Starting phenix.real_space_refine on Mon Mar 11 10:27:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/03_2024/6xss_22305.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/03_2024/6xss_22305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/03_2024/6xss_22305.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/03_2024/6xss_22305.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/03_2024/6xss_22305.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xss_22305/03_2024/6xss_22305.pdb" } resolution = 3.7 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= 0.003 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 8 5.16 5 C 4956 2.51 5 N 1464 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 129": "OD1" <-> "OD2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "C ASP 129": "OD1" <-> "OD2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C GLU 258": "OE1" <-> "OE2" Residue "D ASP 129": "OD1" <-> "OD2" Residue "D GLU 165": "OE1" <-> "OE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D GLU 228": "OE1" <-> "OE2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D GLU 258": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8048 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 8, 'TRANS': 251} Chain: "B" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 8, 'TRANS': 251} Chain: "C" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 8, 'TRANS': 251} Chain: "D" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 8, 'TRANS': 251} Time building chain proxies: 4.46, per 1000 atoms: 0.55 Number of scatterers: 8048 At special positions: 0 Unit cell: (121.119, 121.119, 77.31, 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 8 16.00 O 1620 8.00 N 1464 7.00 C 4956 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: 3.24 Conformation dependent library (CDL) restraints added in 1.4 seconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 95.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 1 through 14 removed outlier: 3.811A pdb=" N VAL A 5 " --> pdb=" O ALA A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.839A pdb=" N LEU A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 65 Processing helix chain 'A' and resid 68 through 99 removed outlier: 3.600A pdb=" N ARG A 72 " --> pdb=" O MET A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 124 Processing helix chain 'A' and resid 127 through 155 Processing helix chain 'A' and resid 156 through 180 Processing helix chain 'A' and resid 183 through 211 Processing helix chain 'A' and resid 212 through 236 Processing helix chain 'A' and resid 239 through 260 Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 16 through 31 Processing helix chain 'B' and resid 34 through 49 removed outlier: 3.839A pdb=" N LEU B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 65 Processing helix chain 'B' and resid 68 through 99 removed outlier: 3.600A pdb=" N ARG B 72 " --> pdb=" O MET B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 124 Processing helix chain 'B' and resid 127 through 155 Processing helix chain 'B' and resid 156 through 180 Processing helix chain 'B' and resid 183 through 211 Processing helix chain 'B' and resid 212 through 236 Processing helix chain 'B' and resid 239 through 260 Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 34 through 49 removed outlier: 3.839A pdb=" N LEU C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 48 " --> pdb=" O VAL C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 65 Processing helix chain 'C' and resid 68 through 99 removed outlier: 3.600A pdb=" N ARG C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 124 Processing helix chain 'C' and resid 127 through 155 Processing helix chain 'C' and resid 156 through 180 Processing helix chain 'C' and resid 183 through 211 Processing helix chain 'C' and resid 212 through 236 Processing helix chain 'C' and resid 239 through 260 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 16 through 31 Processing helix chain 'D' and resid 34 through 49 removed outlier: 3.839A pdb=" N LEU D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 65 Processing helix chain 'D' and resid 68 through 99 removed outlier: 3.600A pdb=" N ARG D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 124 Processing helix chain 'D' and resid 127 through 155 Processing helix chain 'D' and resid 156 through 180 Processing helix chain 'D' and resid 183 through 211 Processing helix chain 'D' and resid 212 through 236 Processing helix chain 'D' and resid 239 through 260 804 hydrogen bonds defined for protein. 