Starting phenix.real_space_refine on Fri Apr 5 19:10:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ey2_28666/04_2024/8ey2_28666.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ey2_28666/04_2024/8ey2_28666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ey2_28666/04_2024/8ey2_28666.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ey2_28666/04_2024/8ey2_28666.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ey2_28666/04_2024/8ey2_28666.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ey2_28666/04_2024/8ey2_28666.pdb" } resolution = 3.5 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= 1.000 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 46 5.16 5 C 3108 2.51 5 N 836 2.21 5 O 918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 197": "OD1" <-> "OD2" Residue "A ASP 289": "OD1" <-> "OD2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 34": "OD1" <-> "OD2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 289": "OD1" <-> "OD2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 4908 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2370 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 2367 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 306, 2367 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} bond proxies already assigned to first conformer: 2416 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 84 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 84 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "B" Number of atoms: 2370 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 2367 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 306, 2367 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} bond proxies already assigned to first conformer: 2416 Time building chain proxies: 5.48, per 1000 atoms: 1.12 Number of scatterers: 4908 At special positions: 0 Unit cell: (72.483, 86.849, 74.442, 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 46 16.00 O 918 8.00 N 836 7.00 C 3108 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: 1.79 Conformation dependent library (CDL) restraints added in 1.7 seconds 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 7 sheets defined 27.8% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 41 through 43 No H-bonds generated for 'chain 'A' and resid 41 through 43' Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 200 through 215 Processing helix chain 'A' and resid 226 through 237 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 292 through 300 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 200 through 215 Processing helix chain 'B' and resid 226 through 237 Processing helix chain 'B' and resid 243 through 250 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 275 removed outlier: 3.549A pdb=" N MET B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 75 removed outlier: 3.960A pdb=" N VAL A 68 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASN A 28 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 75 removed outlier: 3.960A pdb=" N VAL A 68 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.072A pdb=" N LYS A 102 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N TYR A 161 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLY A 149 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 148 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE A 152 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 11.604A pdb=" N THR A 111 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR A 118 " --> pdb=" O PRO A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.072A pdb=" N LYS A 102 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N TYR A 161 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA A 173 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 75 removed outlier: 3.949A pdb=" N VAL B 68 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ASN B 28 " --> pdb=" O PRO B 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 101 through 103 removed outlier: 6.120A pdb=" N LYS B 102 " --> pdb=" O PHE B 159 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE B 152 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 11.637A pdb=" N THR B 111 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TYR B 118 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 162 through 166 removed outlier: 6.904A pdb=" N ALA B 173 " --> pdb=" O HIS B 164 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 576 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: 1.30 Time building geometry restraints manager: 1.97 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: 1612 1.34 - 1.46: 1160 1.46 - 1.58: 2176 1.58 - 1.70: 0 1.70 - 1.81: 68 Bond restraints: 5016 Sorted by residual: bond pdb=" CG LEU B 32 " pdb=" CD1 LEU B 32 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.08e+00 bond pdb=" CB MET A 264 " pdb=" CG MET A 264 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.04e-01 bond pdb=" CG LEU B 272 " pdb=" CD1 LEU B 272 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.03e-01 bond pdb=" CG LEU C -1 " pdb=" CD2 LEU C -1 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 6.95e-01 bond pdb=" CB THR B 175 " pdb=" CG2 THR B 175 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.59e-01 ... (remaining 5011 not shown) Histogram of bond angle deviations from ideal: 96.83 - 104.25: 82 104.25 - 111.68: 2314 111.68 - 119.10: 1694 119.10 - 126.53: 2660 126.53 - 133.96: 60 Bond angle restraints: 6810 Sorted by residual: angle pdb=" N VAL B 13 " pdb=" CA VAL B 13 " pdb=" C VAL B 13 " ideal model delta sigma weight residual 112.96 109.13 3.83 1.00e+00 1.00e+00 1.46e+01 angle pdb=" N VAL A 13 " pdb=" CA VAL A 13 " pdb=" C VAL A 13 " ideal model delta sigma weight residual 112.96 109.20 3.76 1.00e+00 1.00e+00 1.41e+01 angle pdb=" CA LEU C -1 " pdb=" CB LEU C -1 " pdb=" CG LEU C -1 " ideal model delta sigma weight residual 116.30 125.99 -9.69 3.50e+00 8.16e-02 7.67e+00 angle pdb=" CA LEU D -1 " pdb=" CB LEU D -1 " pdb=" CG LEU D -1 " ideal model delta sigma weight residual 116.30 125.27 -8.97 3.50e+00 8.16e-02 6.57e+00 angle pdb=" C VAL C -2 " pdb=" N LEU C -1 " pdb=" CA LEU C -1 " ideal model delta sigma weight residual 121.26 124.71 -3.45 1.59e+00 3.96e-01 4.70e+00 ... (remaining 6805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.12: 2616 14.12 - 28.24: 240 28.24 - 42.35: 88 42.35 - 56.47: 12 56.47 - 70.59: 6 Dihedral angle restraints: 2962 sinusoidal: 1142 harmonic: 1820 Sorted by residual: dihedral pdb=" CA GLN C 0 " pdb=" C GLN C 0 " pdb=" N SER C 1 " pdb=" CA SER C 1 " ideal model delta harmonic sigma weight residual 180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA LEU C -1 " pdb=" C LEU C -1 " pdb=" N GLN C 0 " pdb=" CA GLN C 0 " ideal model delta harmonic sigma weight residual -180.00 -158.79 -21.21 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA THR B 175 " pdb=" C THR B 175 " pdb=" N ASP B 176 " pdb=" CA ASP B 176 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 2959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 447 0.031 - 0.062: 218 0.062 - 0.093: 74 0.093 - 0.123: 27 0.123 - 0.154: 2 Chirality restraints: 768 Sorted by residual: chirality pdb=" CG LEU D -1 " pdb=" CB LEU D -1 " pdb=" CD1 LEU D -1 " pdb=" CD2 LEU D -1 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA VAL C -2 " pdb=" N VAL C -2 " pdb=" C VAL C -2 " pdb=" CB VAL C -2 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE B 281 " pdb=" N ILE B 281 " pdb=" C ILE B 281 " pdb=" CB ILE B 281 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.24e-01 ... (remaining 765 not shown) Planarity restraints: 884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 51 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO A 52 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 51 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO B 52 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 52 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 52 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 3 " 0.011 2.00e-02 2.50e+03 1.11e-02 2.15e+00 pdb=" CG PHE D 3 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE D 3 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE D 3 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 3 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 3 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 3 " 0.002 2.00e-02 2.50e+03 ... (remaining 881 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 134 2.70 - 3.25: 4949 3.25 - 3.80: 8026 3.80 - 4.35: 10191 4.35 - 4.90: 17041 Nonbonded interactions: 40341 Sorted by model distance: nonbonded pdb=" OG1 THR A 292 " pdb=" OD2 ASP A 295 " model vdw 2.149 2.440 nonbonded pdb=" OG1 THR B 292 " pdb=" OD2 ASP B 295 " model vdw 2.152 2.440 nonbonded pdb=" OH TYR A 209 " pdb=" OG SER A 254 " model vdw 2.177 2.440 nonbonded pdb=" O THR A 26 " pdb=" OG SER C 1 " model vdw 2.194 2.440 nonbonded pdb=" OG1 THR B 45 " pdb=" OD1 ASP B 48 " model vdw 2.217 2.440 ... (remaining 40336 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 1 through 116 or resid 118 through 306)) selection = (chain 'B' and (resid 1 through 116 or resid 118 through 306)) } ncs_group { reference = 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=0.17 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: 0.480 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: 2.660 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.850 Find NCS groups from input model: 0.290 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 0.034 5016 Z= 0.189 Angle : 0.600 9.693 6810 Z= 0.315 Chirality : 0.042 0.154 768 Planarity : 0.005 0.055 884 Dihedral : 13.039 70.588 1798 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.29 (0.35), residues: 628 helix: 1.88 (0.44), residues: 150 sheet: -1.02 (0.54), residues: 102 loop : -0.82 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 218 HIS 0.007 0.001 HIS A 41 PHE 0.026 0.001 PHE D 3 TYR 0.024 0.002 TYR A 239 ARG 0.002 0.000 ARG D 4 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8298 (p0) cc_final: 0.7777 (p0) REVERT: A 49 MET cc_start: 0.5976 (mmt) cc_final: 0.5328 (tpp) REVERT: A 100 LYS cc_start: 0.8860 (mtpt) cc_final: 0.8622 (mtpp) REVERT: A 121 SER cc_start: 0.8685 (m) cc_final: 0.8476 (p) REVERT: A 214 ASN cc_start: 0.8538 (t0) cc_final: 0.8086 (t0) REVERT: A 232 LEU cc_start: 0.7767 (mt) cc_final: 0.7127 (mp) REVERT: A 286 LEU cc_start: 0.8563 (mt) cc_final: 0.8051 (pt) REVERT: C 4 ARG cc_start: 0.8201 (ttt90) cc_final: 0.7848 (ttp80) REVERT: B 34 ASP cc_start: 0.8166 (p0) cc_final: 0.7786 (p0) REVERT: B 121 SER cc_start: 0.8664 (m) cc_final: 0.8438 (p) REVERT: B 214 ASN cc_start: 0.8604 (t0) cc_final: 0.8103 (t0) REVERT: B 232 LEU cc_start: 0.7754 (mt) cc_final: 0.7142 (mp) REVERT: B 286 LEU cc_start: 0.8542 (mt) cc_final: 0.8058 (pt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1813 time to fit residues: 39.2943 Evaluate side-chains 136 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5016 Z= 0.219 Angle : 0.648 8.846 6810 Z= 0.330 Chirality : 0.043 0.159 768 Planarity : 0.005 0.045 884 Dihedral : 5.067 20.492 680 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.38 % Allowed : 11.90 % Favored : 85.71 % 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: -0.70 (0.33), residues: 628 helix: 0.86 (0.38), residues: 170 sheet: -1.07 (0.53), residues: 102 loop : -0.92 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 218 HIS 0.006 0.001 HIS B 41 PHE 0.015 0.001 PHE D 3 TYR 0.014 0.002 TYR B 209 ARG 0.002 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8270 (p0) cc_final: 0.7677 (p0) REVERT: A 49 MET cc_start: 0.5967 (mmt) cc_final: 0.5584 (tpp) REVERT: A 214 ASN cc_start: 0.8644 (t0) cc_final: 0.8218 (t0) REVERT: A 286 LEU cc_start: 0.8546 (mt) cc_final: 0.8027 (pt) REVERT: C 4 ARG cc_start: 0.8329 (ttt90) cc_final: 0.7881 (ttp80) REVERT: B 286 LEU cc_start: 0.8532 (mt) cc_final: 0.8035 (pt) outliers start: 13 outliers final: 7 residues processed: 131 average time/residue: 0.1599 time to fit residues: 27.1848 Evaluate side-chains 122 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 147 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5016 Z= 0.273 Angle : 0.640 7.842 6810 Z= 0.326 Chirality : 0.043 0.143 768 Planarity : 0.004 0.042 884 Dihedral : 