Starting phenix.real_space_refine on Mon Sep 23 12:20:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7h_23212/09_2024/7l7h_23212.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7h_23212/09_2024/7l7h_23212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7h_23212/09_2024/7l7h_23212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7h_23212/09_2024/7l7h_23212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7h_23212/09_2024/7l7h_23212.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7h_23212/09_2024/7l7h_23212.cif" } resolution = 4.0 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: 3 Type Number sf(0) Gaussians C 1518 2.51 5 N 424 2.21 5 O 488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2430 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 304 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "B" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 304 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "C" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 304 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "D" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 304 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "E" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 304 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "F" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 304 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "G" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 302 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 43} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 304 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Time building chain proxies: 1.92, per 1000 atoms: 0.79 Number of scatterers: 2430 At special positions: 0 Unit cell: (101.65, 82.39, 40.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 488 8.00 N 424 7.00 C 1518 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: 0.56 Conformation dependent library (CDL) restraints added in 333.9 milliseconds 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 592 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 64 removed outlier: 7.461A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL C 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 40 removed outlier: 6.443A pdb=" N TYR B 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 49 removed outlier: 6.830A pdb=" N VAL B 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL C 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 38 through 39 removed outlier: 3.513A pdb=" N TYR F 39 " --> pdb=" O LEU G 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 48 through 49 removed outlier: 6.402A pdb=" N VAL E 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL F 48 " --> pdb=" O VAL G 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 57 removed outlier: 3.639A pdb=" N THR H 54 " --> pdb=" O ALA G 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 63 through 64 removed outlier: 6.755A pdb=" N VAL G 63 " --> pdb=" O THR H 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 7 hydrogen bonds defined for protein. 21 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: 0.60 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 424 1.29 - 1.36: 392 1.36 - 1.43: 117 1.43 - 1.50: 507 1.50 - 1.58: 998 Bond restraints: 2438 Sorted by residual: bond pdb=" CA THR D 54 " pdb=" CB THR D 54 " ideal model delta sigma weight residual 1.526 1.469 0.057 1.53e-02 4.27e+03 1.40e+01 bond pdb=" CB THR D 44 " pdb=" CG2 THR D 44 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.89e+00 bond pdb=" CB GLU A 61 " pdb=" CG GLU A 61 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.55e+00 bond pdb=" CA THR F 44 " pdb=" CB THR F 44 " ideal model delta sigma weight residual 1.534 1.508 0.025 1.45e-02 4.76e+03 3.07e+00 bond pdb=" CG LEU C 38 " pdb=" CD1 LEU C 38 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.97e+00 ... (remaining 2433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 2821 1.86 - 3.72: 390 3.72 - 5.58: 71 5.58 - 7.43: 21 7.43 - 9.29: 6 Bond angle restraints: 3309 Sorted by residual: angle pdb=" N LYS B 60 " pdb=" CA LYS B 60 " pdb=" C LYS B 60 " ideal model delta sigma weight residual 114.04 107.66 6.38 1.24e+00 6.50e-01 2.65e+01 angle pdb=" N ALA A 78 " pdb=" CA ALA A 78 " pdb=" C ALA A 78 " ideal model delta sigma weight residual 110.42 117.53 -7.11 1.46e+00 4.69e-01 2.37e+01 angle pdb=" C VAL B 37 " pdb=" N LEU B 38 " pdb=" CA LEU B 38 " ideal model delta sigma weight residual 121.31 