2412 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: 2.54 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2960 1.34 - 1.46: 365 1.46 - 1.57: 4755 1.57 - 1.69: 0 1.69 - 1.80: 16 Bond restraints: 8096 Sorted by residual: bond pdb=" N ASN A 15 " pdb=" CA ASN A 15 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.32e-02 5.74e+03 9.92e-01 bond pdb=" N ASN B 15 " pdb=" CA ASN B 15 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.32e-02 5.74e+03 9.81e-01 bond pdb=" N ASN C 15 " pdb=" CA ASN C 15 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.32e-02 5.74e+03 9.63e-01 bond pdb=" N ASN D 15 " pdb=" CA ASN D 15 " ideal model delta sigma weight residual 1.459 1.471 -0.013 1.32e-02 5.74e+03 9.34e-01 bond pdb=" C GLY D 49 " pdb=" O GLY D 49 " ideal model delta sigma weight residual 1.240 1.229 0.012 1.29e-02 6.01e+03 7.97e-01 ... (remaining 8091 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.17: 150 107.17 - 113.86: 4703 113.86 - 120.56: 3613 120.56 - 127.25: 2414 127.25 - 133.95: 52 Bond angle restraints: 10932 Sorted by residual: angle pdb=" CA LEU A 222 " pdb=" CB LEU A 222 " pdb=" CG LEU A 222 " ideal model delta sigma weight residual 116.30 129.90 -13.60 3.50e+00 8.16e-02 1.51e+01 angle pdb=" CA LEU D 222 " pdb=" CB LEU D 222 " pdb=" CG LEU D 222 " ideal model delta sigma weight residual 116.30 129.89 -13.59 3.50e+00 8.16e-02 1.51e+01 angle pdb=" CA LEU C 222 " pdb=" CB LEU C 222 " pdb=" CG LEU C 222 " ideal model delta sigma weight residual 116.30 129.89 -13.59 3.50e+00 8.16e-02 1.51e+01 angle pdb=" CA LEU B 222 " pdb=" CB LEU B 222 " pdb=" CG LEU B 222 " ideal model delta sigma weight residual 116.30 129.84 -13.54 3.50e+00 8.16e-02 1.50e+01 angle pdb=" N GLY C 49 " pdb=" CA GLY C 49 " pdb=" C GLY C 49 " ideal model delta sigma weight residual 114.85 110.60 4.25 1.35e+00 5.49e-01 9.90e+00 ... (remaining 10927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 4804 17.34 - 34.68: 360 34.68 - 52.02: 40 52.02 - 69.37: 4 69.37 - 86.71: 12 Dihedral angle restraints: 5220 sinusoidal: 2156 harmonic: 3064 Sorted by residual: dihedral pdb=" N ASN C 15 " pdb=" C ASN C 15 " pdb=" CA ASN C 15 " pdb=" CB ASN C 15 " ideal model delta harmonic sigma weight residual 122.80 132.00 -9.20 0 2.50e+00 1.60e-01 1.35e+01 dihedral pdb=" N ASN A 15 " pdb=" C ASN A 15 " pdb=" CA ASN A 15 " pdb=" CB ASN A 15 " ideal model delta harmonic sigma weight residual 122.80 131.99 -9.19 0 2.50e+00 1.60e-01 1.35e+01 dihedral pdb=" N ASN B 15 " pdb=" C ASN B 15 " pdb=" CA ASN B 15 " pdb=" CB ASN B 15 " ideal model delta harmonic sigma weight residual 122.80 131.96 -9.16 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 5217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1198 0.066 - 0.131: 94 0.131 - 0.197: 4 0.197 - 0.263: 0 0.263 - 0.328: 4 Chirality restraints: 1300 Sorted by residual: chirality pdb=" CA ASN C 15 " pdb=" N ASN C 15 " pdb=" C ASN C 15 " pdb=" CB ASN C 15 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA ASN A 15 " pdb=" N ASN A 15 " pdb=" C ASN A 15 " pdb=" CB ASN A 15 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ASN B 15 " pdb=" N ASN B 15 " pdb=" C ASN B 15 " pdb=" CB ASN B 15 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 1297 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 14 " 0.006 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" C LEU D 14 " -0.023 2.00e-02 2.50e+03 pdb=" O LEU D 14 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN D 15 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 14 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.70e+00 pdb=" C LEU C 14 " -0.023 2.00e-02 2.50e+03 pdb=" O LEU C 14 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN C 15 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 