Starting phenix.real_space_refine on Mon Mar 11 13:36:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ot9_13057/03_2024/7ot9_13057.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ot9_13057/03_2024/7ot9_13057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ot9_13057/03_2024/7ot9_13057.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ot9_13057/03_2024/7ot9_13057.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ot9_13057/03_2024/7ot9_13057.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ot9_13057/03_2024/7ot9_13057.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 55 5.16 5 C 5650 2.51 5 N 1395 2.21 5 O 1310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "E ARG 180": "NH1" <-> "NH2" Residue "E GLU 182": "OE1" <-> "OE2" Residue "E ARG 301": "NH1" <-> "NH2" Residue "E GLU 347": "OE1" <-> "OE2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D ARG 62": "NH1" <-> "NH2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D ARG 301": "NH1" <-> "NH2" Residue "D GLU 347": "OE1" <-> "OE2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B GLU 347": "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: 8410 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1682 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain breaks: 2 Chain: "E" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1682 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain breaks: 2 Chain: "D" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1682 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain breaks: 2 Chain: "C" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1682 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain breaks: 2 Chain: "B" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1682 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain breaks: 2 Time building chain proxies: 4.64, per 1000 atoms: 0.55 Number of scatterers: 8410 At special positions: 0 Unit cell: (126.312, 125.204, 60.94, 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 55 16.00 O 1310 8.00 N 1395 7.00 C 5650 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: 3.50 Conformation dependent library (CDL) restraints added in 1.7 seconds 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 86.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 9 through 48 Proline residue: A 33 - end of helix removed outlier: 4.468A pdb=" N LEU A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLY A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 59 Processing helix chain 'A' and resid 62 through 79 Processing helix chain 'A' and resid 167 through 180 Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 198 through 230 removed outlier: 3.997A pdb=" N GLY A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 removed outlier: 3.749A pdb=" N LEU A 281 " --> pdb=" O TRP A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 307 through 322 Processing helix chain 'A' and resid 325 through 346 Proline residue: A 331 - end of helix Processing helix chain 'E' and resid 9 through 48 Proline residue: E 33 - end of helix removed outlier: 4.468A pdb=" N LEU E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLY E 37 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY E 42 " --> pdb=" O PHE E 38 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 59 Processing helix chain 'E' and resid 62 through 79 Processing helix chain 'E' and resid 167 through 180 Processing helix chain 'E' and resid 180 through 196 Processing helix chain 'E' and resid 198 through 230 removed outlier: 3.996A pdb=" N GLY E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 289 removed outlier: 3.749A pdb=" N LEU E 281 " --> pdb=" O TRP E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 