Starting phenix.real_space_refine on Mon Sep 23 12:14:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol6_16952/09_2024/8ol6_16952.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol6_16952/09_2024/8ol6_16952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol6_16952/09_2024/8ol6_16952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol6_16952/09_2024/8ol6_16952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol6_16952/09_2024/8ol6_16952.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol6_16952/09_2024/8ol6_16952.cif" } resolution = 3.8 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= 0.428 sd= 1.733 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 10 5.16 5 C 1470 2.51 5 N 390 2.21 5 O 390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2260 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.33, per 1000 atoms: 0.59 Number of scatterers: 2260 At special positions: 0 Unit cell: (73.528, 66.256, 40.4, 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 10 16.00 O 390 8.00 N 390 7.00 C 1470 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 - 3.00 Amino acid : True - 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: 0.49 Conformation dependent library (CDL) restraints added in 268.0 milliseconds 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 520 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 6.444A pdb=" N VAL A 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL C 18 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL E 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL G 18 " --> pdb=" O PHE I 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 35 removed outlier: 6.118A pdb=" N ILE A 31 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU C 34 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLY A 33 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU E 34 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET C 35 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU G 34 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET E 35 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU I 34 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET G 35 " --> pdb=" O LEU I 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 20 removed outlier: 6.364A pdb=" N VAL B 18 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL D 18 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL F 18 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL H 18 " --> pdb=" O PHE J 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 35 removed outlier: 6.955A pdb=" N LEU D 34 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET B 35 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU F 34 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET D 35 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU H 34 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET F 35 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU J 34 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET H 35 " --> pdb=" O LEU J 34 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 40 through 41 29 hydrogen bonds defined for protein. 87 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: 0.44 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 740 1.34 - 1.46: 310 1.46 - 1.57: 1220 1.57 - 1.68: 0 1.68 - 1.80: 20 Bond restraints: 2290 Sorted by residual: bond pdb=" C VAL H 36 " pdb=" O VAL H 36 " ideal model delta sigma weight residual 1.236 1.245 -0.009 1.19e-02 7.06e+03 5.62e-01 bond pdb=" C VAL B 36 " pdb=" O VAL B 36 " ideal model delta sigma weight residual 1.236 1.245 -0.009 1.19e-02 7.06e+03 5.50e-01 bond pdb=" C VAL C 36 " pdb=" O VAL C 36 " ideal model delta sigma weight residual 1.236 1.245 -0.009 1.19e-02 7.06e+03 5.46e-01 bond pdb=" C VAL E 36 " pdb=" O VAL E 36 " ideal model delta sigma weight