14 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" C LEU A 14 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU A 14 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN A 15 " 0.008 2.00e-02 2.50e+03 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 49 2.45 - 3.07: 5477 3.07 - 3.68: 12994 3.68 - 4.29: 17762 4.29 - 4.90: 28573 Nonbonded interactions: 64855 Sorted by model distance: nonbonded pdb=" CB ALA D 94 " pdb=" CD2 LEU D 148 " model vdw 1.843 3.880 nonbonded pdb=" CB ALA A 94 " pdb=" CD2 LEU A 148 " model vdw 1.843 3.880 nonbonded pdb=" CB ALA C 94 " pdb=" CD2 LEU C 148 " model vdw 1.843 3.880 nonbonded pdb=" CB ALA B 94 " pdb=" CD2 LEU B 148 " model vdw 1.844 3.880 nonbonded pdb=" NH2 ARG A 83 " pdb=" OE1 GLU A 142 " model vdw 1.982 2.520 ... (remaining 64850 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 0.650 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: 3.770 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 24.870 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.003 0.023 8096 Z= 0.176 Angle : 0.628 13.605 10932 Z= 0.356 Chirality : 0.038 0.328 1300 Planarity : 0.003 0.024 1468 Dihedral : 12.310 86.708 3196 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 28.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % 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: -0.32 (0.23), residues: 1032 helix: 0.08 (0.14), residues: 976 sheet: None (None), residues: 0 loop : -3.14 (1.01), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 4 TYR 0.002 0.001 TYR D 24 ARG 0.006 0.000 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.8100 (m-40) cc_final: 0.7624 (t0) REVERT: A 60 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8225 (mmtm) REVERT: A 119 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 168 ARG cc_start: 0.7831 (mtt180) cc_final: 0.7436 (ttp-110) REVERT: A 180 ASN cc_start: 0.7917 (m-40) cc_final: 0.7545 (p0) REVERT: A 191 LYS cc_start: 0.9054 (mttt) cc_final: 0.8101 (mmmt) REVERT: A 195 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8076 (mm-30) REVERT: A 209 LYS cc_start: 0.8246 (mttt) cc_final: 0.7892 (tmmt) REVERT: A 210 THR cc_start: 0.6614 (m) cc_final: 0.6301 (p) REVERT: B 31 ASP cc_start: 0.8454 (t0) cc_final: 0.8217 (t0) REVERT: B 60 LYS cc_start: 0.8389 (mmtt) cc_final: 0.8171 (mmtm) REVERT: B 154 THR cc_start: 0.6910 (p) cc_final: 0.6669 (t) REVERT: B 168 ARG cc_start: 0.7799 (mtt180) cc_final: 0.7465 (ttp-110) REVERT: B 180 ASN cc_start: 0.7867 (m-40) cc_final: 0.7468 (p0) REVERT: B 191 LYS cc_start: 0.9054 (mttt) cc_final: 0.8037 (mmmt) REVERT: B 195 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8049 (mm-30) REVERT: B 210 THR cc_start: 0.6841 (m) cc_final: 0.6595 (p) REVERT: B 224 ARG cc_start: 0.8521 (mtt90) cc_final: 0.7813 (mtp-110) REVERT: C 60 LYS cc_start: 0.8401 (mmtt) cc_final: 0.8135 (mmmt) REVERT: C 168 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7152 (ttp-110) REVERT: C 180 ASN cc_start: 0.7347 (m-40) cc_final: 0.7145 (p0) REVERT: C 195 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8081 (mm-30) REVERT: C 224 ARG cc_start: 0.8344 (mtt90) cc_final: 0.7877 (tmt-80) REVERT: C 254 GLN cc_start: 0.8336 (mt0) cc_final: 0.7708 (tm-30) REVERT: D 15 ASN cc_start: 0.8079 (m-40) cc_final: 0.7650 (t0) REVERT: D 119 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7599 (tm-30) REVERT: D 168 ARG cc_start: 0.7835 (mtt180) cc_final: 0.7321 (ttp-110) REVERT: D 180 ASN cc_start: 0.7872 (m-40) cc_final: 0.7525 (p0) REVERT: D 191 LYS cc_start: 0.9031 (mttt) cc_final: 0.8042 (mmmt) REVERT: D 195 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8098 (mm-30) REVERT: D 201 VAL cc_start: 0.9307 (m) cc_final: 0.9104 (m) REVERT: D 224 ARG cc_start: 0.8439 (mtt90) cc_final: 0.7784 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.3253 time to fit residues: 120.5578 Evaluate side-chains 159 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN C 15 ASN C 131 ASN C 234 GLN D 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8096 Z= 0.229 Angle : 0.678 10.767 10932 Z= 0.323 Chirality : 0.037 0.153 1300 Planarity : 0.004 0.042 1468 Dihedral : 3.400 12.030 1148 