Processing helix chain 'E' and resid 307 through 322 Processing helix chain 'E' and resid 325 through 346 Proline residue: E 331 - end of helix Processing helix chain 'D' and resid 9 through 48 Proline residue: D 33 - end of helix removed outlier: 4.468A pdb=" N LEU D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLY D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY D 42 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 59 Processing helix chain 'D' and resid 62 through 79 Processing helix chain 'D' and resid 167 through 180 Processing helix chain 'D' and resid 180 through 196 Processing helix chain 'D' and resid 198 through 230 removed outlier: 3.997A pdb=" N GLY D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 289 removed outlier: 3.748A pdb=" N LEU D 281 " --> pdb=" O TRP D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 Processing helix chain 'D' and resid 307 through 322 Processing helix chain 'D' and resid 325 through 346 Proline residue: D 331 - end of helix Processing helix chain 'C' and resid 9 through 48 Proline residue: C 33 - end of helix removed outlier: 4.468A pdb=" N LEU C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLY C 37 " --> pdb=" O PRO C 33 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 59 Processing helix chain 'C' and resid 62 through 79 Processing helix chain 'C' and resid 167 through 180 Processing helix chain 'C' and resid 180 through 196 Processing helix chain 'C' and resid 198 through 230 removed outlier: 3.997A pdb=" N GLY C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 289 removed outlier: 3.749A pdb=" N LEU C 281 " --> pdb=" O TRP C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 Processing helix chain 'C' and resid 307 through 322 Processing helix chain 'C' and resid 325 through 346 Proline residue: C 331 - end of helix Processing helix chain 'B' and resid 9 through 48 Proline residue: B 33 - end of helix removed outlier: 4.468A pdb=" N LEU B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLY B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 59 Processing helix chain 'B' and resid 62 through 79 Processing helix chain 'B' and resid 167 through 180 Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 198 through 230 removed outlier: 3.997A pdb=" N GLY B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 289 removed outlier: 3.749A pdb=" N LEU B 281 " --> pdb=" O TRP B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 307 through 322 Processing helix chain 'B' and resid 325 through 346 Proline residue: B 331 - end of helix 695 hydrogen bonds defined for protein. 2055 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: 2.25 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2565 1.34 - 1.46: 1319 1.46 - 1.57: 4606 1.57 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 8590 Sorted by residual: bond pdb=" C ALA C 41 " pdb=" N GLY C 42 " ideal model delta sigma weight residual 1.331 1.316 0.015 1.46e-02 4.69e+03 1.01e+00 bond pdb=" C ALA D 41 " pdb=" N GLY D 42 " ideal model delta sigma weight residual 1.331 1.316 0.014 1.46e-02 4.69e+03 9.84e-01 bond pdb=" C ALA A 41 " pdb=" N GLY A 42 " ideal model delta sigma weight residual 1.331 1.316 0.014 1.46e-02 4.69e+03 9.59e-01 bond pdb=" C ALA B 41 " pdb=" N GLY B 42 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.46e-02 4.69e+03 9.11e-01 bond pdb=" C ALA E 41 " pdb=" N GLY E 42 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.46e-02 4.69e+03 9.03e-01 ... (remaining 8585 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.21: 237 106.21 - 113.15: 5038 113.15 - 120.09: 2809 120.09 - 127.03: 3492 127.03 - 133.98: 154 Bond angle restraints: 11730 Sorted by residual: angle pdb=" N