residual 1.236 1.245 -0.009 1.19e-02 7.06e+03 5.11e-01 bond pdb=" C VAL I 36 " pdb=" O VAL I 36 " ideal model delta sigma weight residual 1.236 1.245 -0.008 1.19e-02 7.06e+03 5.08e-01 ... (remaining 2285 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.78: 2726 0.78 - 1.55: 314 1.55 - 2.33: 10 2.33 - 3.11: 10 3.11 - 3.88: 20 Bond angle restraints: 3080 Sorted by residual: angle pdb=" C VAL A 39 " pdb=" N VAL A 40 " pdb=" CA VAL A 40 " ideal model delta sigma weight residual 122.90 120.00 2.90 1.28e+00 6.10e-01 5.14e+00 angle pdb=" C VAL D 39 " pdb=" N VAL D 40 " pdb=" CA VAL D 40 " ideal model delta sigma weight residual 122.90 120.01 2.89 1.28e+00 6.10e-01 5.10e+00 angle pdb=" C VAL J 39 " pdb=" N VAL J 40 " pdb=" CA VAL J 40 " ideal model delta sigma weight residual 122.90 120.01 2.89 1.28e+00 6.10e-01 5.10e+00 angle pdb=" C VAL I 39 " pdb=" N VAL I 40 " pdb=" CA VAL I 40 " ideal model delta sigma weight residual 122.90 120.01 2.89 1.28e+00 6.10e-01 5.09e+00 angle pdb=" C VAL B 39 " pdb=" N VAL B 40 " pdb=" CA VAL B 40 " ideal model delta sigma weight residual 122.90 120.02 2.88 1.28e+00 6.10e-01 5.06e+00 ... (remaining 3075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.06: 1040 7.06 - 14.12: 140 14.12 - 21.18: 60 21.18 - 28.23: 40 28.23 - 35.29: 10 Dihedral angle restraints: 1290 sinusoidal: 470 harmonic: 820 Sorted by residual: dihedral pdb=" N MET I 35 " pdb=" CA MET I 35 " pdb=" CB MET I 35 " pdb=" CG MET I 35 " ideal model delta sinusoidal sigma weight residual 60.00 86.58 -26.58 3 1.50e+01 4.44e-03 3.90e+00 dihedral pdb=" N MET D 35 " pdb=" CA MET D 35 " pdb=" CB MET D 35 " pdb=" CG MET D 35 " ideal model delta sinusoidal sigma weight residual 60.00 86.58 -26.58 3 1.50e+01 4.44e-03 3.90e+00 dihedral pdb=" N MET E 35 " pdb=" CA MET E 35 " pdb=" CB MET E 35 " pdb=" CG MET E 35 " ideal model delta sinusoidal sigma weight residual 60.00 86.56 -26.56 3 1.50e+01 4.44e-03 3.89e+00 ... (remaining 1287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 189 0.023 - 0.046: 71 0.046 - 0.069: 51 0.069 - 0.092: 17 0.092 - 0.115: 42 Chirality restraints: 370 Sorted by residual: chirality pdb=" CA ILE E 32 " pdb=" N ILE E 32 " pdb=" C ILE E 32 " pdb=" CB ILE E 32 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.29e-01 chirality pdb=" CA ILE I 32 " pdb=" N ILE I 32 " pdb=" C ILE I 32 " pdb=" CB ILE I 32 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.28e-01 chirality pdb=" CA ILE C 32 " pdb=" N ILE C 32 " pdb=" C ILE C 32 " pdb=" CB ILE C 32 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.28e-01 ... (remaining 367 not shown) Planarity restraints: 390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 39 " 0.003 2.00e-02 2.50e+03 5.75e-03 3.30e-01 pdb=" C VAL A 39 " -0.010 2.00e-02 2.50e+03 pdb=" O VAL A 39 " 0.004 2.00e-02 2.50e+03 pdb=" N VAL A 40 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 39 " -0.003 2.00e-02 2.50e+03 5.68e-03 3.23e-01 pdb=" C VAL D 39 " 0.010 2.00e-02 2.50e+03 pdb=" O VAL D 39 " -0.004 2.00e-02 2.50e+03 pdb=" N VAL D 40 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 39 " 0.003 2.00e-02 2.50e+03 5.67e-03 3.21e-01 pdb=" C VAL I 39 " -0.010 2.00e-02 2.50e+03 pdb=" O VAL I 39 " 0.004 2.00e-02 2.50e+03 pdb=" N VAL I 40 " 0.003 2.00e-02 2.50e+03 ... (remaining 387 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 451 2.78 - 3.31: 1967 3.31 - 3.84: 3629 3.84 - 4.37: 3971 4.37 - 4.90: 7939 Nonbonded interactions: 17957 Sorted by model distance: nonbonded pdb=" NZ LYS E 28 " pdb=" OXT ALA H 42 " model vdw 2.255 3.120 nonbonded pdb=" NZ LYS C 28 " pdb=" OXT ALA F 42 " model vdw 2.255 3.120 nonbonded pdb=" NZ LYS G 28 " pdb=" OXT ALA J 42 " model vdw 2.255 3.120 nonbonded pdb=" NZ LYS H 28 " pdb=" OXT ALA I 42 " model vdw 2.257 3.120 nonbonded pdb=" NZ LYS D 28 " pdb=" OXT ALA E 42 " model vdw 2.257 3.120 ... (remaining 17952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.790 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.000 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 : 0.004 0.011 2290 Z= 0.240 Angle : 0.560 3.884 3080 Z= 0.354 Chirality : 0.048 0.115 370 Planarity : 0.001 0.006 390 Dihedral : 9.684 35.293 770 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % 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: -2.28 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 13 PHE 0.004 0.001 PHE F 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.259 Fit side-chains REVERT: B 18 VAL cc_start: 0.9485 (t) cc_final: 0.9191 (p) REVERT: C 39 VAL cc_start: 0.9441 (t) cc_final: 0.9160 (t) REVERT: D 15 GLN cc_start: 0.8563 (tt0) cc_final: 0.8333 (tm-30) REVERT: E 22 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7935 (mm-30) REVERT: F 15 GLN cc_start: 0.8632 (tt0) cc_final: 0.8385 (tm-30) REVERT: G 22 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7722 (mm-30) REVERT: H 15 GLN cc_start: 0.8679 (tt0) cc_final: 0.8357 (tm-30) REVERT: I 22 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7677 (mm-30) REVERT: I 40 VAL cc_start: 0.9100 (t) cc_final: 0.8892 (p) REVERT: J 14 HIS cc_start: 0.8525 (m170) cc_final: 0.6694 (p-80) REVERT: J 16 LYS cc_start: 0.8538 (mttp) cc_final: 0.8223 (mmtt) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1346 time to fit residues: 19.1696 Evaluate side-chains 81 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2290 Z= 0.302 Angle : 0.587 6.719 3080 Z= 0.300 Chirality : 0.051 0.122 370 Planarity : 0.002 0.015 390 Dihedral : 9.865 69.292 310 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 7.39 % Allowed : 26.09 % Favored : 66.52 % 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: -2.29 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 13 PHE 0.004 0.001 PHE C 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.254 Fit side-chains REVERT: A 39 VAL cc_start: 0.9207 (t) cc_final: 0.8962 (t) REVERT: C 39 VAL cc_start: 0.9454 (t) cc_final: 0.9187 (t) REVERT: D 22 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7720 (tp30) REVERT: E 22 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7885 (mm-30) REVERT: F 22 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7982 (tp30) REVERT: G 16 LYS cc_start: 0.8089 (mttp) cc_final: 0.7788 (mtpp) REVERT: G 22 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7680 (mm-30) REVERT: G 39 VAL cc_start: 0.9394 (t) cc_final: 0.9154 (t) REVERT: H 22 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7901 (tp30) REVERT: I 16 LYS cc_start: 0.8311 (mttp) cc_final: 0.7512 (mmtt) REVERT: I 22 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7595 (mm-30) REVERT: I 35 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8529 (ptm) REVERT: J 14 HIS cc_start: 0.8709 (m170) cc_final: 0.6722 (p-80) REVERT: J 16 LYS cc_start: 0.8639 (mttp) cc_final: 0.8242 (mmtt) outliers start: 17 outliers final: 3 residues processed: 102 average time/residue: 0.0914 time to fit residues: 11.5900 Evaluate side-chains 97 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain I residue 35 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 0.0770 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 0.0010 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 overall best weight: 2.6150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2290 Z= 0.219 Angle : 0.510 5.859 3080 Z= 0.265 Chirality : 0.053 0.117 370 Planarity : 0.002 0.017 390 Dihedral : 10.079 78.044 310 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 8.70 % Allowed : 27.83 % Favored : 63.48 % 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: -2.37 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 13 PHE 0.005 0.001 PHE E 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9183 (t) cc_final: 0.8946 (t) REVERT: E 16 LYS cc_start: 0.8249 (mttp) cc_final: 0.7953 (mtpp) REVERT: G 22 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7679 (mm-30) REVERT: G 39 VAL cc_start: 0.9399 (t) cc_final: 0.9156 (t) REVERT: H 18 VAL cc_start: 0.9493 (t) cc_final: 0.9096 (p) REVERT: H 22 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7889 (tp30) REVERT: I 16 LYS cc_start: 0.8282 (mttp) cc_final: 0.7490 (mmtt) REVERT: I 22 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7509 (mm-30) REVERT: J 14 HIS cc_start: 0.8754 (m170) cc_final: 0.6613 (p-80) REVERT: J 15 GLN cc_start: 0.8614 (tm-30) cc_final: 0.7946 (tm-30) REVERT: J 16 LYS cc_start: 0.8559 (mttp) cc_final: 0.7951 (tptt) outliers start: 20 outliers final: 3 residues processed: 106 average time/residue: 0.0931 time to fit residues: 12.1566 Evaluate side-chains 99 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain G residue 41 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.1980 chunk 28 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2290 Z= 0.310 Angle : 0.536 4.859 3080 Z= 0.278 Chirality : 0.052 0.115 370 Planarity : 0.002 0.014 390 Dihedral : 10.404 84.819 310 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 9.13 % Allowed : 27.39 % Favored : 63.48 % 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: -2.45 (0.47), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 13 PHE 0.004 0.001 PHE C 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: E 16 LYS cc_start: 0.8305 (mttp) cc_final: 0.8071 (mtpp) REVERT: G 22 GLU cc_start: 0.8234 (mm-30) cc_final: 0.8013 (tp30) REVERT: G 39 VAL cc_start: 0.9453 (t) cc_final: 0.9212 (t) REVERT: H 22 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7957 (tp30) REVERT: I 16 LYS cc_start: 0.8386 (mttp) cc_final: 0.7516 (mmtt) REVERT: I 22 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7635 (mm-30) REVERT: J 14 HIS cc_start: 0.8734 (m170) cc_final: 0.6626 (p-80) REVERT: J 16 LYS cc_start: 0.8548 (mttp) cc_final: 0.8140 (mmtt) outliers start: 21 outliers final: 8 residues processed: 107 average time/residue: 0.0912 time to fit residues: 11.9834 Evaluate side-chains 104 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain G residue 41 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2290 Z= 0.219 Angle : 0.508 4.760 3080 Z= 0.266 Chirality : 0.053 0.119 370 Planarity : 0.002 0.021 390 Dihedral : 10.321 87.043 310 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 8.70 % Allowed : 27.39 % Favored : 63.91 % 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: -2.50 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 13 PHE 0.004 0.001 PHE C 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9220 (t) cc_final: 0.8956 (t) REVERT: E 16 LYS cc_start: 0.8379 (mttp) cc_final: 0.8065 (mtpp) REVERT: E 22 GLU cc_start: 0.8448 (tp30) cc_final: 0.7854 (tp30) REVERT: E 39 VAL cc_start: 0.9458 (t) cc_final: 0.9198 (t) REVERT: F 22 GLU cc_start: 0.8377 (tp30) cc_final: 0.7883 (tp30) REVERT: G 22 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7853 (tp30) REVERT: H 22 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7800 (tp30) REVERT: I 16 LYS cc_start: 0.8414 (mttp) cc_final: 0.7491 (mmtt) REVERT: I 22 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7533 (tp30) REVERT: J 14 HIS cc_start: 0.8733 (m170) cc_final: 0.6542 (p-80) REVERT: J 16 LYS cc_start: 0.8596 (mttp) cc_final: 0.8187 (mmtt) outliers start: 20 outliers final: 7 residues processed: 107 average time/residue: 0.0918 time to fit residues: 12.1244 Evaluate side-chains 103 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain G residue 41 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2290 Z= 0.291 Angle : 0.541 4.434 3080 Z= 0.282 Chirality : 0.053 0.121 370 Planarity : 0.002 0.021 390 Dihedral : 10.155 79.493 310 