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.58 % Allowed : 13.83 % Favored : 84.59 % 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: 1.29 (0.24), residues: 1032 helix: 1.12 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -4.00 (1.04), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 4 TYR 0.010 0.003 TYR A 24 ARG 0.007 0.001 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 176 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.8365 (m-40) cc_final: 0.7784 (t0) REVERT: A 131 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.8007 (t0) REVERT: A 168 ARG cc_start: 0.7823 (mtt180) cc_final: 0.7298 (ttp-110) REVERT: A 180 ASN cc_start: 0.7874 (m-40) cc_final: 0.7663 (p0) REVERT: A 195 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8047 (mm-30) REVERT: A 224 ARG cc_start: 0.8556 (mtt90) cc_final: 0.7841 (mtp-110) REVERT: B 168 ARG cc_start: 0.7759 (mtt180) cc_final: 0.7223 (ttp-110) REVERT: B 180 ASN cc_start: 0.7783 (m-40) cc_final: 0.7424 (p0) REVERT: B 195 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8076 (mm-30) REVERT: B 210 THR cc_start: 0.6885 (m) cc_final: 0.6685 (p) REVERT: B 224 ARG cc_start: 0.8531 (mtt90) cc_final: 0.7825 (mtp-110) REVERT: C 60 LYS cc_start: 0.8427 (mmtt) cc_final: 0.8135 (mmmt) REVERT: C 69 ASP cc_start: 0.8331 (p0) cc_final: 0.7992 (p0) REVERT: C 168 ARG cc_start: 0.8030 (mtt180) cc_final: 0.7033 (ttp-110) REVERT: C 188 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8232 (mm-30) REVERT: C 195 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8090 (mm-30) REVERT: C 224 ARG cc_start: 0.8335 (mtt90) cc_final: 0.7878 (tmt-80) REVERT: C 254 GLN cc_start: 0.8241 (mt0) cc_final: 0.7622 (tm-30) REVERT: D 15 ASN cc_start: 0.8355 (m-40) cc_final: 0.7785 (t0) REVERT: D 168 ARG cc_start: 0.7709 (mtt180) cc_final: 0.7203 (ttp-110) REVERT: D 180 ASN cc_start: 0.7827 (m-40) cc_final: 0.7494 (p0) REVERT: D 195 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8124 (mm-30) REVERT: D 224 ARG cc_start: 0.8439 (mtt90) cc_final: 0.7829 (mtp-110) outliers start: 13 outliers final: 7 residues processed: 178 average time/residue: 0.2636 time to fit residues: 60.1424 Evaluate side-chains 151 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain D residue 113 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.9980 chunk 29 optimal weight: 0.0270 chunk 78 optimal weight: 0.5980 chunk 64 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8096 Z= 0.186 Angle : 0.649 11.478 10932 Z= 0.304 Chirality : 0.034 0.139 1300 Planarity : 0.004 0.042 1468 Dihedral : 3.363 12.169 1148 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.55 % Allowed : 15.17 % Favored : 82.28 % 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: 2.11 (0.25), residues: 1032 helix: 1.65 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -4.00 (0.94), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 4 TYR 0.014 0.003 TYR C 24 ARG 0.007 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 167 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.8340 (m-40) cc_final: 0.7805 (t0) REVERT: A 168 ARG cc_start: 0.7648 (mtt180) cc_final: 0.7181 (ttp-110) REVERT: A 195 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8039 (mm-30) REVERT: A 224 ARG cc_start: 0.8531 (mtt90) cc_final: 0.7785 (mtp-110) REVERT: B 168 ARG cc_start: 0.7658 (mtt180) cc_final: 0.7232 (ttp-110) REVERT: B 180 ASN cc_start: 0.7777 (m-40) cc_final: 0.7450 (p0) REVERT: B 195 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8059 (mm-30) REVERT: B 224 ARG cc_start: 0.8535 (mtt90) cc_final: 0.7817 (mtp-110) REVERT: C 60 LYS cc_start: 0.8437 (mmtt) cc_final: 0.8157 (mmmt) REVERT: C 69 ASP cc_start: 0.8365 (p0) cc_final: 0.7998 (p0) REVERT: C 124 ASP cc_start: 0.8371 (t0) cc_final: 0.8137 (t70) REVERT: C 149 GLU cc_start: 0.8214 (pt0) cc_final: 0.7761 (tm-30) REVERT: C 165 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8474 (pt0) REVERT: C 168 ARG cc_start: 0.7981 (mtt180) cc_final: 0.7218 (ttp-110) REVERT: C 188 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8175 (mm-30) REVERT: C 195 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8078 (mm-30) REVERT: C 224 ARG