Starting phenix.real_space_refine on Fri Apr 5 12:01:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owd_17234/04_2024/8owd_17234.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owd_17234/04_2024/8owd_17234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owd_17234/04_2024/8owd_17234.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owd_17234/04_2024/8owd_17234.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owd_17234/04_2024/8owd_17234.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owd_17234/04_2024/8owd_17234.pdb" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 970 2.51 5 N 265 2.21 5 O 285 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 1525 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "B" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "C" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "D" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "E" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Time building chain proxies: 1.05, per 1000 atoms: 0.69 Number of scatterers: 1525 At special positions: 0 Unit cell: (45.15, 85.05, 40.95, 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 5 16.00 O 285 8.00 N 265 7.00 C 970 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: 0.68 Conformation dependent library (CDL) restraints added in 279.2 milliseconds 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 340 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA3, first strand: chain 'A' and resid 17 through 22 removed outlier: 6.204A pdb=" N VAL A 18 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ALA B 21 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE A 20 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL B 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ALA C 21 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N PHE B 20 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL C 18 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ALA D 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N PHE C 20 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL D 18 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA E 21 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE D 20 " --> pdb=" O ALA E 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.059A pdb=" N ILE A 31 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE B 31 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE C 31 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE D 31 " --> pdb=" O ILE E 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 35 through 36 24 hydrogen bonds defined for protein. 72 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: 0.35 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 507 1.33 - 1.45: 283 1.45 - 1.56: 755 1.56 - 1.68: 0 1.68 - 1.80: 10 Bond restraints: 1555 Sorted by residual: bond pdb=" CA LYS C 16 " pdb=" C LYS C 16 " ideal model delta sigma weight residual 1.526 1.492 0.034 1.03e-02 9.43e+03 1.09e+01 bond pdb=" CA LYS B 16 " pdb=" C LYS B 16 " ideal model delta sigma weight residual 1.526 1.493 0.033 1.03e-02 9.43e+03 1.05e+01 bond pdb=" CA LYS A 16 " pdb=" C LYS A 16 " ideal model delta sigma weight residual 1.526 1.493 0.033 1.03e-02 9.43e+03 1.05e+01 bond pdb=" CA LYS D 16 " pdb=" C LYS D 16 " ideal model delta sigma weight residual 1.526 1.493 0.033 1.03e-02 9.43e+03 1.05e+01 bond pdb=" CA LYS E 16 " pdb=" C LYS E 16 " ideal model delta sigma weight residual 1.526 1.494 0.033 1.03e-02 9.43e+03 1.00e+01 ... (remaining 1550 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.07: 89 107.07 - 113.60: 711 113.60 - 120.13: 705 120.13 - 126.66: 560 126.66 - 133.19: 20 Bond angle restraints: 2085 Sorted by residual: angle pdb=" N GLY D 25 " pdb=" CA GLY D 25 " pdb=" C GLY D 25 " ideal model delta sigma weight residual 111.54 133.19 -21.65 1.36e+00 5.41e-01 2.53e+02 angle pdb=" N GLY C 25 " pdb=" CA GLY C 25 " pdb=" C GLY C 25 " ideal model delta sigma weight residual 111.54 133.15 -21.61 1.36e+00 5.41e-01 2.52e+02 angle pdb=" N GLY B 25 " pdb=" CA GLY B 25 " pdb=" C GLY B 25 " ideal model delta sigma weight residual 111.54 133.14 -21.60 1.36e+00 5.41e-01 2.52e+02 angle pdb=" N GLY E 25 " pdb=" CA GLY E 25 " pdb=" C GLY E 25 " ideal model delta sigma weight residual 111.54 133.13 -21.59 1.36e+00 5.41e-01 2.52e+02 angle pdb=" N GLY A 25 " pdb=" CA GLY A 25 " pdb=" C GLY A 25 " ideal model delta sigma weight residual 111.54 133.13 -21.59 1.36e+00 5.41e-01 2.52e+02 ... (remaining 2080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 745 14.98 - 29.96: 40 29.96 - 44.93: 35 44.93 - 59.91: 45 59.91 - 74.89: 5 Dihedral angle restraints: 870 sinusoidal: 330 harmonic: 540 Sorted by residual: dihedral pdb=" C ARG B 5 " pdb=" N ARG B 5 " pdb=" CA ARG B 5 " pdb=" CB ARG B 5 " ideal model delta harmonic sigma weight residual -122.60 -132.38 9.78 0 2.50e+00 1.60e-01 1.53e+01 dihedral pdb=" C ARG C 5 " pdb=" N ARG C 5 " pdb=" CA ARG C 5 " pdb=" CB ARG C 5 " ideal model delta harmonic sigma weight residual -122.60 -132.37 9.77 0 2.50e+00 1.60e-01 1.53e+01 dihedral pdb=" C ARG E 5 " pdb=" N ARG E 5 " pdb=" CA ARG E 5 " pdb=" CB ARG E 5 " ideal model delta harmonic sigma weight residual -122.60 -132.35 9.75 0 2.50e+00 1.60e-01 1.52e+01 ... (remaining 867 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.069: 126 0.069 - 0.136: 54 0.136 - 0.204: 15 0.204 - 0.272: 6 0.272 - 0.339: 19 Chirality restraints: 220 Sorted by residual: chirality pdb=" CB VAL A 12 " pdb=" CA VAL A 12 " pdb=" CG1 VAL A 12 " pdb=" CG2 VAL A 12 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CB VAL C 12 " pdb=" CA VAL C 12 " pdb=" CG1 VAL C 12 " pdb=" CG2 VAL C 12 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CB VAL E 12 " pdb=" CA VAL E 12 " pdb=" CG1 VAL E 12 " pdb=" CG2 VAL E 12 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 217 not shown) Planarity restraints: 275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 24 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C VAL B 24 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL B 24 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY B 25 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 24 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C VAL D 24 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL D 24 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY D 25 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 24 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C VAL C 24 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL C 24 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY C 25 " 0.011 2.00e-02 2.50e+03 ... (remaining 272 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.98: 776 2.98 - 3.46: 1452 3.46 - 3.94: 2619 3.94 - 4.42: 2948 4.42 - 4.90: 5446 Nonbonded interactions: 13241 Sorted by model distance: nonbonded pdb=" NZ LYS C 28 " pdb=" OD2 ASP D 23 " model vdw 2.506 2.520 nonbonded pdb=" NZ LYS B 28 " pdb=" OD2 ASP C 23 " model vdw 2.517 2.520 nonbonded pdb=" NZ LYS D 28 " pdb=" OD2 ASP E 23 " model vdw 2.543 2.520 nonbonded pdb=" NZ LYS A 28 " pdb=" OD2 ASP B 23 " model vdw 2.586 2.520 nonbonded pdb=" O ASP E 1 " pdb=" OE1 GLU E 3 " model vdw 2.591 3.040 ... (remaining 13236 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: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 2.790 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.350 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 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 : 0.012 0.035 1555 Z= 0.813 Angle : 2.438 21.645 2085 Z= 1.629 Chirality : 0.118 0.339 220 Planarity : 0.005 0.019 275 Dihedral : 21.081 74.889 530 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 16.13 % Allowed : 19.35 % Favored : 64.52 % 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: -0.81 (0.54), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.61 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 14 PHE 0.015 0.005 PHE C 20 TYR 0.005 0.002 TYR D 10 ARG 0.009 0.005 ARG B 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 57 time to evaluate : 0.168 Fit side-chains REVERT: A 11 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7071 (tt0) REVERT: A 13 HIS cc_start: 0.6825 (OUTLIER) cc_final: 0.6551 (m-70) REVERT: A 22 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: A 23 ASP cc_start: 0.8691 (t0) cc_final: 0.8261 (t0) REVERT: B 11 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7204 (tt0) REVERT: B 13 HIS cc_start: 0.6499 (OUTLIER) cc_final: 0.6124 (m170) REVERT: B 17 LEU cc_start: 0.8770 (mp) cc_final: 0.8437 (mt) REVERT: B 22 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: B 23 ASP cc_start: 0.8988 (t0) cc_final: 0.8316 (t0) REVERT: B 28 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7986 (mttt) REVERT: C 11 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7229 (tt0) REVERT: C 13 HIS cc_start: 0.6280 (OUTLIER) cc_final: 0.5932 (m-70) REVERT: C 22 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: C 23 ASP cc_start: 0.8924 (t0) cc_final: 0.7842 (t0) REVERT: D 11 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7212 (tt0) REVERT: D 13 HIS cc_start: 0.6744 (OUTLIER) cc_final: 0.6357 (m170) REVERT: D 22 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8309 (tm-30) REVERT: D 23 ASP cc_start: 0.8949 (t0) cc_final: 0.8229 (t0) REVERT: D 28 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8079 (mttt) REVERT: E 5 ARG cc_start: 0.7617 (ttp80) cc_final: 0.6557 (tpp-160) REVERT: E 11 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7436 (tt0) REVERT: E 13 HIS cc_start: 0.6167 (OUTLIER) cc_final: 0.5802 (m170) REVERT: E 22 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8331 (tm-30) REVERT: E 23 ASP cc_start: 0.8805 (t0) cc_final: 0.7989 (t0) REVERT: E 28 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.6245 (mmtt) outliers start: 25 outliers final: 5 residues processed: 77 average time/residue: 0.1731 time to fit residues: 14.5306 Evaluate side-chains 75 residues out of total 155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 52 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 28 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN E 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 1555 Z= 0.254 Angle : 0.605 7.364 2085 Z= 0.314 Chirality : 0.051 0.129 220 Planarity : 0.002 0.013 275 Dihedral : 17.435 56.604 262 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 11.61 % Allowed : 21.94 % Favored : 66.45 % 