Starting phenix.real_space_refine on Sun Mar 10 14:51:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7h_23212/03_2024/7l7h_23212.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7h_23212/03_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_23212/03_2024/7l7h_23212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7h_23212/03_2024/7l7h_23212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7h_23212/03_2024/7l7h_23212.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7h_23212/03_2024/7l7h_23212.pdb" } 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 Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 1.64, per 1000 atoms: 0.67 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 483.1 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: 0.26 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: 0.40 Time building geometry restraints manager: 1.01 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: 102.85 - 108.57: 188 108.57 - 114.29: 1401 114.29 - 120.01: 679 120.01 - 125.73: 1014 125.73 - 131.46: 27 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 2.440 nonbonded pdb=" OG1 THR B 44 " pdb=" O GLU B 46 " model vdw 2.233 2.440 nonbonded pdb=" OG1 THR H 44 " pdb=" O GLU H 46 " model vdw 2.266 2.440 nonbonded pdb=" OG1 THR G 44 " pdb=" O GLU G 46 " model vdw 2.279 2.440 nonbonded pdb=" OG1 THR D 44 " pdb=" O GLU D 46 " model vdw 2.286 2.440 ... (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 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: 0.000 Extract box with map and model: 0.510 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.120 Find NCS groups from input model: 0.180 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.760 ------------------------------------------------------------------------------- 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 : 0.312 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: 0.1461 time to fit residues: 15.8355 Evaluate side-chains 70 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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: 8.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2438 Z= 0.226 Angle : 0.850 8.606 3309 Z= 0.466 Chirality : 0.055 0.153 447 Planarity : 0.003 0.012 408 Dihedral : 8.544 43.804 360 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.40 % Favored : 75.60 % Rotamer: Outliers : 9.41 % Allowed : 25.88 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.36 (0.34), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.26), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 TYR 0.024 0.004 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 79 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 55 time to evaluate : 0.274 Fit side-chains REVERT: A 39 TYR cc_start: 0.5218 (t80) cc_final: 0.4747 (t80) REVERT: A 45 LYS cc_start: 0.8215 (tttt) cc_final: 0.7823 (mptt) REVERT: A 57 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7458 (mp0) REVERT: C 57 GLU cc_start: 0.7352 (tt0) cc_final: 0.6826 (tm-30) REVERT: C 62 GLN cc_start: 0.8351 (mp10) cc_final: 0.8007 (mp10) REVERT: C 65 ASN cc_start: 0.7242 (m-40) cc_final: 0.6276 (t0) REVERT: D 57 GLU cc_start: 0.7486 (tt0) cc_final: 0.7065 (tm-30) REVERT: F 45 LYS cc_start: 0.7938 (tttt) cc_final: 0.7659 (mmtt) REVERT: F 58 LYS cc_start: 0.5519 (mttt) cc_final: 0.4875 (tptp) REVERT: F 62 GLN cc_start: 0.7577 (mp10) cc_final: 0.7163 (mp10) outliers start: 24 outliers final: 22 residues processed: 73 average time/residue: 0.1402 time to fit residues: 12.0452 Evaluate side-chains 70 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 48 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 B residue 59 THR 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 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 44 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: 6.9990 chunk 24 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 79 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: 0.5878 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2438 Z= 0.229 Angle : 0.799 5.903 3309 Z= 0.440 Chirality : 0.055 0.137 447 Planarity : 0.003 0.015 408 Dihedral : 8.316 42.772 360 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 30.06 % Favored : 69.94 % Rotamer: Outliers : 11.37 % Allowed : 26.67 % Favored : 61.96 % 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: -5.25 (0.35), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.27), 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 81 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 52 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 39 TYR cc_start: 0.5333 (t80) cc_final: 0.4839 (t80) REVERT: A 45 LYS cc_start: 0.8256 (tttt) cc_final: 0.7804 (mptt) REVERT: A 57 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7545 (mp0) REVERT: B 62 GLN cc_start: 0.7771 (mp10) cc_final: 0.7436 (mp10) REVERT: C 57 GLU cc_start: 0.7086 (tt0) cc_final: 0.6768 (tm-30) REVERT: C 62 GLN cc_start: 0.8157 (mp10) cc_final: 0.7916 (mp10) REVERT: C 65 ASN cc_start: 0.7246 (m-40) cc_final: 0.6287 (t0) REVERT: F 45 LYS cc_start: 0.7861 (tttt) cc_final: 0.7610 (mmtt) REVERT: F 58 LYS cc_start: 0.5482 (mttt) cc_final: 0.4854 (tptp) REVERT: F 62 GLN cc_start: 0.7544 (mp10) cc_final: 0.7205 (mp10) outliers start: 29 outliers final: 25 residues processed: 77 average time/residue: 0.1300 time to fit residues: 11.9094 Evaluate side-chains 73 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 48 