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.62 % Favored : 91.03 % Rotamer: Outliers : 11.74 % Allowed : 24.78 % Favored : 63.48 % 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: -2.45 (0.47), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 13 PHE 0.004 0.001 PHE E 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9238 (t) cc_final: 0.8985 (t) REVERT: E 16 LYS cc_start: 0.8370 (mttp) cc_final: 0.8080 (mtpp) REVERT: G 39 VAL cc_start: 0.9469 (t) cc_final: 0.9206 (t) REVERT: H 22 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7978 (tp30) REVERT: I 16 LYS cc_start: 0.8422 (mttp) cc_final: 0.7470 (mmtt) REVERT: I 22 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7649 (mm-30) REVERT: J 15 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8228 (tm-30) REVERT: J 16 LYS cc_start: 0.8508 (mttp) cc_final: 0.7949 (mmtt) outliers start: 27 outliers final: 13 residues processed: 112 average time/residue: 0.0858 time to fit residues: 12.0538 Evaluate side-chains 111 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 12 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 35 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2290 Z= 0.200 Angle : 0.525 5.151 3080 Z= 0.273 Chirality : 0.054 0.126 370 Planarity : 0.002 0.020 390 Dihedral : 9.868 70.291 310 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.14 % Favored : 95.52 % Rotamer: Outliers : 10.00 % Allowed : 28.70 % Favored : 61.30 % 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: -2.52 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 13 PHE 0.004 0.001 PHE A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9212 (t) cc_final: 0.8954 (t) REVERT: E 16 LYS cc_start: 0.8392 (mttp) cc_final: 0.8106 (mtpp) REVERT: E 22 GLU cc_start: 0.8433 (tp30) cc_final: 0.7859 (tp30) REVERT: F 22 GLU cc_start: 0.8389 (tp30) cc_final: 0.7859 (tp30) REVERT: G 22 GLU cc_start: 0.8157 (tp30) cc_final: 0.7534 (tp30) REVERT: G 39 VAL cc_start: 0.9471 (t) cc_final: 0.9204 (t) REVERT: H 15 GLN cc_start: 0.8618 (tt0) cc_final: 0.8195 (tt0) REVERT: I 16 LYS cc_start: 0.8456 (mttp) cc_final: 0.7500 (mmtt) REVERT: I 23 ASP cc_start: 0.7259 (p0) cc_final: 0.6172 (m-30) REVERT: J 15 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8038 (tm-30) REVERT: J 16 LYS cc_start: 0.8473 (mttp) cc_final: 0.7750 (tptt) outliers start: 23 outliers final: 15 residues processed: 108 average time/residue: 0.0854 time to fit residues: 11.5178 Evaluate side-chains 110 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain I residue 40 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.0030 chunk 22 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2290 Z= 0.285 Angle : 0.551 5.972 3080 Z= 0.287 Chirality : 0.053 0.151 370 Planarity : 0.002 0.019 390 Dihedral : 9.682 60.454 310 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.24 % Favored : 92.41 % Rotamer: Outliers : 10.00 % Allowed : 29.13 % Favored : 60.87 % 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: -2.61 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 13 PHE 0.004 0.001 PHE C 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9291 (t) cc_final: 0.9051 (t) REVERT: B 39 VAL cc_start: 0.9196 (t) cc_final: 0.8937 (t) REVERT: E 16 LYS cc_start: 0.8427 (mttp) cc_final: 0.8137 (mtpp) REVERT: E 22 GLU cc_start: 0.8461 (tp30) cc_final: 0.7868 (tp30) REVERT: F 22 GLU cc_start: 0.8406 (tp30) cc_final: 0.7869 (tp30) REVERT: F 39 VAL cc_start: 0.9499 (t) cc_final: 0.9252 (t) REVERT: G 22 GLU cc_start: 0.8211 (tp30) cc_final: 0.7573 (tp30) REVERT: G 39 VAL cc_start: 0.9500 (t) cc_final: 0.9261 (t) REVERT: H 15 GLN cc_start: 0.8657 (tt0) cc_final: 0.8136 (tt0) REVERT: I 16 LYS cc_start: 0.8436 (mttp) cc_final: 0.7452 (mmtt) REVERT: J 15 GLN cc_start: 0.8563 (tm-30) cc_final: 0.7902 (tm-30) REVERT: J 16 LYS cc_start: 0.8411 (mttp) cc_final: 0.7702 (tptt) outliers