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: -2.67 (0.42), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.32), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 6 PHE 0.010 0.001 PHE E 4 TYR 0.006 0.002 TYR B 10 ARG 0.003 0.001 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 42 time to evaluate : 0.172 Fit side-chains REVERT: A 22 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7912 (tm-30) REVERT: B 11 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: B 13 HIS cc_start: 0.6246 (OUTLIER) cc_final: 0.5982 (m170) REVERT: C 11 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7396 (tt0) REVERT: C 13 HIS cc_start: 0.6274 (OUTLIER) cc_final: 0.5975 (m-70) REVERT: D 11 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7187 (tt0) REVERT: D 28 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8160 (mttp) REVERT: E 5 ARG cc_start: 0.7522 (ttp80) cc_final: 0.6331 (tpp-160) REVERT: E 13 HIS cc_start: 0.6438 (OUTLIER) cc_final: 0.6187 (m170) REVERT: E 28 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.6631 (mmmt) outliers start: 18 outliers final: 5 residues processed: 59 average time/residue: 0.1870 time to fit residues: 12.0588 Evaluate side-chains 47 residues out of total 155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 34 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 28 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 HIS ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1555 Z= 0.312 Angle : 0.558 6.029 2085 Z= 0.296 Chirality : 0.050 0.127 220 Planarity : 0.003 0.020 275 Dihedral : 12.700 51.203 235 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 7.74 % Allowed : 24.52 % Favored : 67.74 % 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: -3.11 (0.41), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.32), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 13 PHE 0.009 0.001 PHE A 4 TYR 0.006 0.002 TYR B 10 ARG 0.003 0.001 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 36 time to evaluate : 0.175 Fit side-chains REVERT: A 26 SER cc_start: 0.8419 (m) cc_final: 0.8210 (m) REVERT: B 3 GLU cc_start: 0.7414 (mp0) cc_final: 0.6785 (mp0) REVERT: B 11 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: C 11 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: D 5 ARG cc_start: 0.8497 (tpp80) cc_final: 0.8180 (ttt-90) REVERT: D 11 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7560 (tt0) REVERT: D 28 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8123 (mttp) REVERT: E 5 ARG cc_start: 0.7697 (ttp80) cc_final: 0.7014 (mmp-170) outliers start: 12 outliers final: 7 residues processed: 48 average time/residue: 0.1454 time to fit residues: 7.8509 Evaluate side-chains 43 residues out of total 155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 12 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1555 Z= 0.245 Angle : 0.560 6.533 2085 Z= 0.278 Chirality : 0.050 0.130 220 Planarity : 0.002 0.013 275 Dihedral : 10.994 51.673 225 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 6.45 % Allowed : 25.16 % Favored : 68.39 % 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: -3.24 (0.41), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.31), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 13 PHE 0.007 0.001 PHE A 4 TYR 0.004 0.001 TYR B 10 ARG 0.002 0.001 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 0.176 Fit side-chains REVERT: A 26 SER cc_start: 0.8340 (m) cc_final: 0.8066 (p) REVERT: B 3 GLU cc_start: 0.7472 (mp0) cc_final: 0.6845 (mp0) REVERT: B 11 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: C 11 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7252 (tt0) REVERT: D 5 ARG cc_start: 0.8450 (tpp80) cc_final: 0.8109 (ttt-90) REVERT: D 28 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7961 (mttp) REVERT: E 5 ARG cc_start: 0.7711 (ttp80) cc_final: 0.6841 (tpm170) REVERT: E 11 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7229 (tt0) outliers start: 10 outliers final: 5 residues processed: 42 average time/residue: 0.1501 time to fit residues: 7.0937 Evaluate side-chains 39 residues out of total 155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 30 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 12 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 1555 Z= 0.479 Angle : 0.638 6.599 2085 Z= 0.332 Chirality : 0.051 0.130 220 Planarity : 0.004 0.046 275 Dihedral : 11.215 58.651 222 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 7.10 % Allowed : 23.87 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.39), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.30), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 13 PHE 0.011 0.002 PHE A 4 TYR 0.007 0.002 TYR B 10 ARG 0.003 0.001 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.160 Fit side-chains REVERT: A 22 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: B 3 GLU cc_start: 0.7546 (mp0) cc_final: 0.6923 (mp0) REVERT: C 3 GLU cc_start: 0.7054 (mp0) cc_final: 0.6564 (mp0) REVERT: C 11 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7316 (tt0) REVERT: D 3 GLU cc_start: 0.7344 (mp0) cc_final: 0.6685 (mp0) REVERT: D 28 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7934 (mttp) REVERT: E 5 ARG cc_start: 0.7749 (ttp80) cc_final: 