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 59 THR 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 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 44 THR 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: 0.0870 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 8 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5763 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2438 Z= 0.132 Angle : 0.628 4.480 3309 Z= 0.347 Chirality : 0.052 0.146 447 Planarity : 0.002 0.012 408 Dihedral : 6.085 30.991 359 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.18 % Favored : 84.82 % Rotamer: Outliers : 9.41 % Allowed : 29.02 % Favored : 61.57 % 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: -4.75 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 TYR 0.012 0.001 TYR B 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 78 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 54 time to evaluate : 0.266 Fit side-chains REVERT: A 45 LYS cc_start: 0.8171 (tttt) cc_final: 0.7607 (mptt) REVERT: B 62 GLN cc_start: 0.7957 (mp10) cc_final: 0.7748 (mp10) REVERT: C 57 GLU cc_start: 0.7126 (tt0) cc_final: 0.6722 (tm-30) REVERT: C 65 ASN cc_start: 0.7107 (m-40) cc_final: 0.6295 (t0) REVERT: D 57 GLU cc_start: 0.7522 (tt0) cc_final: 0.7059 (tm-30) REVERT: E 50 HIS cc_start: 0.4887 (OUTLIER) cc_final: 0.4313 (m90) REVERT: E 57 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7110 (mp0) REVERT: F 45 LYS cc_start: 0.7934 (tttt) cc_final: 0.7553 (mmtt) REVERT: G 62 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7432 (tm-30) REVERT: H 38 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6599 (tt) outliers start: 24 outliers final: 14 residues processed: 76 average time/residue: 0.1061 time to fit residues: 9.6623 Evaluate side-chains 62 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 46 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 72 THR 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 G residue 75 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 52 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 overall best weight: 2.6184 ------------------------------------------------------------------------------- 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: 0.5841 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2438 Z= 0.199 Angle : 0.729 5.118 3309 Z= 0.403 Chirality : 0.055 0.166 447 Planarity : 0.003 0.012 408 Dihedral : 6.892 39.820 357 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.89 % Favored : 74.11 % Rotamer: Outliers : 12.94 % Allowed : 23.92 % Favored : 63.14 % 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: -4.74 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 TYR 0.016 0.003 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 81 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 48 time to evaluate : 0.263 Fit side-chains REVERT: A 39 TYR cc_start: 0.5251 (t80) cc_final: 0.4801 (t80) REVERT: A 45 LYS cc_start: 0.8226 (tttt) cc_final: 0.7731 (mptt) REVERT: A 57 GLU cc_start: 0.7737 (mp0) cc_final: 0.7395 (mp0) REVERT: C 57 GLU cc_start: 0.7297 (tt0) cc_final: 0.6710 (tm-30) REVERT: C 65 ASN cc_start: 0.7207 (m-40) cc_final: 0.6280 (t0) REVERT: D 57 GLU cc_start: 0.7446 (tt0) cc_final: 0.6997 (tm-30) REVERT: E 50 HIS cc_start: 0.5133 (OUTLIER) cc_final: 0.4598 (m90) REVERT: F 39 TYR cc_start: 0.5380 (m-80) cc_final: 0.5149 (m-80) REVERT: F 45 LYS cc_start: 0.7914 (tttt) cc_final: 0.7496 (mmtt) REVERT: G 62 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7553 (tm-30) REVERT: H 38 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6823 (tt) outliers start: 33 outliers final: 28 residues processed: 77 average time/residue: 0.1176 time to fit residues: 10.8906 Evaluate side-chains 75 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 45 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR 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 44 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 44 THR 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 44 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 65 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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: 0.5834 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2438 Z= 0.180 Angle : 0.688 5.269 3309 Z= 0.379 Chirality : 0.054 0.137 447 Planarity : 0.002 0.011 408 Dihedral : 6.798 41.033 357 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.13 % Favored : 78.87 % Rotamer: Outliers : 13.33 % Allowed : 23.92 % 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: -4.64 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 TYR 0.014 0.002 TYR G 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 75 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 41 time to evaluate : 0.220 Fit side-chains REVERT: A 39 TYR cc_start: 0.5328 (t80) cc_final: 0.4946 (t80) REVERT: A 45 LYS cc_start: 0.8249 (tttt) cc_final: 0.7711 (mptt) REVERT: A 57 GLU cc_start: 0.7982 (mp0) cc_final: 0.7502 (mp0) REVERT: C 57 GLU cc_start: 0.7396 (tt0) cc_final: 0.6869 (tm-30) REVERT: C 65 ASN cc_start: 0.7257 (m-40) cc_final: 0.6294 (t0) REVERT: D 57 GLU cc_start: 0.7474 (tt0) cc_final: 0.7045 (tm-30) REVERT: E 45 LYS cc_start: 0.8234 (mttt) cc_final: 0.7974 (mttm) REVERT: E 50 HIS cc_start: 0.5160 (OUTLIER) cc_final: 0.4588 (m90) REVERT: F 45 LYS cc_start: 0.7858 (tttt) cc_final: 0.7513 (mmtt) REVERT: G 62 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7570 (tm-30) REVERT: