp30) cc_final: 0.6772 (tp30) outliers start: 24 outliers final: 10 residues processed: 130 average time/residue: 1.1315 time to fit residues: 153.7053 Evaluate side-chains 133 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain F residue 27 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5384 Z= 0.158 Angle : 0.457 6.536 7255 Z= 0.241 Chirality : 0.036 0.137 854 Planarity : 0.002 0.025 908 Dihedral : 3.629 14.259 705 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.13 % Allowed : 20.29 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.88 (0.33), residues: 675 helix: 2.92 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.71 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 38 HIS 0.009 0.001 HIS A 210 PHE 0.022 0.001 PHE C 52 TYR 0.011 0.002 TYR B 17 ARG 0.006 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 0.513 Fit side-chains REVERT: A 6 GLU cc_start: 0.7681 (pt0) cc_final: 0.7401 (pt0) REVERT: A 10 GLN cc_start: 0.7354 (mt0) cc_final: 0.7144 (mt0) REVERT: A 88 GLN cc_start: 0.7776 (tp40) cc_final: 0.7089 (tm-30) REVERT: A 163 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6844 (mm-30) REVERT: B 11 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7307 (mtm-85) REVERT: B 48 GLN cc_start: 0.8297 (mt0) cc_final: 0.8058 (mt0) REVERT: B 63 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6246 (pm20) REVERT: B 99 THR cc_start: 0.8115 (t) cc_final: 0.7806 (p) REVERT: B 194 GLU cc_start: 0.7369 (tp30) cc_final: 0.6819 (tp30) REVERT: B 205 SER cc_start: 0.8583 (p) cc_final: 0.8359 (p) REVERT: B 209 LYS cc_start: 0.8380 (tttp) cc_final: 0.8105 (ttpt) REVERT: C 54 MET cc_start: 0.7205 (mmm) cc_final: 0.6661 (mmm) REVERT: D 6 LYS cc_start: 0.5340 (ptpp) cc_final: 0.4784 (ptmt) REVERT: E 47 GLU cc_start: 0.7376 (tp30) cc_final: 0.6784 (tp30) outliers start: 23 outliers final: 11 residues processed: 127 average time/residue: 1.0843 time to fit residues: 143.9128 Evaluate side-chains 136 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain F residue 27 MET Chi-restraints excluded: chain G residue 37 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.3980 chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5384 Z= 0.140 Angle : 0.450 6.845 7255 Z= 0.238 Chirality : 0.036 0.135 854 Planarity : 0.002 0.025 908 Dihedral : 3.569 13.942 705 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.95 % Allowed : 20.65 % Favored : 75.40 % 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: 2.98 (0.33), residues: 675 helix: 2.98 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -1.68 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 38 HIS 0.007 0.001 HIS A 210 PHE 0.020 0.001 PHE C 52 TYR 0.012 0.002 TYR B 17 ARG 0.006 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 0.629 Fit side-chains REVERT: A 6 GLU cc_start: 0.7582 (pt0) cc_final: 0.7317 (pt0) REVERT: A 10 GLN cc_start: 0.7279 (mt0) cc_final: 0.7070 (mt0) REVERT: A 88 GLN cc_start: 0.7740 (tp40) cc_final: 0.7099 (tm-30) REVERT: A 156 ILE cc_start: 0.7199 (tp) cc_final: 0.6851 (tt) REVERT: A 163 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6795 (mm-30) REVERT: B 11 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7313 (mtm-85) REVERT: B 48 GLN cc_start: 0.8263 (mt0) cc_final: 0.8041 (mt0) REVERT: B 63 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6245 (pm20) REVERT: B 99 THR cc_start: 0.8096 (t) cc_final: 0.7796 (p) REVERT: B 163 GLU cc_start: 0.7515 (pt0) cc_final: 0.7171 (pt0) REVERT: B 194 GLU cc_start: 0.7359 (tp30) cc_final: 0.6813 (tp30) REVERT: B 209 LYS cc_start: 0.8348 (tttp) cc_final: 0.8068 (ttpt) REVERT: C 54 MET cc_start: 0.7225 (mmm) cc_final: 0.6667 (mmm) REVERT: D 6 LYS cc_start: 0.5261 (ptpp) cc_final: 0.4723 (ptmt) REVERT: E 47 GLU cc_start: 0.7355 (tp30) cc_final: 0.6780 (tp30) outliers start: 22 outliers final: 11 residues processed: 132 average time/residue: 1.0922 time to fit residues: 150.6804 Evaluate side-chains 137 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain F residue 27 MET Chi-restraints excluded: chain G residue 37 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 36 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5384 Z= 0.133 Angle : 0.454 7.159 7255 Z= 0.240 Chirality : 0.036 0.139 854 Planarity : 0.002 0.028 908 Dihedral : 3.517 13.855 705 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.59 % Allowed : 21.36 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.33), residues: 675 helix: 3.02 (0.22), residues: 517 sheet: None (None), residues: 0 loop : -1.63 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 38 HIS 0.010 0.001 HIS A 210 PHE 0.021 0.001 PHE C 52 TYR 0.013 0.002 TYR B 17 ARG 0.007 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 0.610 Fit side-chains REVERT: A 6 GLU cc_start: 0.7599 (pt0) cc_final: 0.7324 (pt0) REVERT: A 10 GLN cc_start: 0.7272 (mt0) cc_final: 0.7025 (mt0) REVERT: A 88 GLN cc_start: 0.7683 (tp40) cc_final: 0.7031 (tm-30) REVERT: A 96 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6780 (tm-30) REVERT: A 156 ILE cc_start: 0.7188 (tp) cc_final: 0.6842 (tt) REVERT: B 48 GLN cc_start: 0.8273 (mt0) cc_final: 0.8033 (mt0) REVERT: B 63 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6253 (pm20) REVERT: B 99 THR cc_start: 0.8092 (t) cc_final: 0.7793 (p) REVERT: B 163 GLU cc_start: 0.7454 (pt0) cc_final: 0.7120 (pt0) REVERT: B 194 GLU cc_start: 0.7345 (tp30) cc_final: 0.6801 (tp30) REVERT: B 209 LYS cc_start: 0.8392 (tttp) cc_final: 0.8113 (ttpt) REVERT: C 54 MET cc_start: 0.7261 (mmm) cc_final: 0.6690 (mmm) REVERT: D 6 LYS cc_start: 0.5241 (ptpp) cc_final: 0.4704 (ptmt) REVERT: E 47 GLU cc_start: 0.7318 (tp30) cc_final: 0.6738 (tp30) outliers start: 20 outliers final: 9 residues processed: 127 average time/residue: 1.1081 time to fit residues: 146.9806 Evaluate side-chains 131 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain F residue 27 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 0.0570 chunk 55 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 30 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5384 Z= 0.130 Angle : 0.450 7.483 7255 Z= 0.239 Chirality : 0.036 0.139 854 Planarity : 0.003 0.027 908 Dihedral : 3.501 15.291 705 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.87 % Allowed : 23.34 % Favored : 73.79 % 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: 3.08 (0.33), residues: 675 helix: 3.04 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -1.61 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 38 HIS 0.010 0.001 HIS A 210 PHE 0.021 0.001 PHE C 52 TYR 0.014 0.002 TYR B 17 ARG 0.008 0.001 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 0.595 Fit side-chains REVERT: A 6 GLU cc_start: 0.7501 (pt0) cc_final: 0.7254 (pt0) REVERT: A 10 GLN cc_start: 0.7254 (mt0) cc_final: 0.7025 (mt0) REVERT: A 34 ASP cc_start: 0.7689 (m-30) cc_final: 0.7425 (m-30) REVERT: A 88 GLN cc_start: 0.7677 (tp40) cc_final: 0.7004 (tm-30) REVERT: A 96 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6777 (tm-30) REVERT: A 156 ILE cc_start: 0.7140 (tp) cc_final: 0.6874 (tt) REVERT: B 48 GLN cc_start: 0.8267 (mt0) cc_final: 0.8035 (mt0) REVERT: B 63 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6233 (pm20) REVERT: B 99 THR cc_start: 0.8091 (t) cc_final: 0.7803 (p) REVERT: B 163 