cc_start: 0.8334 (mtt90) cc_final: 0.7863 (tmt-80) REVERT: D 15 ASN cc_start: 0.8341 (m-40) cc_final: 0.7827 (t0) REVERT: D 168 ARG cc_start: 0.7624 (mtt180) cc_final: 0.7124 (ttp-110) REVERT: D 180 ASN cc_start: 0.7795 (m-40) cc_final: 0.7517 (p0) REVERT: D 195 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8109 (mm-30) REVERT: D 224 ARG cc_start: 0.8431 (mtt90) cc_final: 0.7826 (mtp-110) outliers start: 21 outliers final: 11 residues processed: 176 average time/residue: 0.2371 time to fit residues: 54.2536 Evaluate side-chains 149 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 154 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.0370 chunk 10 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8096 Z= 0.209 Angle : 0.647 11.250 10932 Z= 0.308 Chirality : 0.035 0.156 1300 Planarity : 0.004 0.044 1468 Dihedral : 3.358 11.449 1148 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.91 % Allowed : 16.87 % Favored : 80.22 % 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: 2.51 (0.25), residues: 1032 helix: 1.92 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -4.23 (0.87), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 4 TYR 0.014 0.003 TYR C 24 ARG 0.004 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 157 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.8430 (m-40) cc_final: 0.7882 (t0) REVERT: A 168 ARG cc_start: 0.7665 (mtt180) cc_final: 0.7186 (ttp-110) REVERT: A 195 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8050 (mm-30) REVERT: A 224 ARG cc_start: 0.8534 (mtt90) cc_final: 0.7826 (mtp-110) REVERT: B 123 ARG cc_start: 0.8096 (tpm170) cc_final: 0.7649 (mmm-85) REVERT: B 168 ARG cc_start: 0.7673 (mtt180) cc_final: 0.7226 (ttp-110) REVERT: B 180 ASN cc_start: 0.7805 (m-40) cc_final: 0.7436 (p0) REVERT: B 195 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8085 (mm-30) REVERT: B 224 ARG cc_start: 0.8540 (mtt90) cc_final: 0.7752 (mtp-110) REVERT: B 228 GLU cc_start: 0.8736 (tt0) cc_final: 0.8506 (pt0) REVERT: C 60 LYS cc_start: 0.8468 (mmtt) cc_final: 0.8181 (mmmt) REVERT: C 69 ASP cc_start: 0.8431 (p0) cc_final: 0.8096 (p0) REVERT: C 124 ASP cc_start: 0.8392 (t0) cc_final: 0.8125 (t70) REVERT: C 149 GLU cc_start: 0.8230 (pt0) cc_final: 0.7759 (tm-30) REVERT: C 168 ARG cc_start: 0.7923 (mtt180) cc_final: 0.7084 (ttp-110) REVERT: C 188 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8203 (mm-30) REVERT: C 195 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8113 (mm-30) REVERT: C 224 ARG cc_start: 0.8345 (mtt90) cc_final: 0.7866 (tmt-80) REVERT: D 15 ASN cc_start: 0.8422 (m-40) cc_final: 0.7861 (t0) REVERT: D 168 ARG cc_start: 0.7629 (mtt180) cc_final: 0.7188 (ttp-110) REVERT: D 180 ASN cc_start: 0.7838 (m-40) cc_final: 0.7548 (p0) REVERT: D 195 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8131 (mm-30) REVERT: D 224 ARG cc_start: 0.8434 (mtt90) cc_final: 0.7791 (mtp-110) outliers start: 24 outliers final: 15 residues processed: 162 average time/residue: 0.2504 time to fit residues: 51.9651 Evaluate side-chains 156 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 154 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 ASN D 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8096 Z= 0.250 Angle : 0.672 11.129 10932 Z= 0.320 Chirality : 0.035 0.126 1300 Planarity : 0.004 0.045 1468 Dihedral : 3.384 11.351 1148 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.64 % Allowed : 17.11 % Favored : 79.25 % 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: 2.56 (0.25), residues: 1032 helix: 1.97 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -4.66 (0.78), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 4 TYR 0.014 0.003 TYR B 24 ARG 0.005 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 151 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.8582 (m-40) cc_final: 0.8023 (t0) REVERT: A 168 ARG cc_start: 0.7652 (mtt180) cc_final: 0.7046 (ttp-110) REVERT: A 195 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8118 (mm-30) REVERT: A 224 ARG cc_start: 0.8614 (mtt90) cc_final: 0.7514 (mtp-110) REVERT: B 123 ARG cc_start: 0.8074 (tpm170) cc_final: 0.7636 (mmm-85) REVERT: B 168 ARG cc_start: 