128.32 -7.01 1.49e+00 4.50e-01 2.21e+01 angle pdb=" N ALA E 78 " pdb=" CA ALA E 78 " pdb=" C ALA E 78 " ideal model delta sigma weight residual 110.42 116.94 -6.52 1.46e+00 4.69e-01 2.00e+01 angle pdb=" N VAL H 77 " pdb=" CA VAL H 77 " pdb=" C VAL H 77 " ideal model delta sigma weight residual 112.17 107.93 4.24 9.50e-01 1.11e+00 1.99e+01 ... (remaining 3304 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 1220 17.23 - 34.46: 156 34.46 - 51.69: 29 51.69 - 68.92: 1 68.92 - 86.14: 1 Dihedral angle restraints: 1407 sinusoidal: 463 harmonic: 944 Sorted by residual: dihedral pdb=" CA VAL A 37 " pdb=" C VAL A 37 " pdb=" N LEU A 38 " pdb=" CA LEU A 38 " ideal model delta harmonic sigma weight residual 180.00 152.04 27.96 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLY G 68 " pdb=" C GLY G 68 " pdb=" N ALA G 69 " pdb=" CA ALA G 69 " ideal model delta harmonic sigma weight residual 180.00 153.44 26.56 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA VAL F 66 " pdb=" C VAL F 66 " pdb=" N GLY F 67 " pdb=" CA GLY F 67 " ideal model delta harmonic sigma weight residual 180.00 154.80 25.20 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 1404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 200 0.051 - 0.102: 158 0.102 - 0.153: 69 0.153 - 0.204: 17 0.204 - 0.255: 3 Chirality restraints: 447 Sorted by residual: chirality pdb=" CB VAL E 71 " pdb=" CA VAL E 71 " pdb=" CG1 VAL E 71 " pdb=" CG2 VAL E 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB VAL H 40 " pdb=" CA VAL H 40 " pdb=" CG1 VAL H 40 " pdb=" CG2 VAL H 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB THR C 44 " pdb=" CA THR C 44 " pdb=" OG1 THR C 44 " pdb=" CG2 THR C 44 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 444 not shown) Planarity restraints: 408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 39 " 0.025 2.00e-02 2.50e+03 1.60e-02 5.14e+00 pdb=" CG TYR F 39 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR F 39 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR F 39 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR F 39 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR F 39 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR F 39 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR F 39 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 44 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C THR B 44 " -0.037 2.00e-02 2.50e+03 pdb=" O THR B 44 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS B 45 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 52 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C VAL F 52 " -0.035 2.00e-02 2.50e+03 pdb=" O VAL F 52 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA F 53 " 0.012 2.00e-02 2.50e+03 ... (remaining 405 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 319 2.74 - 3.28: 2220 3.28 - 3.82: 3663 3.82 - 4.36: 3947 4.36 - 4.90: 7666 Nonbonded interactions: 17815 Sorted by model distance: nonbonded pdb=" OG1 THR A 44 " pdb=" O GLU A 46 " model vdw 2.199 3.040 nonbonded pdb=" OG1 THR B 44 " pdb=" O GLU B 46 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR H 44 " pdb=" O GLU H 46 " model vdw 2.266 3.040 nonbonded pdb=" OG1 THR G 44 " pdb=" O GLU G 46 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR D 44 " pdb=" O GLU D 46 " model vdw 2.286 3.040 ... (remaining 17810 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' and (resid 36 or (resid 37 and (name N or name CA or name C or name O \ or name CB )) or resid 38 through 79)) selection = (chain 'B' and (resid 36 or (resid 37 and (name N or name CA or name C or name O \ or name CB )) or resid 38 through 79)) selection = (chain 'C' and (resid 36 or (resid 37 and (name N or name CA or name C or name O \ or name CB )) or resid 38 through 79)) selection = (chain 'D' and (resid 36 or (resid 37 and (name N or name CA or name C or name O \ or name CB )) or resid 38 through 79)) selection = (chain 'E' and (resid 36 or (resid 37 and (name N or name CA or name C or name O \ or name CB )) or resid 38 through 79)) selection = (chain 'F' and (resid 36 or (resid 37 and (name N or name CA or name C or name O \ or name CB )) or resid 38 through 79)) selection = chain 'G' selection = (chain 'H' and (resid 36 or (resid 37 and (name N or name CA or name C or name O \ or name CB )) or resid 38 through 79)) } 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: 0.070 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.970 Find NCS groups from input model: 0.130 