5.208 22.133 680 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.23 % Favored : 93.61 % Rotamer: Outliers : 3.85 % Allowed : 14.84 % Favored : 81.32 % 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: -0.72 (0.33), residues: 628 helix: 0.95 (0.39), residues: 170 sheet: -1.23 (0.52), residues: 102 loop : -0.93 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 218 HIS 0.006 0.001 HIS B 41 PHE 0.015 0.002 PHE B 181 TYR 0.022 0.002 TYR B 161 ARG 0.002 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8256 (p0) cc_final: 0.7834 (p0) REVERT: A 95 ASN cc_start: 0.8794 (t0) cc_final: 0.8573 (t0) REVERT: A 214 ASN cc_start: 0.8704 (t0) cc_final: 0.8274 (t0) REVERT: A 235 MET cc_start: 0.7714 (ptt) cc_final: 0.7480 (ptp) REVERT: A 286 LEU cc_start: 0.8537 (mt) cc_final: 0.8036 (pt) REVERT: C 4 ARG cc_start: 0.8477 (ttt90) cc_final: 0.7938 (ttp80) REVERT: B 34 ASP cc_start: 0.8184 (p0) cc_final: 0.7758 (p0) REVERT: B 95 ASN cc_start: 0.8710 (t0) cc_final: 0.8324 (t0) REVERT: B 286 LEU cc_start: 0.8477 (mt) cc_final: 0.7995 (pt) outliers start: 21 outliers final: 18 residues processed: 119 average time/residue: 0.1353 time to fit residues: 21.7168 Evaluate side-chains 129 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain C residue -1 LEU Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 265 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 53 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5016 Z= 0.168 Angle : 0.595 7.206 6810 Z= 0.302 Chirality : 0.041 0.148 768 Planarity : 0.004 0.037 884 Dihedral : 5.054 25.246 680 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.20 % Allowed : 17.03 % Favored : 80.77 % 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: -0.72 (0.33), residues: 628 helix: 1.07 (0.39), residues: 174 sheet: -1.66 (0.57), residues: 78 loop : -0.96 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 218 HIS 0.009 0.001 HIS B 41 PHE 0.010 0.001 PHE A 181 TYR 0.030 0.002 TYR B 161 ARG 0.001 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8220 (p0) cc_final: 0.7795 (p0) REVERT: A 95 ASN cc_start: 0.8790 (t0) cc_final: 0.8439 (t0) REVERT: A 100 LYS cc_start: 0.8882 (mtpt) cc_final: 0.8633 (mtpp) REVERT: A 214 ASN cc_start: 0.8706 (t0) cc_final: 0.8274 (t0) REVERT: A 286 LEU cc_start: 0.8501 (mt) cc_final: 0.8004 (pt) REVERT: C 4 ARG cc_start: 0.8493 (ttt90) cc_final: 0.7953 (ttp80) REVERT: B 34 ASP cc_start: 0.8182 (p0) cc_final: 0.7751 (p0) REVERT: B 95 ASN cc_start: 0.8743 (t0) cc_final: 0.8338 (t0) REVERT: B 286 LEU cc_start: 0.8483 (mt) cc_final: 0.7964 (pt) outliers start: 12 outliers final: 10 residues processed: 117 average time/residue: 0.1529 time to fit residues: 23.4440 Evaluate side-chains 115 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 245 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5016 Z= 0.285 Angle : 0.662 9.239 6810 Z= 0.336 Chirality : 0.043 0.164 768 Planarity : 0.004 0.036 884 Dihedral : 5.256 23.986 680 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.30 % Allowed : 15.93 % Favored : 80.77 % 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: -0.79 (0.33), residues: 628 helix: 1.02 (0.39), residues: 172 sheet: -1.79 (0.57), residues: 78 loop : -0.98 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 218 HIS 0.008 0.002 HIS B 41 PHE 0.011 0.002 PHE B 181 TYR 0.035 0.003 TYR A 161 ARG 0.003 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 0.597 Fit side-chains REVERT: A 34 ASP cc_start: 0.8268 (p0) cc_final: 0.7840 (p0) REVERT: A 95 ASN cc_start: 0.8781 (t0) cc_final: 0.8569 (t0) REVERT: A 214 ASN cc_start: 0.8733 (t0) cc_final: 0.8274 (t0) REVERT: A 286 LEU cc_start: 0.8522 (mt) cc_final: 0.8026 (pt) REVERT: C 4 ARG cc_start: 0.8598 (ttt90) cc_final: 0.8030 (ttp80) REVERT: B 34 ASP cc_start: 0.8246 (p0) cc_final: 0.7811 (p0) REVERT: B 95 ASN cc_start: 0.8683 (t0) cc_final: 0.8331 (t0) REVERT: B 286 LEU cc_start: 0.8512 (mt) cc_final: 0.7998 (pt) outliers start: 18 outliers final: 17 residues processed: 117 average time/residue: 0.1345 time to fit residues: 21.3338 Evaluate side-chains 125 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 