0.7200 (mmp-170) REVERT: E 11 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7567 (tt0) REVERT: E 22 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7840 (tm-30) outliers start: 11 outliers final: 5 residues processed: 44 average time/residue: 0.1486 time to fit residues: 7.3350 Evaluate side-chains 40 residues out of total 155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 30 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 22 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1555 Z= 0.221 Angle : 0.554 6.394 2085 Z= 0.273 Chirality : 0.050 0.131 220 Planarity : 0.002 0.015 275 Dihedral : 9.862 55.607 219 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 7.74 % Allowed : 21.94 % Favored : 70.32 % 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: -3.44 (0.39), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.30), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 13 PHE 0.005 0.001 PHE E 4 TYR 0.004 0.001 TYR C 10 ARG 0.002 0.000 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 31 time to evaluate : 0.174 Fit side-chains REVERT: A 22 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7245 (tm-30) REVERT: B 3 GLU cc_start: 0.7647 (mp0) cc_final: 0.6993 (mp0) REVERT: B 22 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: C 3 GLU cc_start: 0.7036 (mp0) cc_final: 0.6826 (mp0) REVERT: C 11 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: D 3 GLU cc_start: 0.7482 (mp0) cc_final: 0.6839 (mp0) REVERT: D 5 ARG cc_start: 0.8384 (tpp80) cc_final: 0.7979 (ttt-90) REVERT: D 22 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: E 3 GLU cc_start: 0.7457 (mp0) cc_final: 0.7142 (mp0) REVERT: E 5 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7090 (mmp-170) REVERT: E 11 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: E 22 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: E 28 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.6713 (mmmt) outliers start: 12 outliers final: 5 residues processed: 43 average time/residue: 0.1435 time to fit residues: 6.9087 Evaluate side-chains 42 residues out of total 155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 30 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain C residue 11 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 28 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1555 Z= 0.308 Angle : 0.584 7.385 2085 Z= 0.289 Chirality : 0.050 0.130 220 Planarity : 0.002 0.023 275 Dihedral : 9.759 58.327 215 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 9.03 % Allowed : 20.00 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.39), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.30), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 13 PHE 0.007 0.001 PHE A 4 TYR 0.004 0.001 TYR B 10 ARG 0.001 0.001 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 32 time to evaluate : 0.178 Fit side-chains REVERT: A 22 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: B 3 GLU cc_start: 0.7658 (mp0) cc_final: 0.7004 (mp0) REVERT: B 22 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7441 (tm-30) REVERT: C 3 GLU cc_start: 0.7119 (mp0) cc_final: 0.6863 (mp0) REVERT: C 22 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: D 3 GLU cc_start: 0.7397 (mp0) cc_final: 0.6784 (mp0) REVERT: D 22 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: E 5 ARG cc_start: 0.7731 (ttp80) cc_final: 0.7185 (mmp-170) REVERT: E 11 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: E 22 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: E 28 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.6716 (mmmt) outliers start: 14 outliers final: 6 residues processed: 46 average time/residue: 0.1479 time to fit residues: 7.6335 Evaluate side-chains 42 residues out of total 155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 29 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 28 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 16 optimal weight: 0.0970 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 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: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1555 Z= 0.203 Angle : 0.559 6.675 2085 Z= 0.271 Chirality : 0.050 0.131 220 Planarity : 0.002 0.021 275 Dihedral : 8.577 59.653 212 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 8.39 % Allowed : 18.71 % Favored : 72.90 % 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: -3.50 (0.40), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.31), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 13 PHE 0.005 0.001 PHE E 4 TYR 0.004 0.001 TYR C 10 ARG 0.005 0.001 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 34 time to evaluate : 0.177 Fit side-chains REVERT: A 22 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: B 3 GLU cc_start: 0.7645 (mp0) cc_final: 0.6981 (mp0) REVERT: B 22 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: C 3 GLU cc_start: 0.7120 (mp0) cc_final: 0.6867 (mp0) REVERT: C 22 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: D 3 GLU cc_start: 0.7447 (mp0) cc_final: 0.6853 (mp0) REVERT: D 22 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7329 (tm-30) REVERT: E 3 GLU cc_start: 0.7457 (mp0) cc_final: 0.7094 (mp0) REVERT: E 5 ARG cc_start: 0.7663 (ttp80) cc_final: 0.7188 (mmp-170) REVERT: E 11 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: E 22 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7733 (tm-30) REVERT: E 28 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.6761 (mmmt) outliers start: 13 outliers final: 6 residues processed: 46 average time/residue: 0.1305 time to fit residues: 6.8361 Evaluate side-chains 45 residues out of total 155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 32 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 28 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 1555 Z= 0.376 Angle : 0.625 7.657 2085 Z= 0.309 Chirality : 0.051 0.136 220 Planarity : 0.003 0.029 275 Dihedral : 8.742 58.876 212 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 8.39 % Allowed : 18.71 % Favored : 72.90 % 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: -3.50 (0.40), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.31), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 13 PHE 0.008 0.001 PHE A 4 TYR 0.005 0.002 TYR B 10 ARG 0.005 0.001 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 29 time to evaluate : 0.123 Fit side-chains REVERT: A 22 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: B 3 GLU cc_start: 0.7665 (mp0) cc_final: 0.7015 (mp0) REVERT: B 22 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: C 3 GLU cc_start: 0.7138 (mp0) cc_final: 0.6551 (mp0) REVERT: C 22 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: D 3 GLU cc_start: 0.7388 (mp0) cc_final: 0.6820 (mp0) REVERT: D 22 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7376 (tm-30) REVERT: E 3 GLU cc_start: 0.7458 (mp0) cc_final: 0.7040 (mp0) REVERT: E 5 ARG cc_start: 0.7622 (ttp80) cc_final: 0.7139 (mmp-170) REVERT: E 11 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: E 22 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: E 28 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.6681 (mmmt) outliers start: 13 outliers final: 6 residues processed: 42 average time/residue: 0.0949 time to fit residues: 4.5441 Evaluate side-chains 42 residues out of total 155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 29 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 0.0770 chunk 7 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 overall best weight: 3.0544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 1555 Z= 0.381 Angle : 0.631 7.832 2085 Z= 0.311 Chirality : 0.050 0.137 220 Planarity : 0.003 0.030 275 Dihedral : 8.307 49.130 212 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 8.39 % Allowed : 19.35 % Favored : 72.26 % 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: -3.52 (0.40), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.31), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 13 PHE 0.008 0.001 PHE A 4 TYR 0.005 0.002 TYR B 10 ARG 0.005 0.001 ARG D 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 380 Ramachandran restraints generated. 190 Oldfield, 0 Emsley, 190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 31 time to evaluate : 0.173 Fit side-chains REVERT: A 22 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7240 (tm-30) REVERT: B 3 GLU cc_start: 0.7677 (mp0) cc_final: 0.7026 (mp0) REVERT: B 22 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7552 (tm-30) REVERT: C 3 GLU cc_start: 0.7129 (mp0) cc_final: 0.6537 (mp0) REVERT: C 22 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: D 3 GLU cc_start: 0.7340 (mp0) cc_final: 0.6779 (mp0) REVERT: D 22 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: E 3 GLU cc_start: 0.7467 (mp0) cc_final: 0.7045 (mp0) REVERT: E 5 ARG cc_start: 0.7630 (ttp80) cc_final: 0.7126 (mmp-170) REVERT: E 11 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7871 (tt0) REVERT: E 22 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7690 (tm-30) outliers start: 13 outliers final: 6 residues processed: 44 average time/residue: 0.1285 time to fit residues: 6.4646 Evaluate side-chains 41 residues out of total 155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 29 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 22 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 3 optimal weight: 0.0370 chunk 10 optimal weight: 2.9990 overall best weight: 2.0864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 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 = 0.3578 r_free = 0.3578 target = 0.082823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.074451 restraints weight = 3128.797| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.62 r_work: 0.3353 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1555 Z= 0.278 Angle : 0.607 8.196 2085 Z= 0.292 Chirality : 0.050 0.137 220 Planarity : 0.002 0.021 275 Dihedral : 7.737 42.395 212 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 7.74 % Allowed : 20.00 % Favored : 72.26 % 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: -3.51 (0.41), residues: 190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.31), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 13 PHE 0.006 0.001 PHE A 4 TYR 0.004 0.001 TYR C 10 ARG 0.004 0.001 ARG D 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 905.77 seconds wall clock time: 18 minutes 53.31 seconds (1133.31 seconds total)