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5872 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 : 0.008 0.073 2438 Z= 0.542 Angle : 1.471 9.292 3309 Z= 0.882 Chirality : 0.079 0.255 447 Planarity : 0.006 0.021 408 Dihedral : 15.099 86.144 815 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 36.31 % Favored : 63.69 % Rotamer: Outliers : 3.53 % Allowed : 17.25 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.00 (0.32), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.56 (0.24), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 50 TYR 0.037 0.006 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.271 Fit side-chains REVERT: A 39 TYR cc_start: 0.5199 (t80) cc_final: 0.4885 (t80) REVERT: A 45 LYS cc_start: 0.8316 (tttt) cc_final: 0.7992 (mptt) REVERT: A 57 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7576 (mp0) REVERT: B 39 TYR cc_start: 0.6141 (m-80) cc_final: 0.5798 (m-80) REVERT: B 57 GLU cc_start: 0.7606 (tt0) cc_final: 0.7280 (tt0) REVERT: B 62 GLN cc_start: 0.7537 (mt0) cc_final: 0.7328 (mp10) REVERT: C 45 LYS cc_start: 0.7943 (tttt) cc_final: 0.7654 (mttp) REVERT: C 57 GLU cc_start: 0.7546 (tt0) cc_final: 0.6735 (tm-30) REVERT: C 62 GLN cc_start: 0.8055 (mp10) cc_final: 0.7715 (mp10) REVERT: C 65 ASN cc_start: 0.6956 (m-40) cc_final: 0.6148 (t0) REVERT: D 57 GLU cc_start: 0.7576 (tt0) cc_final: 0.7180 (tm-30) REVERT: E 43 LYS cc_start: 0.6426 (ttmt) cc_final: 0.5756 (tttp) REVERT: F 45 LYS cc_start: 0.7892 (tttt) cc_final: 0.7668 (mttt) REVERT: F 58 LYS cc_start: 0.5783 (mttt) cc_final: 0.5209 (tptp) outliers start: 9 outliers final: 8 residues processed: 94 average time/residue: 0.1463 time to fit residues: 15.8775 Evaluate side-chains 70 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain H residue 52 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2438 Z= 0.315 Angle : 0.952 7.304 3309 Z= 0.527 Chirality : 0.059 0.147 447 Planarity : 0.004 0.013 408 Dihedral : 9.528 49.840 360 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.49 % Favored : 73.51 % Rotamer: Outliers : 8.24 % Allowed : 26.67 % Favored : 65.10 % 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: -5.70 (0.33), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.34 (0.25), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 TYR 0.030 0.005 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 60 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 39 TYR cc_start: 0.5296 (t80) cc_final: 0.4796 (t80) REVERT: A 45 LYS cc_start: 0.8286 (tttt) cc_final: 0.7846 (mptt) REVERT: A 57 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7658 (mp0) REVERT: A 62 GLN cc_start: 0.7722 (pp30) cc_final: 0.7488 (pp30) REVERT: C 57 GLU cc_start: 0.7444 (tt0) cc_final: 0.7013 (tm-30) REVERT: C 62 GLN cc_start: 0.8339 (mp10) cc_final: 0.8005 (mp10) REVERT: C 65 ASN cc_start: 0.7298 (m-40) cc_final: 0.6316 (t0) REVERT: F 45 LYS cc_start: 0.7944 (tttt) cc_final: 0.7687 (mmtt) REVERT: F 58 LYS cc_start: 0.5608 (mttt) cc_final: 0.4944 (tptp) REVERT: F 62 GLN cc_start: 0.7593 (mp10) cc_final: 0.7238 (tm-30) REVERT: G 62 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7769 (tm-30) outliers start: 21 outliers final: 18 residues processed: 75 average time/residue: 0.1362 time to fit residues: 12.0683 Evaluate side-chains 71 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 53 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 0.0010 chunk 28 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 overall best weight: 3.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5882 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2438 Z= 0.233 Angle : 0.807 6.425 3309 Z= 0.448 Chirality : 0.056 0.142 447 Planarity : 0.003 0.015 408 Dihedral : 8.431 50.447 359 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.98 % Favored : 72.02 % Rotamer: Outliers : 10.59 % Allowed : 24.31 % Favored : 65.10 % 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: -5.39 (0.34), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.10 (0.26), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 TYR 0.021 0.003 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 57 time to evaluate : 0.265 Fit side-chains REVERT: A 38 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6871 (mt) REVERT: A 39 TYR cc_start: 0.5207 (t80) cc_final: 0.4690 (t80) REVERT: A 45 LYS cc_start: 0.8335 (tttt) cc_final: 0.7790 (mptt) REVERT: A 57 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7801 (mp0) REVERT: C 57 GLU cc_start: 0.7264 (tt0) cc_final: 0.6819 (tm-30) REVERT: C 62 GLN cc_start: 0.8087 (mp10) cc_final: 0.7767 (mp10) REVERT: C 65 ASN cc_start: 0.7247 (m-40) cc_final: 0.6369 (t0) REVERT: D 57 GLU cc_start: 0.7581 (tt0) cc_final: 0.7201 (tm-30) REVERT: E 50 HIS cc_start: 0.5198 (OUTLIER) cc_final: 0.4751 (m90) REVERT: F 45 LYS cc_start: 0.7908 (tttt) cc_final: 0.7530 (mmtt) REVERT: F 58 LYS cc_start: 0.5719 (mttt) cc_final: 0.5003 (tptp) REVERT: F 62 GLN cc_start: 0.7496 (mp10) cc_final: 0.7103 (mp10) REVERT: H 38 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6705 (tt) REVERT: H 61 GLU cc_start: 0.7523 (tp30) cc_final: 0.7110 (tp30) outliers start: 27 outliers final: 19 residues processed: 79 average time/residue: 0.1232 time to fit residues: 11.5992 Evaluate side-chains 70 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 48 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 0.1980 chunk 29 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 6.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5960 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 2438 Z= 0.378 Angle : 0.973 7.509 3309 Z= 0.540 Chirality : 0.062 0.201 447 Planarity : 0.004 0.013 408 Dihedral : 9.565 38.588 359 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 33.63 % Favored : 66.37 % Rotamer: Outliers : 14.12 % Allowed : 21.57 % Favored : 64.31 % 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: -5.78 (0.34), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.40 (0.26), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 50 TYR 0.027 0.005 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 53 time to evaluate : 0.274 Fit side-chains REVERT: A 38 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6795 (tt) REVERT: A 39 TYR cc_start: 0.5205 (t80) cc_final: 0.4905 (t80) REVERT: A 45 LYS cc_start: 0.8394 (tttt) cc_final: 0.7836 (mptt) REVERT: C 57 GLU cc_start: 0.7175 (tt0) cc_final: 0.6628 (tm-30) REVERT: C 65 ASN cc_start: 0.7259 (m-40) cc_final: 0.6295 (t0) REVERT: D 57 GLU cc_start: 0.7562 (tt0) cc_final: 0.7101 (tm-30) REVERT: D 62 GLN cc_start: 0.8564 (tm-30) cc_final: 0.7573 (tm-30) REVERT: E 50 HIS cc_start: 0.5010 (OUTLIER) cc_final: 0.4532 (m90) REVERT: F 45 LYS cc_start: 0.7877 (tttt) cc_final: 0.7530 (mmtt) REVERT: F 62 GLN cc_start: 0.7608 (mp10) cc_final: 0.7277 (mp10) REVERT: G 62 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7622 (tm-30) REVERT: H 38 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6857 (tt) outliers start: 36 outliers final: 30 residues processed: 81 average time/residue: 0.1201 time to fit residues: 11.6189 Evaluate side-chains 81 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 48 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5815 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2438 Z= 0.159 Angle : 0.722 5.638 3309 Z= 0.398 Chirality : 0.055 0.146 447 Planarity : 0.002 0.012 408 Dihedral : 6.863 25.719 359 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.35 % Favored : 80.65 % Rotamer: Outliers : 7.45 % Allowed : 29.80 % Favored : 62.75 % 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: -5.14 (0.35), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 TYR 0.011 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 52 time to evaluate : 0.243 Fit side-chains REVERT: A 38 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6905 (mt) REVERT: A 45 LYS cc_start: 0.8220 (tttt) cc_final: 0.7586 (mptt) REVERT: A 57 GLU cc_start: 0.7769 (mp0) cc_final: 0.7547 (mp0) REVERT: B 57 GLU cc_start: 0.7416 (tt0) cc_final: 0.7113 (mp0) REVERT: C 57 GLU cc_start: 0.7152 (tt0) cc_final: 0.6706 (tm-30) REVERT: C 65 ASN cc_start: 0.7181 (m-40) cc_final: 0.6273 (t0) REVERT: D 57 GLU cc_start: 0.7477 (tt0) cc_final: 0.7053 (tm-30) REVERT: D 62 GLN cc_start: 0.8463 (tm-30) cc_final: 0.7616 (tm-30) REVERT: F 45 LYS cc_start: 0.7870 (tttt) cc_final: 0.7472 (mmtt) REVERT: G 62 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7449 (tm-30) REVERT: H 38 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6704 (tt) outliers start: 19 outliers final: 12 residues processed: 68 average time/residue: 0.1197 time to fit residues: 9.8111 Evaluate side-chains 60 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 46 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 52 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 20.0000 chunk 30 optimal weight: 0.0970 chunk 25 optimal weight: 20.0000 chunk 14 optimal weight: 0.1980 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 overall best weight: 4.