GLU cc_start: 0.7528 (pt0) cc_final: 0.7225 (pt0) REVERT: B 194 GLU cc_start: 0.7346 (tp30) cc_final: 0.6803 (tp30) REVERT: B 209 LYS cc_start: 0.8360 (tttp) cc_final: 0.8058 (ttpp) REVERT: C 54 MET cc_start: 0.7249 (mmm) cc_final: 0.6695 (mmm) REVERT: D 6 LYS cc_start: 0.5243 (ptpp) cc_final: 0.4701 (ptmt) REVERT: E 47 GLU cc_start: 0.7298 (tp30) cc_final: 0.6726 (tp30) outliers start: 16 outliers final: 9 residues processed: 127 average time/residue: 1.1347 time to fit residues: 150.2989 Evaluate side-chains 133 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain F residue 27 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 chunk 42 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 49 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5384 Z= 0.148 Angle : 0.467 7.237 7255 Z= 0.246 Chirality : 0.036 0.138 854 Planarity : 0.002 0.027 908 Dihedral : 3.549 15.804 705 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.51 % Allowed : 23.88 % Favored : 73.61 % 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: 3.02 (0.33), residues: 675 helix: 3.01 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.61 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 38 HIS 0.010 0.001 HIS A 210 PHE 0.024 0.001 PHE C 52 TYR 0.014 0.002 TYR B 17 ARG 0.007 0.000 ARG B 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 0.604 Fit side-chains REVERT: A 6 GLU cc_start: 0.7496 (pt0) cc_final: 0.7250 (pt0) REVERT: A 10 GLN cc_start: 0.7265 (mt0) cc_final: 0.7019 (mt0) REVERT: A 34 ASP cc_start: 0.7690 (m-30) cc_final: 0.7428 (m-30) REVERT: A 88 GLN cc_start: 0.7671 (tp40) cc_final: 0.6959 (tm-30) REVERT: A 96 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6781 (tm-30) REVERT: A 156 ILE cc_start: 0.7191 (tp) cc_final: 0.6927 (tt) REVERT: B 11 ARG cc_start: 0.7815 (ttm-80) cc_final: 0.7482 (ttt90) REVERT: B 48 GLN cc_start: 0.8265 (mt0) cc_final: 0.8045 (mt0) REVERT: B 63 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6220 (pm20) REVERT: B 99 THR cc_start: 0.8106 (t) cc_final: 0.7823 (p) REVERT: B 163 GLU cc_start: 0.7507 (pt0) cc_final: 0.7221 (pt0) REVERT: B 194 GLU cc_start: 0.7349 (tp30) cc_final: 0.6811 (tp30) REVERT: B 209 LYS cc_start: 0.8388 (tttp) cc_final: 0.8087 (ttpp) REVERT: C 54 MET cc_start: 0.7261 (mmm) cc_final: 0.6705 (mmm) REVERT: D 6 LYS cc_start: 0.5288 (ptpp) cc_final: 0.4748 (ptmt) REVERT: E 47 GLU cc_start: 0.7293 (tp30) cc_final: 0.6735 (tp30) outliers start: 14 outliers final: 10 residues processed: 127 average time/residue: 1.0996 time to fit residues: 145.8728 Evaluate side-chains 131 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain F residue 27 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN A 154 ASN B 27 ASN B 44 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.139867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.111835 restraints weight = 6175.472| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.69 r_work: 0.3108 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5384 Z= 0.162 Angle : 0.478 7.423 7255 Z= 0.251 Chirality : 0.037 0.140 854 Planarity : 0.003 0.026 908 Dihedral : 3.589 16.880 705 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.59 % Allowed : 23.70 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.33), residues: 675 helix: 3.04 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.62 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 38 HIS 0.010 0.001 HIS A 210 PHE 0.026 0.001 PHE C 52 TYR 0.014 0.002 TYR B 17 ARG 0.007 0.001 ARG B 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2687.70 seconds wall clock time: 48 minutes 11.55 seconds (2891.55 seconds total)