VAL E 198 " pdb=" CA VAL E 198 " pdb=" C VAL E 198 " ideal model delta sigma weight residual 113.53 108.12 5.41 9.80e-01 1.04e+00 3.05e+01 angle pdb=" N VAL B 198 " pdb=" CA VAL B 198 " pdb=" C VAL B 198 " ideal model delta sigma weight residual 113.53 108.15 5.38 9.80e-01 1.04e+00 3.01e+01 angle pdb=" N VAL C 198 " pdb=" CA VAL C 198 " pdb=" C VAL C 198 " ideal model delta sigma weight residual 113.53 108.16 5.37 9.80e-01 1.04e+00 3.01e+01 angle pdb=" N VAL A 198 " pdb=" CA VAL A 198 " pdb=" C VAL A 198 " ideal model delta sigma weight residual 113.53 108.16 5.37 9.80e-01 1.04e+00 3.00e+01 angle pdb=" N VAL D 198 " pdb=" CA VAL D 198 " pdb=" C VAL D 198 " ideal model delta sigma weight residual 113.53 108.16 5.37 9.80e-01 1.04e+00 3.00e+01 ... (remaining 11725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 4470 17.70 - 35.40: 410 35.40 - 53.10: 45 53.10 - 70.80: 10 70.80 - 88.49: 15 Dihedral angle restraints: 4950 sinusoidal: 1845 harmonic: 3105 Sorted by residual: dihedral pdb=" CA ASN A 293 " pdb=" C ASN A 293 " pdb=" N VAL A 294 " pdb=" CA VAL A 294 " ideal model delta harmonic sigma weight residual -180.00 -160.95 -19.05 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASN C 293 " pdb=" C ASN C 293 " pdb=" N VAL C 294 " pdb=" CA VAL C 294 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASN D 293 " pdb=" C ASN D 293 " pdb=" N VAL D 294 " pdb=" CA VAL D 294 " ideal model delta harmonic sigma weight residual 180.00 -160.99 -19.01 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 4947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 840 0.031 - 0.062: 479 0.062 - 0.092: 124 0.092 - 0.123: 37 0.123 - 0.154: 10 Chirality restraints: 1490 Sorted by residual: chirality pdb=" CB ILE E 300 " pdb=" CA ILE E 300 " pdb=" CG1 ILE E 300 " pdb=" CG2 ILE E 300 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CB ILE A 300 " pdb=" CA ILE A 300 " pdb=" CG1 ILE A 300 " pdb=" CG2 ILE A 300 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CB ILE B 300 " pdb=" CA ILE B 300 " pdb=" CG1 ILE B 300 " pdb=" CG2 ILE B 300 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.84e-01 ... (remaining 1487 not shown) Planarity restraints: 1385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 42 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C GLY C 42 " 0.040 2.00e-02 2.50e+03 pdb=" O GLY C 42 " -0.015 2.00e-02 2.50e+03 pdb=" N THR C 43 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 42 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" C GLY B 42 " -0.040 2.00e-02 2.50e+03 pdb=" O GLY B 42 " 0.015 2.00e-02 2.50e+03 pdb=" N THR B 43 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 42 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C GLY D 42 " 0.040 2.00e-02 2.50e+03 pdb=" O GLY D 42 " -0.015 2.00e-02 2.50e+03 pdb=" N THR D 43 " -0.014 2.00e-02 2.50e+03 ... (remaining 1382 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 103 2.69 - 3.24: 8869 3.24 - 3.80: 13722 3.80 - 4.35: 15471 4.35 - 4.90: 27598 Nonbonded interactions: 65763 Sorted by model distance: nonbonded pdb=" O TRP D 344 " pdb=" NH1 ARG C 194 " model vdw 2.138 2.520 nonbonded pdb=" OG1 THR C 48 " pdb=" OH TYR C 178 " model vdw 2.140 2.440 nonbonded pdb=" OG1 THR E 48 " pdb=" OH TYR E 178 " model vdw 2.140 2.440 nonbonded pdb=" OG1 THR D 48 " pdb=" OH TYR D 178 " model vdw 2.141 2.440 nonbonded pdb=" OG1 THR A 48 " pdb=" OH TYR A 178 " model vdw 2.141 2.440 ... (remaining 65758 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' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.940 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: 3.310 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 25.160 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 