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2438 Z= 0.282 Angle : 0.841 6.500 3309 Z= 0.466 Chirality : 0.059 0.144 447 Planarity : 0.003 0.013 408 Dihedral : 8.164 32.348 358 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 30.95 % Favored : 69.05 % Rotamer: Outliers : 12.55 % Allowed : 26.27 % Favored : 61.18 % 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: -5.31 (0.35), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 TYR 0.028 0.004 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 52 time to evaluate : 0.263 Fit side-chains REVERT: A 38 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6885 (mt) REVERT: A 45 LYS cc_start: 0.8286 (tttt) cc_final: 0.7738 (mptt) REVERT: C 57 GLU cc_start: 0.7251 (tt0) cc_final: 0.6727 (tm-30) REVERT: D 57 GLU cc_start: 0.7541 (tt0) cc_final: 0.7054 (tm-30) REVERT: E 50 HIS cc_start: 0.5044 (OUTLIER) cc_final: 0.4527 (m90) REVERT: F 45 LYS cc_start: 0.7853 (tttt) cc_final: 0.7435 (mmtt) REVERT: G 62 GLN cc_start: 0.8332 (tm-30) cc_final: 0.7909 (tm-30) REVERT: H 38 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6757 (tt) outliers start: 32 outliers final: 27 residues processed: 81 average time/residue: 0.1169 time to fit residues: 11.3953 Evaluate side-chains 75 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 45 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 17 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 19 optimal weight: 0.4980 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5871 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2438 Z= 0.220 Angle : 0.787 6.375 3309 Z= 0.435 Chirality : 0.056 0.138 447 Planarity : 0.003 0.011 408 Dihedral : 7.695 30.730 358 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.40 % Favored : 75.60 % Rotamer: Outliers : 12.55 % Allowed : 26.27 % Favored : 61.18 % 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: -5.07 (0.36), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 TYR 0.021 0.003 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 52 time to evaluate : 0.275 Fit side-chains REVERT: A 38 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6813 (mt) REVERT: A 45 LYS cc_start: 0.8220 (tttt) cc_final: 0.7657 (mptt) REVERT: C 57 GLU cc_start: 0.7265 (tt0) cc_final: 0.6748 (tm-30) REVERT: D 57 GLU cc_start: 0.7609 (tt0) cc_final: 0.7043 (tm-30) REVERT: D 62 GLN cc_start: 0.8487 (tm-30) cc_final: 0.7483 (tm-30) REVERT: E 43 LYS cc_start: 0.6766 (ttmt) cc_final: 0.6499 (tttt) REVERT: E 50 HIS cc_start: 0.5047 (OUTLIER) cc_final: 0.4522 (m90) REVERT: F 45 LYS cc_start: 0.7951 (tttt) cc_final: 0.7473 (mmtt) REVERT: F 62 GLN cc_start: 0.7732 (mp10) cc_final: 0.7113 (tm-30) REVERT: G 62 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7754 (tm-30) REVERT: H 38 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6700 (tt) REVERT: H 60 LYS cc_start: 0.7712 (mttt) cc_final: 0.7044 (mmtm) outliers start: 32 outliers final: 28 residues processed: 78 average time/residue: 0.1295 time to fit residues: 12.0885 Evaluate side-chains 81 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 50 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 52 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5919 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2438 Z= 0.294 Angle : 0.863 6.670 3309 Z= 0.477 Chirality : 0.058 0.142 447 Planarity : 0.004 0.020 408 Dihedral : 8.435 32.290 358 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 32.44 % Favored : 67.56 % Rotamer: Outliers : 14.12 % Allowed : 25.49 % Favored : 60.39 % 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: -5.29 (0.36), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 TYR 0.028 0.004 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 48 time to evaluate : 0.274 Fit side-chains REVERT: A 45 LYS cc_start: 0.8324 (tttt) cc_final: 0.7750 (mptt) REVERT: A 57 GLU cc_start: 0.8185 (mp0) cc_final: 0.7845 (mp0) REVERT: C 57 GLU cc_start: 0.7098 (tt0) cc_final: 0.6448 (tm-30) REVERT: D 57 GLU cc_start: 0.7736 (tt0) cc_final: 0.6986 (tm-30) REVERT: D 62 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8100 (tm-30) REVERT: E 43 LYS cc_start: 0.6749 (ttmt) cc_final: 0.6205 (tttt) REVERT: E 50 HIS cc_start: 0.4994 (OUTLIER) cc_final: 0.4507 (m90) REVERT: F 45 LYS cc_start: 0.7873 (tttt) cc_final: 0.7387 (mmtt) REVERT: G 62 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7911 (tm-30) REVERT: H 38 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6966 (tp) REVERT: H 60 LYS cc_start: 0.7864 (mttt) cc_final: 0.7121 (mmtm) outliers