H 38 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6750 (tt) outliers start: 34 outliers final: 31 residues processed: 70 average time/residue: 0.1423 time to fit residues: 11.7858 Evaluate side-chains 74 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 41 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR 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 44 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain F residue 44 THR 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 F residue 72 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 44 THR 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 44 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 65 ASN 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: 9.9990 chunk 26 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 0.0040 chunk 12 optimal weight: 0.2980 chunk 9 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 overall best weight: 2.6598 ------------------------------------------------------------------------------- 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: 0.5851 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2438 Z= 0.194 Angle : 0.700 5.269 3309 Z= 0.386 Chirality : 0.054 0.133 447 Planarity : 0.003 0.012 408 Dihedral : 7.043 41.395 357 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.38 % Favored : 72.62 % Rotamer: Outliers : 16.47 % Allowed : 21.57 % Favored : 61.96 % 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: -4.68 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 TYR 0.016 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 88 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 46 time to evaluate : 0.288 Fit side-chains REVERT: A 45 LYS cc_start: 0.8266 (tttt) cc_final: 0.7752 (mptt) REVERT: A 57 GLU cc_start: 0.7780 (mp0) cc_final: 0.7565 (mp0) REVERT: A 65 ASN cc_start: 0.6663 (OUTLIER) cc_final: 0.6054 (t0) REVERT: C 57 GLU cc_start: 0.7332 (tt0) cc_final: 0.6690 (tm-30) REVERT: C 65 ASN cc_start: 0.7223 (m-40) cc_final: 0.6307 (t0) REVERT: D 57 GLU cc_start: 0.7420 (tt0) cc_final: 0.6904 (tm-30) REVERT: E 43 LYS cc_start: 0.6559 (ttmt) cc_final: 0.6263 (tttt) REVERT: E 50 HIS cc_start: 0.5251 (OUTLIER) cc_final: 0.4670 (m90) REVERT: F 45 LYS cc_start: 0.7920 (tttt) cc_final: 0.7510 (mmtt) REVERT: F 61 GLU cc_start: 0.8241 (tp30) cc_final: 0.8029 (tp30) REVERT: G 62 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7655 (tm-30) REVERT: H 38 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6721 (tt) outliers start: 42 outliers final: 38 residues processed: 79 average time/residue: 0.1289 time to fit residues: 12.1253 Evaluate side-chains 87 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 46 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 44 THR 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 40 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR 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 D residue 65 ASN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain F residue 44 THR 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 F residue 72 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 44 THR 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 44 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 65 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.0670 chunk 24 optimal weight: 20.0000 chunk 28 optimal weight: 0.0870 chunk 29 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.0898 ------------------------------------------------------------------------------- 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: 0.5781 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2438 Z= 0.141 Angle : 0.625 5.187 3309 Z= 0.344 Chirality : 0.053 0.145 447 Planarity : 0.002 0.014 408 Dihedral : 5.998 34.866 357 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.56 % Favored : 82.44 % Rotamer: Outliers : 10.98 % Allowed : 25.88 % Favored : 63.14 % 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: -4.41 (0.38), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 TYR 0.011 0.001 TYR B 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 73 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 45 time to evaluate : 0.264 Fit side-chains REVERT: A 45 LYS cc_start: 0.8099 (tttt) cc_final: 0.7574 (mptt) REVERT: C 57 GLU cc_start: 0.7281 (tt0) cc_final: 0.6670 (tm-30) REVERT: C 65 ASN cc_start: 0.7062 (m-40) cc_final: 0.6316 (t0) REVERT: D 57 GLU cc_start: 0.7479 (tt0) cc_final: 0.6962 (tm-30) REVERT: D 62 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7752 (tm-30) REVERT: E 50 HIS cc_start: 0.5050 (OUTLIER) cc_final: 0.4460 (m90) REVERT: F 45 LYS cc_start: 0.7885 (tttt) cc_final: 0.7481 (mmtm) REVERT: G 57 GLU cc_start: 0.7702 (mp0) cc_final: 0.7367 (mp0) REVERT: G 62 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7531 (tm-30) REVERT: H 38 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6619 (tt) outliers start: 28 outliers final: 25 residues processed: 68 average time/residue: 0.1213 time to fit residues: 10.0222 Evaluate side-chains 70 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 43 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 59 THR 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 D residue 65 ASN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 44 THR 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 F residue 72 THR 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 52 VAL 