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 : 0.005 0.030 8590 Z= 0.319 Angle : 0.667 6.000 11730 Z= 0.365 Chirality : 0.040 0.154 1490 Planarity : 0.004 0.023 1385 Dihedral : 14.505 88.495 2940 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: 2.47 (0.25), residues: 1075 helix: 2.27 (0.17), residues: 905 sheet: None (None), residues: 0 loop : -2.04 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 344 HIS 0.019 0.007 HIS B 190 PHE 0.011 0.001 PHE C 163 TYR 0.003 0.001 TYR B 178 ARG 0.004 0.000 ARG C 301 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.925 Fit side-chains REVERT: A 170 MET cc_start: 0.6257 (ttm) cc_final: 0.5920 (ttm) REVERT: E 170 MET cc_start: 0.6847 (ttm) cc_final: 0.6643 (ttm) REVERT: E 182 GLU cc_start: 0.8133 (mp0) cc_final: 0.7812 (mp0) REVERT: E 302 MET cc_start: 0.8221 (mpp) cc_final: 0.7746 (mpt) REVERT: D 170 MET cc_start: 0.6758 (ttm) cc_final: 0.6502 (ttm) REVERT: D 182 GLU cc_start: 0.8336 (mp0) cc_final: 0.8060 (mp0) REVERT: C 178 TYR cc_start: 0.9038 (m-80) cc_final: 0.8514 (m-80) REVERT: C 182 GLU cc_start: 0.8276 (mp0) cc_final: 0.7959 (mp0) REVERT: C 302 MET cc_start: 0.7952 (mpp) cc_final: 0.7726 (mpt) REVERT: B 170 MET cc_start: 0.6627 (ttm) cc_final: 0.6325 (ttm) REVERT: B 182 GLU cc_start: 0.8352 (mp0) cc_final: 0.8080 (mp0) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 1.1854 time to fit residues: 144.0425 Evaluate side-chains 87 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.2980 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.0030 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8590 Z= 0.172 Angle : 0.603 7.040 11730 Z= 0.297 Chirality : 0.037 0.121 1490 Planarity : 0.004 0.029 1385 Dihedral : 4.392 20.774 1155 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.26 % Allowed : 13.03 % 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: 2.96 (0.26), residues: 1075 helix: 2.79 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -2.15 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 344 HIS 0.013 0.004 HIS A 190 PHE 0.008 0.001 PHE B 163 TYR 0.004 0.001 TYR A 178 ARG 0.002 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.860 Fit side-chains REVERT: A 170 MET cc_start: 0.6518 (ttm) cc_final: 0.6309 (ttm) REVERT: E 302 MET cc_start: 0.8251 (mpp) cc_final: 0.7652 (mpt) REVERT: D 170 MET cc_start: 0.6734 (ttm) cc_final: 0.6514 (ttm) REVERT: D 182 GLU cc_start: 0.8304 (mp0) cc_final: 0.8009 (mp0) REVERT: C 178 TYR cc_start: 0.8996 (m-80) cc_final: 0.8518 (m-80) REVERT: C 182 GLU cc_start: 0.8217 (mp0) cc_final: 0.7894 (mp0) REVERT: C 302 MET cc_start: 0.8192 (mpp) cc_final: 0.7981 (mpt) REVERT: B 170 MET cc_start: 0.6719 (ttm) cc_final: 0.6421 (ttm) outliers start: 11 outliers final: 8 residues processed: 104 average time/residue: 1.1993 time to fit residues: 132.9573 Evaluate side-chains 98 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain B residue 64 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8590 Z= 0.293 Angle : 0.606 7.372 11730 Z= 0.295 Chirality : 0.038 0.112 1490 Planarity : 0.005 0.041 1385 Dihedral : 4.292 21.011 1155 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.09 % Allowed : 18.74 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.25), residues: 1075 helix: 2.74 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -2.22 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 344 HIS 0.012 0.004 HIS E 190 PHE 0.007 0.001 PHE A 163 TYR 0.005 0.002 TYR B 178 ARG 0.002 0.000 ARG E 301 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: E 182 GLU cc_start: 0.8095 (mp0) cc_final: 0.7764 (mp0) REVERT: E 302 MET cc_start: 0.8328 (mpp) cc_final: 0.7659 (mpt) REVERT: D 182 GLU cc_start: 0.8306 (mp0) cc_final: 0.7989 (mp0) REVERT: D 294 VAL cc_start: 0.6789 (OUTLIER) cc_final: 0.6556 (t) REVERT: C 178 TYR cc_start: 0.9069 (m-80) cc_final: 0.8378 (m-80) REVERT: C 182 GLU cc_start: 0.8237 (mp0) cc_final: 0.7894 (mp0) REVERT: C 302 MET cc_start: 0.8177 (mpp) cc_final: 0.7898 (mpt) outliers start: 27 outliers final: 10 residues processed: 106 average time/residue: 1.1648 time to fit residues: 132.0172 Evaluate side-chains 99 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 305 ASP Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8590 Z= 0.172 Angle : 0.561 7.923 11730 Z= 0.273 Chirality : 0.036 0.113 1490 Planarity : 0.004 0.030 1385 Dihedral : 4.225 20.522 1155 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.83 % Allowed : 23.31 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.10 (0.26), residues: 1075 helix: 2.88 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -2.04 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 344 HIS 0.008 0.003 HIS E 190 PHE 0.007 0.001 PHE B 163 TYR 0.003 0.001 TYR E 178 ARG 0.001 0.000 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: E 302 MET cc_start: 0.8317 (mpp) cc_final: 0.7594 (mpt) REVERT: D 182 GLU cc_start: 0.8267 (mp0) cc_final: 0.7956 (mp0) REVERT: D 294 VAL cc_start: 0.6741 (OUTLIER) cc_final: 0.6526 (t) REVERT: C 178 TYR cc_start: 0.9011 (m-80) cc_final: 0.8429 (m-80) REVERT: C 182 GLU cc_start: 0.8159 (mp0) cc_final: 0.7806 (mp0) REVERT: C 302 MET cc_start: 0.8149 (mpp) cc_final: 0.7785 (mpt) outliers start: 16 outliers final: 11 residues processed: 105 average time/residue: 1.1035 time to fit residues: 124.1630 Evaluate side-chains 102 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain B residue 294 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8590 Z= 0.175 Angle : 0.533 8.194 11730 Z= 0.263 Chirality : 0.036 0.136 1490 Planarity : 0.004 0.032 1385 Dihedral : 4.149 20.151 1155 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.94 % Allowed : 26.63 % Favored : 71.43 % 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: 3.21 (0.26), residues: 1075 helix: 2.95 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.97 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 277 HIS 0.008 0.003 HIS E 190 PHE 0.006 0.001 PHE B 163 TYR 0.005 0.001 TYR E 178 ARG 0.001 0.000 ARG C 301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 182 GLU cc_start: 0.8254 (mp0) cc_final: 0.7937 (mp0) REVERT: D 294 VAL cc_start: 0.6573 (OUTLIER) cc_final: 0.6347 (t) REVERT: C 178 TYR cc_start: 0.9029 (m-80) cc_final: 0.8341 (m-80) REVERT: C 182 GLU cc_start: 0.8161 (mp0) cc_final: 0.7816 (mp0) REVERT: C 302 MET cc_start: 0.8322 (mpp) cc_final: 0.7849 (mpt) outliers start: 17 outliers final: 13 residues processed: 104 average time/residue: 1.1363 time to fit residues: 126.4383 Evaluate side-chains 105 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8590 Z= 0.204 Angle : 0.535 8.617 11730 Z= 0.263 Chirality : 0.036 0.119 1490 Planarity : 0.004 0.033 1385 Dihedral : 4.142 20.245 1155 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.17 % Allowed : 27.66 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.22 (0.26), residues: 1075 helix: 2.96 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -2.02 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 344 HIS 0.008 0.003 HIS E 190 PHE 0.006 0.001 PHE A 34 TYR 0.004 0.001 TYR B 178 ARG 0.007 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8219 (mp0) cc_final: 0.7772 (mp0) REVERT: E 284 TRP cc_start: 0.6624 (m100) cc_final: 0.6231 (m100) REVERT: D 182 GLU cc_start: 0.8263 (mp0) cc_final: 0.7938 (mp0) REVERT: D 294 VAL cc_start: 0.6539 (OUTLIER) cc_final: 0.6308 (t) REVERT: C 178 TYR cc_start: 0.9030 (m-80) cc_final: 0.8341 (m-80) REVERT: C 182 GLU cc_start: 0.8165 (mp0) cc_final: 0.7820 (mp0) REVERT: C 302 MET cc_start: 0.8253 (mpp) cc_final: 0.7843 (mpt) REVERT: B 182 GLU cc_start: 0.8001 (mp0) cc_final: 0.7762 (mp0) outliers start: 19 outliers final: 14 residues processed: 104 average time/residue: 1.1243 time to fit residues: 125.1987 Evaluate side-chains 106 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8590 Z= 0.170 Angle : 0.527 9.759 11730 Z= 0.258 Chirality : 0.036 0.123 1490 Planarity : 0.004 0.032 1385 Dihedral : 4.084 19.873 1155 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.63 % Allowed : 28.11 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.26), residues: 1075 helix: 3.04 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.94 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 344 HIS 0.006 0.003 HIS E 190 PHE 0.006 0.001 PHE B 163 TYR 0.004 0.001 TYR B 178 ARG 0.002 0.000 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8207 (mp0) cc_final: 0.7765 (mp0) REVERT: E 284 TRP cc_start: 0.6540 (m100) cc_final: 0.6195 (m100) REVERT: D 182 GLU cc_start: 0.8232 (mp0) cc_final: 0.7897 (mp0) REVERT: D 294 VAL cc_start: 0.6455 (OUTLIER) cc_final: 0.6234 (t) REVERT: D 313 SER cc_start: 0.9300 (t) cc_final: 0.8766 (m) REVERT: C 178 TYR cc_start: 0.9006 (m-80) cc_final: 0.8461 (m-80) REVERT: C 182 GLU cc_start: 0.8207 (mp0) cc_final: 0.7855 (mp0) REVERT: C 284 TRP cc_start: 0.6481 (m100) cc_final: 0.5980 (m100) REVERT: C 302 MET cc_start: 0.8295 (mpp) cc_final: 0.7945 (mpt) outliers start: 23 outliers final: 14 residues processed: 110 average time/residue: 1.0468 time to fit residues: 123.5411 Evaluate side-chains 107 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8590 Z= 0.164 Angle : 0.555 11.190 11730 Z= 0.268 Chirality : 0.036 0.128 1490 Planarity : 0.004 0.032 1385 Dihedral : 4.049 19.745 1155 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.29 % Allowed : 28.80 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.26), residues: 1075 helix: 3.09 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.90 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 344 HIS 0.006 0.003 HIS E 190 PHE 0.011 0.001 PHE A 34 TYR 0.004 0.001 TYR B 178 ARG 0.002 0.000 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8205 (mp0) cc_final: 0.7770 (mp0) REVERT: E 182 GLU cc_start: 0.8067 (mp0) cc_final: 0.7633 (mp0) REVERT: E 284 TRP cc_start: 0.6532 (m100) cc_final: 0.6208 (m100) REVERT: D 182 GLU cc_start: 0.8223 (mp0) cc_final: 0.7888 (mp0) REVERT: D 313 SER cc_start: 0.9301 (t) cc_final: 0.8768 (m) REVERT: C 178 TYR cc_start: 0.9005 (m-80) cc_final: 0.8230 (m-80) REVERT: C 182 GLU cc_start: 0.8200 (mp0) cc_final: 0.7835 (mp0) REVERT: C 284 TRP cc_start: 0.6447 (m100) cc_final: 0.5992 (m100) REVERT: C 302 MET cc_start: 0.8338 (mpp) cc_final: 0.8002 (mpt) outliers start: 20 outliers final: 8 residues processed: 112 average time/residue: 1.2208 time to fit residues: 146.6884 Evaluate side-chains 101 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 104 optimal weight: 40.0000 chunk 63 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8590 Z= 0.179 Angle : 0.592 12.484 11730 Z= 0.285 Chirality : 0.036 0.175 1490 Planarity : 0.004 0.032 1385 Dihedral : 4.044 19.668 1155 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.40 % Allowed : 29.26 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.26), residues: 1075 helix: 3.09 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.90 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 49 HIS 0.006 0.003 HIS E 190 PHE 0.009 0.001 PHE A 34 TYR 0.005 0.001 TYR B 178 ARG 0.003 0.000 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8193 (mp0) cc_final: 0.7770 (mp0) REVERT: E 182 GLU cc_start: 