start: 36 outliers final: 33 residues processed: 77 average time/residue: 0.1317 time to fit residues: 11.9728 Evaluate side-chains 82 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 47 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 31 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2438 Z= 0.185 Angle : 0.744 6.649 3309 Z= 0.411 Chirality : 0.054 0.138 447 Planarity : 0.002 0.010 408 Dihedral : 7.103 28.498 358 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.70 % Favored : 75.30 % Rotamer: Outliers : 12.55 % Allowed : 27.06 % Favored : 60.39 % 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: -4.94 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 50 TYR 0.015 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 50 time to evaluate : 0.236 Fit side-chains REVERT: A 45 LYS cc_start: 0.8187 (tttt) cc_final: 0.7593 (mptt) REVERT: A 57 GLU cc_start: 0.8167 (mp0) cc_final: 0.7808 (mp0) REVERT: C 52 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7816 (m) REVERT: C 57 GLU cc_start: 0.7111 (tt0) cc_final: 0.6787 (tm-30) REVERT: E 43 LYS cc_start: 0.6556 (ttmt) cc_final: 0.6018 (mttp) REVERT: E 50 HIS cc_start: 0.5099 (OUTLIER) cc_final: 0.4578 (m90) REVERT: F 45 LYS cc_start: 0.7868 (tttt) cc_final: 0.7417 (mmtt) REVERT: F 62 GLN cc_start: 0.7666 (mp10) cc_final: 0.7105 (tm-30) REVERT: G 62 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7736 (tm-30) REVERT: H 38 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6685 (tt) REVERT: H 60 LYS cc_start: 0.7798 (mttt) cc_final: 0.7118 (mmtm) outliers start: 32 outliers final: 27 residues processed: 78 average time/residue: 0.1255 time to fit residues: 11.6515 Evaluate side-chains 80 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 50 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 2438 Z= 0.406 Angle : 0.982 7.441 3309 Z= 0.544 Chirality : 0.062 0.147 447 Planarity : 0.005 0.015 408 Dihedral : 9.211 33.766 358 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 36.31 % Favored : 63.69 % Rotamer: Outliers : 12.55 % Allowed : 26.27 % Favored : 61.18 % 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: -5.61 (0.35), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.27 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 50 TYR 0.035 0.005 TYR F 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 53 time to evaluate : 0.285 Fit side-chains REVERT: A 45 LYS cc_start: 0.8364 (tttt) cc_final: 0.7807 (mptt) REVERT: C 52 VAL cc_start: 0.8217 (OUTLIER) cc_final: 0.7875 (m) REVERT: C 57 GLU cc_start: 0.7180 (tt0) cc_final: 0.6776 (tm-30) REVERT: D 62 GLN cc_start: 0.8621 (tm-30) cc_final: 0.7527 (tm-30) REVERT: E 43 LYS cc_start: 0.6561 (ttmt) cc_final: 0.5871 (mttt) REVERT: E 45 LYS cc_start: 0.8336 (mttt) cc_final: 0.7330 (mptt) REVERT: E 50 HIS cc_start: 0.5005 (OUTLIER) cc_final: 0.4544 (m90) REVERT: F 45 LYS cc_start: 0.7814 (tttt) cc_final: 0.7374 (mmtt) REVERT: F 62 GLN cc_start: 0.7671 (mp10) cc_final: 0.7302 (tm-30) REVERT: G 62 GLN cc_start: 0.8336 (tm-30) cc_final: 0.7882 (tm-30) REVERT: H 38 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7144 (tp) REVERT: H 60 LYS cc_start: 0.7936 (mttt) cc_final: 0.7185 (mmtm) outliers start: 32 outliers final: 28 residues processed: 77 average time/residue: 0.1373 time to fit residues: 12.4580 Evaluate side-chains 83 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 52 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 1 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 0.0570 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 overall best weight: 3.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.099329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.087835 restraints weight = 6112.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.089612 restraints weight = 3738.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.090834 restraints weight = 2558.902| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2438 Z= 0.257 Angle : 0.847 7.163 3309 Z= 0.469 Chirality : 0.057 0.145 447 Planarity : 0.003 0.015 408 Dihedral : 8.020 33.267 358 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.79 % Favored : 73.21 % Rotamer: Outliers : 11.76 % Allowed : 28.63 % Favored : 59.61 % 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: -5.34 (0.36), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 TYR 0.020 0.003 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1002.24 seconds wall clock time: 18 minutes 37.84 seconds (1117.84 seconds total)