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: 6.9990 chunk 28 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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: 0.5879 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2438 Z= 0.259 Angle : 0.762 5.690 3309 Z= 0.422 Chirality : 0.055 0.133 447 Planarity : 0.003 0.014 408 Dihedral : 7.461 41.769 357 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 29.17 % Favored : 70.83 % Rotamer: Outliers : 14.51 % Allowed : 24.31 % 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: -4.72 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 TYR 0.020 0.004 TYR G 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 85 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 48 time to evaluate : 0.288 Fit side-chains REVERT: A 45 LYS cc_start: 0.8288 (tttt) cc_final: 0.7767 (mptt) REVERT: B 57 GLU cc_start: 0.7517 (mp0) cc_final: 0.7316 (mp0) REVERT: C 57 GLU cc_start: 0.7394 (tt0) cc_final: 0.6747 (tm-30) REVERT: D 57 GLU cc_start: 0.7599 (tt0) cc_final: 0.6999 (tm-30) REVERT: D 62 GLN cc_start: 0.8461 (tm-30) cc_final: 0.7561 (tm-30) REVERT: E 45 LYS cc_start: 0.8271 (mttt) cc_final: 0.8025 (mttp) REVERT: E 50 HIS cc_start: 0.5173 (OUTLIER) cc_final: 0.4586 (m90) REVERT: F 45 LYS cc_start: 0.7925 (tttt) cc_final: 0.7508 (mmtt) REVERT: G 62 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7660 (tm-30) REVERT: H 38 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6734 (tt) outliers start: 37 outliers final: 35 residues processed: 77 average time/residue: 0.1252 time to fit residues: 11.6225 Evaluate side-chains 82 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 45 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 44 THR 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 40 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR 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 D residue 65 ASN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 44 THR 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 F residue 72 THR 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 44 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 65 ASN 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: 0.5980 chunk 20 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 23 optimal weight: 0.0070 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 overall best weight: 4.3204 ------------------------------------------------------------------------------- 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: 0.5893 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2438 Z= 0.282 Angle : 0.822 7.452 3309 Z= 0.454 Chirality : 0.057 0.144 447 Planarity : 0.003 0.017 408 Dihedral : 8.007 43.620 357 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.49 % Favored : 73.51 % Rotamer: Outliers : 14.90 % Allowed : 25.49 % 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: -4.85 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 TYR 0.023 0.004 TYR G 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 86 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 48 time to evaluate : 0.283 Fit side-chains REVERT: A 45 LYS cc_start: 0.8272 (tttt) cc_final: 0.7735 (mptt) REVERT: C 57 GLU cc_start: 0.7389 (tt0) cc_final: 0.6905 (tm-30) REVERT: D 62 GLN cc_start: 0.8482 (tm-30) cc_final: 0.7579 (tm-30) REVERT: E 50 HIS cc_start: 0.5012 (OUTLIER) cc_final: 0.4429 (m90) REVERT: F 45 LYS cc_start: 0.8001 (tttt) cc_final: 0.7538 (mmtt) REVERT: G 62 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7763 (tm-30) REVERT: H 38 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6765 (tt) REVERT: H 60 LYS cc_start: 0.7653 (mttt) cc_final: 0.6946 (mmtm) outliers start: 38 outliers final: 36 residues processed: 78 average time/residue: 0.1279 time to fit residues: 11.8398 Evaluate side-chains 84 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 46 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR 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 40 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 39 TYR 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 44 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 44 THR 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 F residue 72 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 44 THR 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 44 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 65 ASN 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: 10.0000 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.106926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.095926 restraints weight = 6527.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.097505 restraints weight = 4089.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.098598 restraints weight = 2882.166| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.4073 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= 0.307 Angle : 0.874 6.371 3309 Z= 0.481 Chirality : 0.058 0.143 447 Planarity : 0.004 0.017 408 Dihedral : 8.306 44.136 357 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 31.55 % Favored : 68.45 % Rotamer: Outliers : 15.69 % Allowed : 24.71 % 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: -5.06 (0.37), 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 0.003 0.001 HIS D 50 TYR 0.025 0.004 TYR G 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 959.19 seconds wall clock time: 18 minutes 3.57 seconds (1083.57 seconds total)