0.7646 (mtt180) cc_final: 0.7122 (ttp-110) REVERT: B 180 ASN cc_start: 0.7807 (m-40) cc_final: 0.7426 (p0) REVERT: B 195 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8081 (mm-30) REVERT: B 224 ARG cc_start: 0.8550 (mtt90) cc_final: 0.7753 (mtp-110) REVERT: C 60 LYS cc_start: 0.8524 (mmtt) cc_final: 0.8211 (mmmt) REVERT: C 165 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8568 (pt0) REVERT: C 168 ARG cc_start: 0.7851 (mtt180) cc_final: 0.6796 (ttp-110) REVERT: C 195 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8163 (mm-30) REVERT: C 224 ARG cc_start: 0.8374 (mtt90) cc_final: 0.7917 (tmt-80) REVERT: D 15 ASN cc_start: 0.8569 (m-40) cc_final: 0.8044 (t0) REVERT: D 168 ARG cc_start: 0.7753 (mtt180) cc_final: 0.7051 (ttp-110) REVERT: D 180 ASN cc_start: 0.7916 (m-40) cc_final: 0.7552 (p0) REVERT: D 195 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8156 (mm-30) REVERT: D 224 ARG cc_start: 0.8479 (mtt90) cc_final: 0.7865 (mtp-110) outliers start: 30 outliers final: 20 residues processed: 161 average time/residue: 0.2432 time to fit residues: 50.6264 Evaluate side-chains 145 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 192 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 59 optimal weight: 0.0870 chunk 24 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 0.1980 chunk 97 optimal weight: 5.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 GLN D 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8096 Z= 0.186 Angle : 0.665 11.986 10932 Z= 0.311 Chirality : 0.035 0.130 1300 Planarity : 0.004 0.043 1468 Dihedral : 3.418 11.342 1148 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.06 % Allowed : 19.17 % Favored : 78.76 % 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: 2.82 (0.24), residues: 1032 helix: 2.12 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -4.23 (0.79), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 4 TYR 0.011 0.002 TYR B 24 ARG 0.011 0.000 ARG D 179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.8586 (m-40) cc_final: 0.8137 (t0) REVERT: A 168 ARG cc_start: 0.7557 (mtt180) cc_final: 0.7016 (ttp-110) REVERT: A 195 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8038 (mm-30) REVERT: A 224 ARG cc_start: 0.8518 (mtt90) cc_final: 0.7703 (mtp-110) REVERT: B 168 ARG cc_start: 0.7492 (mtt180) cc_final: 0.6968 (ttp-110) REVERT: B 180 ASN cc_start: 0.7821 (m-40) cc_final: 0.7436 (p0) REVERT: B 195 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8099 (mm-30) REVERT: B 224 ARG cc_start: 0.8574 (mtt90) cc_final: 0.7934 (mtp-110) REVERT: C 69 ASP cc_start: 0.8482 (p0) cc_final: 0.8156 (p0) REVERT: C 165 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8444 (pt0) REVERT: C 168 ARG cc_start: 0.7797 (mtt180) cc_final: 0.6885 (ttp-110) REVERT: C 195 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8143 (mm-30) REVERT: C 224 ARG cc_start: 0.8348 (mtt90) cc_final: 0.7891 (tmt-80) REVERT: D 15 ASN cc_start: 0.8570 (m-40) cc_final: 0.8210 (t0) REVERT: D 168 ARG cc_start: 0.7663 (mtt180) cc_final: 0.7002 (ttp-110) REVERT: D 180 ASN cc_start: 0.7863 (m-40) cc_final: 0.7508 (p0) REVERT: D 195 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8140 (mm-30) REVERT: D 224 ARG cc_start: 0.8456 (mtt90) cc_final: 0.7813 (mtp-110) outliers start: 17 outliers final: 11 residues processed: 154 average time/residue: 0.2384 time to fit residues: 47.8630 Evaluate side-chains 145 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 73 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8096 Z= 0.209 Angle : 0.682 12.567 10932 Z= 0.319 Chirality : 0.035 0.137 1300 Planarity : 0.004 0.043 1468 Dihedral : 3.384 11.641 1148 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.03 % Allowed : 19.54 % Favored : 77.43 % 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 (0.24), residues: 1032 helix: 2.14 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -4.40 (0.76), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 4 TYR 0.017 0.003 TYR B 24 ARG 0.009 0.000 ARG D 179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.8640 (m-40) cc_final: 0.8173 (t0) REVERT: A 168 ARG cc_start: 0.7609 (mtt180) cc_final: 