start: 23 outliers final: 14 residues processed: 104 average time/residue: 0.0861 time to fit residues: 11.3054 Evaluate side-chains 108 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain I residue 40 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2290 Z= 0.195 Angle : 0.526 6.653 3080 Z= 0.274 Chirality : 0.054 0.145 370 Planarity : 0.002 0.017 390 Dihedral : 9.467 61.673 310 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.79 % Favored : 95.86 % Rotamer: Outliers : 8.70 % Allowed : 29.57 % Favored : 61.74 % 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: -2.66 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 13 PHE 0.004 0.001 PHE A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9257 (t) cc_final: 0.9024 (t) REVERT: B 39 VAL cc_start: 0.9189 (t) cc_final: 0.8927 (t) REVERT: E 16 LYS cc_start: 0.8526 (mttp) cc_final: 0.8242 (mtpp) REVERT: E 22 GLU cc_start: 0.8452 (tp30) cc_final: 0.7863 (tp30) REVERT: F 22 GLU cc_start: 0.8370 (tp30) cc_final: 0.7883 (tp30) REVERT: G 22 GLU cc_start: 0.8169 (tp30) cc_final: 0.7573 (tp30) REVERT: H 15 GLN cc_start: 0.8561 (tt0) cc_final: 0.8199 (tt0) REVERT: I 16 LYS cc_start: 0.8485 (mttp) cc_final: 0.7489 (mmtt) REVERT: I 23 ASP cc_start: 0.7186 (p0) cc_final: 0.6132 (m-30) REVERT: J 15 GLN cc_start: 0.8473 (tm-30) cc_final: 0.7898 (tm-30) REVERT: J 16 LYS cc_start: 0.8319 (mttp) cc_final: 0.7692 (tptt) outliers start: 20 outliers final: 13 residues processed: 110 average time/residue: 0.0861 time to fit residues: 11.8366 Evaluate side-chains 109 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2290 Z= 0.341 Angle : 0.568 7.476 3080 Z= 0.299 Chirality : 0.054 0.160 370 Planarity : 0.002 0.017 390 Dihedral : 9.406 62.671 310 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.69 % Favored : 88.97 % Rotamer: Outliers : 9.57 % Allowed : 30.87 % Favored : 59.57 % 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: -2.64 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 13 PHE 0.005 0.001 PHE I 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 VAL cc_start: 0.9294 (t) cc_final: 0.9059 (t) REVERT: B 39 VAL cc_start: 0.9227 (t) cc_final: 0.8982 (t) REVERT: E 16 LYS cc_start: 0.8480 (mttp) cc_final: 0.8193 (mtpp) REVERT: G 22 GLU cc_start: 0.8284 (tp30) cc_final: 0.7697 (tp30) REVERT: H 15 GLN cc_start: 0.8657 (tt0) cc_final: 0.8175 (tt0) REVERT: H 39 VAL cc_start: 0.9506 (t) cc_final: 0.9257 (t) REVERT: I 16 LYS cc_start: 0.8484 (mttp) cc_final: 0.7596 (mmtt) REVERT: J 15 GLN cc_start: 0.8529 (tm-30) cc_final: 0.7885 (tm-30) REVERT: J 16 LYS cc_start: 0.8392 (mttp) cc_final: 0.7683 (tptt) outliers start: 22 outliers final: 17 residues processed: 103 average time/residue: 0.0892 time to fit residues: 11.3994 Evaluate side-chains 109 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain I residue 27 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.0970 chunk 16 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.106740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.091867 restraints weight = 4924.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.094195 restraints weight = 2662.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.095974 restraints weight = 1751.887| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2290 Z= 0.272 Angle : 0.566 7.677 3080 Z= 0.300 Chirality : 0.054 0.170 370 Planarity : 0.002 0.023 390 Dihedral : 9.453 64.063 310 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.69 % Allowed : 5.86 % Favored : 93.45 % Rotamer: Outliers : 10.00 % Allowed : 30.43 % Favored : 59.57 % 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: -2.62 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 13 PHE 0.005 0.001 PHE A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 884.66 seconds wall clock time: 16 minutes 36.88 seconds (996.88 seconds total)