263 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 0.0070 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 0.0030 overall best weight: 0.3608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5016 Z= 0.151 Angle : 0.590 8.552 6810 Z= 0.300 Chirality : 0.042 0.232 768 Planarity : 0.004 0.037 884 Dihedral : 5.058 22.175 680 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.20 % Allowed : 18.86 % Favored : 78.94 % 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: -0.67 (0.33), residues: 628 helix: 1.18 (0.39), residues: 174 sheet: -1.72 (0.57), residues: 78 loop : -0.95 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 218 HIS 0.009 0.001 HIS B 41 PHE 0.008 0.001 PHE A 181 TYR 0.032 0.002 TYR B 161 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 0.571 Fit side-chains REVERT: A 34 ASP cc_start: 0.8229 (p0) cc_final: 0.7817 (p0) REVERT: A 49 MET cc_start: 0.6825 (mmt) cc_final: 0.4404 (mmt) REVERT: A 95 ASN cc_start: 0.8791 (t0) cc_final: 0.8409 (t0) REVERT: A 214 ASN cc_start: 0.8716 (t0) cc_final: 0.8292 (t0) REVERT: A 286 LEU cc_start: 0.8498 (mt) cc_final: 0.7981 (pt) REVERT: C 4 ARG cc_start: 0.8562 (ttt90) cc_final: 0.7953 (ttp80) REVERT: B 34 ASP cc_start: 0.8235 (p0) cc_final: 0.7703 (p0) REVERT: B 95 ASN cc_start: 0.8675 (t0) cc_final: 0.8265 (t0) REVERT: B 286 LEU cc_start: 0.8492 (mt) cc_final: 0.7932 (pt) outliers start: 12 outliers final: 8 residues processed: 115 average time/residue: 0.1356 time to fit residues: 21.2405 Evaluate side-chains 113 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5016 Z= 0.173 Angle : 0.608 8.263 6810 Z= 0.314 Chirality : 0.042 0.194 768 Planarity : 0.004 0.037 884 Dihedral : 4.994 22.533 680 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.93 % Allowed : 19.96 % Favored : 77.11 % 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: -0.82 (0.33), residues: 628 helix: 0.96 (0.39), residues: 174 sheet: -1.75 (0.56), residues: 78 loop : -1.00 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 218 HIS 0.004 0.001 HIS A 41 PHE 0.009 0.001 PHE A 181 TYR 0.030 0.002 TYR B 161 ARG 0.001 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 0.629 Fit side-chains REVERT: A 34 ASP cc_start: 0.8243 (p0) cc_final: 0.7822 (p0) REVERT: A 49 MET cc_start: 0.6801 (mmt) cc_final: 0.4400 (mmt) REVERT: A 286 LEU cc_start: 0.8523 (mt) cc_final: 0.7995 (pt) REVERT: C 0 GLN cc_start: 0.6540 (mp10) cc_final: 0.6303 (mp10) REVERT: C 4 ARG cc_start: 0.8549 (ttt90) cc_final: 0.7942 (ttp80) REVERT: B 34 ASP cc_start: 0.8271 (p0) cc_final: 0.7711 (p0) REVERT: B 95 ASN cc_start: 0.8650 (t0) cc_final: 0.8277 (t0) REVERT: B 286 LEU cc_start: 0.8509 (mt) cc_final: 0.7931 (pt) outliers start: 16 outliers final: 12 residues processed: 115 average time/residue: 0.1420 time to fit residues: 22.3336 Evaluate side-chains 118 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 263 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 0.0980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5016 Z= 0.212 Angle : 0.621 8.825 6810 Z= 0.317 Chirality : 0.045 0.447 768 Planarity : 0.004 0.037 884 Dihedral : 5.189 23.151 680 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.93 % Allowed : 20.33 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.33), residues: 628 helix: 1.13 (0.39), residues: 174 sheet: -1.89 (0.54), residues: 82 loop : -1.10 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 218 HIS 0.006 0.001 HIS A 163 PHE 0.032 0.001 PHE A 140 TYR 0.030 0.002 TYR B 161 ARG 0.001 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.593 Fit side-chains REVERT: A 34 ASP cc_start: 0.8279 (p0) cc_final: 0.7847 (p0) REVERT: A 49 MET cc_start: 0.6867 (mmt) cc_final: 0.6640 (mmm) REVERT: A 286 LEU cc_start: 0.8522 (mt) cc_final: 0.7991 (pt) REVERT: C 0 GLN cc_start: 0.6668 (mp10) cc_final: 0.6215 (mp10) REVERT: C 4 ARG cc_start: 0.8541 (ttt90) cc_final: 0.8089 (ttp80) REVERT: B 34 ASP cc_start: 0.8288 (p0) cc_final: 0.7726 (p0) REVERT: B 95 ASN cc_start: 0.8566 (t0) cc_final: 0.8298 (t0) REVERT: B 286 LEU cc_start: 0.8532 (mt) cc_final: 0.7956 (pt) outliers start: 16 outliers final: 14 residues processed: 118 average time/residue: 0.1374 time to fit residues: 22.0798 Evaluate side-chains 119 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 263 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5016 Z= 0.214 Angle : 0.639 10.918 6810 Z= 0.325 Chirality : 0.042 0.136 768 Planarity : 0.004 0.037 884 Dihedral : 5.292 27.225 680 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.75 % Allowed : 20.88 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.33), residues: 628 helix: 0.81 (0.39), residues: 174 sheet: -1.91 (0.54), residues: 82 loop : -1.09 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 218 HIS 0.007 0.001 HIS B 41 PHE 0.027 0.001 PHE A 140 TYR 0.030 0.002 TYR A 161 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.627 Fit side-chains REVERT: A 34 ASP cc_start: 0.8267 (p0) cc_final: 0.7855 (p0) REVERT: A 95 ASN cc_start: 0.8695 (t0) cc_final: 0.8343 (t0) REVERT: A 286 LEU cc_start: 0.8525 (mt) cc_final: 0.7999 (pt) REVERT: C 0 GLN cc_start: 0.7001 (mp10) cc_final: 0.6509 (mp10) REVERT: C 4 ARG cc_start: 0.8519 (ttt90) cc_final: 0.8071 (ttp80) REVERT: B 34 ASP cc_start: 0.8301 (p0) cc_final: 0.7747 (p0) REVERT: B 95 ASN cc_start: 0.8629 (t0) cc_final: 0.8407 (t0) REVERT: B 286 LEU cc_start: 0.8531 (mt) cc_final: 0.7959 (pt) outliers start: 15 outliers final: 13 residues processed: 114 average time/residue: 0.1393 time to fit residues: 21.6713 Evaluate side-chains 117 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain C residue 1 SER Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 263 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 5016 Z= 0.370 Angle : 0.703 11.441 6810 Z= 0.362 Chirality : 0.044 0.146 768 Planarity : 0.004 0.036 884 Dihedral : 5.679 33.015 680 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.99 % Favored : 91.69 % Rotamer: Outliers : 2.75 % Allowed : 21.06 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.13 (0.33), residues: 628 helix: 0.86 (0.39), residues: 172 sheet: -2.06 (0.55), residues: 78 loop : -1.25 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 218 HIS 0.009 0.002 HIS B 41 PHE 0.030 0.002 PHE A 140 TYR 0.030 0.003 TYR A 161 ARG 0.005 0.000 ARG A 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.559 Fit side-chains REVERT: A 95 ASN cc_start: 0.8733 (t0) cc_final: 0.8452 (t0) REVERT: A 286 LEU cc_start: 0.8544 (mt) cc_final: 0.8033 (pt) REVERT: C 0 GLN cc_start: 0.7348 (mp10) cc_final: 0.6753 (mp10) REVERT: C 4 ARG cc_start: 0.8524 (ttt90) cc_final: 0.8020 (ttp80) REVERT: B 34 ASP cc_start: 0.8342 (p0) cc_final: 0.7885 (p0) REVERT: B 95 ASN cc_start: 0.8675 (t0) cc_final: 0.8472 (t0) REVERT: B 286 LEU cc_start: 0.8556 (mt) cc_final: 0.8012 (pt) outliers start: 15 outliers final: 13 residues processed: 116 average time/residue: 0.1429 time to fit residues: 22.5728 Evaluate side-chains 119 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 263 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.0770 chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 0.0970 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.137885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.115550 restraints weight = 18711.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.121412 restraints weight = 6581.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.125212 restraints weight = 3426.439| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5016 Z= 0.174 Angle : 0.643 13.012 6810 Z= 0.327 Chirality : 0.042 0.129 768 Planarity : 0.004 0.038 884 Dihedral : 5.396 30.979 680 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.28 % Allowed : 23.08 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.33), residues: 628 helix: 0.73 (0.39), residues: 174 sheet: -1.94 (0.54), residues: 82 loop : -1.18 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 218 HIS 0.006 0.001 HIS B 41 PHE 0.022 0.001 PHE A 140 TYR 0.030 0.002 TYR B 161 ARG 0.002 0.000 ARG B 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1438.17 seconds wall clock time: 26 minutes 52.42 seconds (1612.42 seconds total)