0.7034 (ttp-110) REVERT: A 195 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8050 (mm-30) REVERT: A 224 ARG cc_start: 0.8494 (mtt90) cc_final: 0.7723 (mtp-110) REVERT: B 168 ARG cc_start: 0.7564 (mtt180) cc_final: 0.7127 (ttp-110) REVERT: B 180 ASN cc_start: 0.7824 (m-40) cc_final: 0.7440 (p0) REVERT: B 195 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8114 (mm-30) REVERT: B 224 ARG cc_start: 0.8665 (mtt90) cc_final: 0.8000 (mtp-110) REVERT: C 165 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8437 (pt0) REVERT: C 168 ARG cc_start: 0.7785 (mtt180) cc_final: 0.6874 (ttp-110) REVERT: C 195 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8181 (mm-30) REVERT: C 224 ARG cc_start: 0.8337 (mtt90) cc_final: 0.7891 (tmt-80) REVERT: D 15 ASN cc_start: 0.8599 (m-40) cc_final: 0.8186 (t0) REVERT: D 168 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7019 (ttp-110) REVERT: D 180 ASN cc_start: 0.7895 (m-40) cc_final: 0.7495 (p0) REVERT: D 195 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8177 (mm-30) REVERT: D 224 ARG cc_start: 0.8503 (mtt90) cc_final: 0.7864 (mtp-110) outliers start: 25 outliers final: 18 residues processed: 144 average time/residue: 0.2427 time to fit residues: 45.3703 Evaluate side-chains 145 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 238 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 78 optimal weight: 0.0870 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 93 optimal weight: 0.0470 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8096 Z= 0.184 Angle : 0.702 13.410 10932 Z= 0.325 Chirality : 0.035 0.147 1300 Planarity : 0.004 0.042 1468 Dihedral : 3.466 13.087 1148 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.55 % Allowed : 19.90 % Favored : 77.55 % 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: 2.89 (0.24), residues: 1032 helix: 2.15 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -3.99 (0.85), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 4 TYR 0.016 0.003 TYR B 24 ARG 0.008 0.000 ARG D 179 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.8583 (m-40) cc_final: 0.8192 (t0) REVERT: A 168 ARG cc_start: 0.7566 (mtt180) cc_final: 0.7006 (ttp-110) REVERT: A 224 ARG cc_start: 0.8488 (mtt90) cc_final: 0.7540 (mtp-110) REVERT: B 168 ARG cc_start: 0.7658 (mtt180) cc_final: 0.7022 (ttp-110) REVERT: B 180 ASN cc_start: 0.7855 (m-40) cc_final: 0.7471 (p0) REVERT: B 224 ARG cc_start: 0.8589 (mtt90) cc_final: 0.7964 (mtp-110) REVERT: C 154 THR cc_start: 0.6290 (p) cc_final: 0.6017 (t) REVERT: C 165 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8437 (pt0) REVERT: C 168 ARG cc_start: 0.7728 (mtt180) cc_final: 0.6849 (ttp-110) REVERT: C 195 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8172 (mm-30) REVERT: C 224 ARG cc_start: 0.8336 (mtt90) cc_final: 0.7887 (tmt-80) REVERT: D 15 ASN cc_start: 0.8609 (m-40) cc_final: 0.8241 (t0) REVERT: D 168 ARG cc_start: 0.7658 (mtt180) cc_final: 0.6988 (ttp-110) REVERT: D 180 ASN cc_start: 0.7921 (m-40) cc_final: 0.7593 (p0) REVERT: D 195 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8207 (mm-30) REVERT: D 224 ARG cc_start: 0.8433 (mtt90) cc_final: 0.7820 (mtp-110) outliers start: 21 outliers final: 15 residues processed: 159 average time/residue: 0.2289 time to fit residues: 47.7636 Evaluate side-chains 147 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 73 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 61 optimal weight: 0.3980 chunk 98 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8096 Z= 0.213 Angle : 0.726 13.813 10932 Z= 0.346 Chirality : 0.036 0.173 1300 Planarity : 0.004 0.041 1468 Dihedral : 3.455 13.276 1148 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.43 % Allowed : 20.63 % Favored : 76.94 % 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: 2.80 (0.24), residues: 1032 helix: 2.10 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -4.25 (0.81), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 4 TYR 0.018 0.004 TYR D 24 ARG 0.007 0.000 ARG D 179 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.8608 (m-40) cc_final: 0.8220 (t0) REVERT: A 168 ARG cc_start: 0.7609 (mtt180) cc_final: 0.7106 (ttp-110) REVERT: A 195 GLU cc_start: 0.8211 (mp0) cc_final: 0.7819 (mp0) REVERT: A 224 ARG cc_start: 0.8503 (mtt90) cc_final: 0.7752 (mtp-110) REVERT: B 168 ARG cc_start: 0.7692 (mtt180) cc_final: 0.7080 (ttp-110) REVERT: B 180 ASN cc_start: 0.7865 (m-40) cc_final: 0.7438 (p0) REVERT: B 195 GLU cc_start: 0.8297 (mp0) cc_final: 0.7916 (mp0) REVERT: B 224 ARG cc_start: 0.8603 (mtt90) cc_final: 0.7967 (mtp-110) REVERT: C 165 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8442 (pt0) REVERT: C 168 ARG cc_start: 0.7746 (mtt180) cc_final: 0.6829 (ttp-110) REVERT: C 195 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8186 (mm-30) REVERT: C 224 ARG cc_start: 0.8345 (mtt90) cc_final: 0.7891 (tmt-80) REVERT: D 15 ASN cc_start: 0.8650 (m-40) cc_final: 0.8273 (t0) REVERT: D 168 ARG cc_start: 0.7719 (mtt180) cc_final: 0.7044 (ttp-110) REVERT: D 180 ASN cc_start: 0.7895 (m-40) cc_final: 0.7537 (p0) REVERT: D 195 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8194 (mm-30) REVERT: D 224 ARG cc_start: 0.8469 (mtt90) cc_final: 0.7806 (mtp-110) outliers start: 20 outliers final: 16 residues processed: 140 average time/residue: 0.2388 time to fit residues: 43.6834 Evaluate side-chains 142 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 238 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 8096 Z= 0.314 Angle : 0.791 13.316 10932 Z= 0.382 Chirality : 0.040 0.195 1300 Planarity : 0.005 0.043 1468 Dihedral : 3.541 11.603 1148 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.18 % Allowed : 21.84 % Favored : 75.97 % 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: 2.38 (0.24), residues: 1032 helix: 1.87 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -5.06 (0.68), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 4 TYR 0.018 0.004 TYR C 24 ARG 0.007 0.001 ARG D 179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ARG cc_start: 0.7814 (mtt180) cc_final: 0.7088 (ttp-110) REVERT: A 195 GLU cc_start: 0.8255 (mp0) cc_final: 0.7813 (mp0) REVERT: A 224 ARG cc_start: 0.8535 (mtt90) cc_final: 0.7806 (mtp-110) REVERT: B 168 ARG cc_start: 0.7648 (mtt180) cc_final: 0.7075 (ttp-110) REVERT: B 180 ASN cc_start: 0.7953 (m-40) cc_final: 0.7469 (p0) REVERT: B 195 GLU cc_start: 0.8283 (mp0) cc_final: 0.7867 (mp0) REVERT: B 224 ARG cc_start: 0.8653 (mtt90) cc_final: 0.8003 (mtp-110) REVERT: C 165 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8464 (pt0) REVERT: C 168 ARG cc_start: 0.7767 (mtt180) cc_final: 0.6929 (ttp-110) REVERT: C 195 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8277 (mm-30) REVERT: C 224 ARG cc_start: 0.8357 (mtt90) cc_final: 0.7905 (tmt-80) REVERT: D 168 ARG cc_start: 0.7661 (mtt180) cc_final: 0.7096 (ttp-110) REVERT: D 180 ASN cc_start: 0.8048 (m-40) cc_final: 0.7550 (p0) REVERT: D 195 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8244 (mm-30) REVERT: D 224 ARG cc_start: 0.8573 (mtt90) cc_final: 0.7877 (mtp-110) outliers start: 18 outliers final: 15 residues processed: 139 average time/residue: 0.2385 time to fit residues: 43.2185 Evaluate side-chains 136 residues out of total 824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 238 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.107566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.075057 restraints weight = 27044.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.077191 restraints weight = 16266.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.078466 restraints weight = 12075.082| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8096 Z= 0.219 Angle : 0.786 14.031 10932 Z= 0.367 Chirality : 0.037 0.165 1300 Planarity : 0.004 0.046 1468 Dihedral : 3.560 13.698 1148 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.70 % Allowed : 23.54 % Favored : 74.76 % 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: 2.49 (0.24), residues: 1032 helix: 1.91 (0.15), residues: 988 sheet: None (None), residues: 0 loop : -4.36 (0.83), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 4 TYR 0.018 0.004 TYR B 24 ARG 0.011 0.000 ARG D 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1773.45 seconds wall clock time: 33 minutes 4.16 seconds (1984.16 seconds total)