0.8071 (mp0) cc_final: 0.7636 (mp0) REVERT: D 182 GLU cc_start: 0.8224 (mp0) cc_final: 0.7887 (mp0) REVERT: D 313 SER cc_start: 0.9300 (t) cc_final: 0.8775 (m) REVERT: C 178 TYR cc_start: 0.8996 (m-80) cc_final: 0.8226 (m-80) REVERT: C 182 GLU cc_start: 0.8199 (mp0) cc_final: 0.7845 (mp0) REVERT: C 284 TRP cc_start: 0.6427 (m100) cc_final: 0.5968 (m100) REVERT: C 302 MET cc_start: 0.8274 (mpp) cc_final: 0.8013 (mpt) outliers start: 21 outliers final: 13 residues processed: 114 average time/residue: 1.0910 time to fit residues: 133.2616 Evaluate side-chains 105 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 352 THR Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 109 optimal weight: 0.0870 chunk 100 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 26 optimal weight: 0.0000 overall best weight: 0.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8590 Z= 0.151 Angle : 0.592 13.606 11730 Z= 0.284 Chirality : 0.035 0.171 1490 Planarity : 0.004 0.033 1385 Dihedral : 3.967 19.286 1155 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.37 % Allowed : 30.29 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.51 (0.26), residues: 1075 helix: 3.15 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.82 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 49 HIS 0.006 0.003 HIS E 190 PHE 0.017 0.001 PHE D 34 TYR 0.003 0.001 TYR B 178 ARG 0.002 0.000 ARG C 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8168 (mp0) cc_final: 0.7755 (mp0) REVERT: A 284 TRP cc_start: 0.6444 (m100) cc_final: 0.6035 (m100) REVERT: A 313 SER cc_start: 0.9282 (t) cc_final: 0.8888 (m) REVERT: E 71 THR cc_start: 0.8835 (m) cc_final: 0.8634 (m) REVERT: E 182 GLU cc_start: 0.8091 (mp0) cc_final: 0.7633 (mp0) REVERT: E 284 TRP cc_start: 0.6555 (m100) cc_final: 0.6126 (m100) REVERT: D 71 THR cc_start: 0.9099 (m) cc_final: 0.8834 (m) REVERT: D 182 GLU cc_start: 0.8184 (mp0) cc_final: 0.7880 (mp0) REVERT: D 313 SER cc_start: 0.9286 (t) cc_final: 0.8738 (m) REVERT: C 178 TYR cc_start: 0.8947 (m-80) cc_final: 0.8324 (m-80) REVERT: C 182 GLU cc_start: 0.8239 (mp0) cc_final: 0.7866 (mp0) REVERT: C 284 TRP cc_start: 0.6476 (m100) cc_final: 0.6050 (m100) REVERT: C 302 MET cc_start: 0.8274 (mpp) cc_final: 0.8014 (mpt) REVERT: B 284 TRP cc_start: 0.6649 (m100) cc_final: 0.6226 (m100) outliers start: 12 outliers final: 8 residues processed: 110 average time/residue: 1.1274 time to fit residues: 132.6937 Evaluate side-chains 104 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 352 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 30.0000 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 0.0370 chunk 63 optimal weight: 0.0980 overall best weight: 0.5062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 209 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 = 0.3732 r_free = 0.3732 target = 0.103163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.074149 restraints weight = 18333.665| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.85 r_work: 0.3039 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8590 Z= 0.160 Angle : 0.613 13.421 11730 Z= 0.293 Chirality : 0.036 0.174 1490 Planarity : 0.004 0.032 1385 Dihedral : 3.976 19.236 1155 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.83 % Allowed : 29.60 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.26), residues: 1075 helix: 3.18 (0.17), residues: 875 sheet: None (None), residues: 0 loop : -1.83 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 277 HIS 0.006 0.003 HIS E 190 PHE 0.015 0.001 PHE D 34 TYR 0.006 0.001 TYR B 178 ARG 0.003 0.000 ARG B 301 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2744.51 seconds wall clock time: 49 minutes 26.07 seconds (2966.07 seconds total)