Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:48:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7h_23212/11_2022/7l7h_23212.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7h_23212/11_2022/7l7h_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_23212/11_2022/7l7h_23212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7h_23212/11_2022/7l7h_23212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7h_23212/11_2022/7l7h_23212.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7h_23212/11_2022/7l7h_23212.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4778/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: 1.76, per 1000 atoms: 0.72 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: 0.95 Conformation dependent library (CDL) restraints added in 395.5 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: 0.12 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: 0.41 Time building geometry restraints manager: 1.04 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 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. 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.590 Check model and map are aligned: 0.030 Convert atoms to be neutral: 0.030 Process input model: 11.600 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5988 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 % 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 *********************** 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 : 0.291 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 94 average time/residue: 0.1449 time to fit residues: 15.8376 Evaluate side-chains 62 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.308 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0263 time to fit residues: 0.7510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 moved from start: 0.3132 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= 0.205 Angle : 0.841 8.779 3309 Z= 0.460 Chirality : 0.054 0.158 447 Planarity : 0.003 0.013 408 Dihedral : 7.020 24.166 352 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.13 % Favored : 78.87 % Rotamer Outliers : 7.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.23 (0.34), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.26), residues: 336 *********************** 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 64 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 45 time to evaluate : 0.292 Fit side-chains outliers start: 19 outliers final: 16 residues processed: 59 average time/residue: 0.1133 time to fit residues: 8.2104 Evaluate side-chains 53 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 37 time to evaluate : 0.284 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0253 time to fit residues: 1.0437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 19 optimal weight: 0.0030 chunk 8 optimal weight: 9.9990 chunk 29 optimal weight: 0.0170 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 overall best weight: 2.0034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.5920 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 2438 Z= 0.177 Angle : 0.743 4.985 3309 Z= 0.409 Chirality : 0.054 0.135 447 Planarity : 0.002 0.015 408 Dihedral : 6.318 19.529 352 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.11 % Favored : 75.89 % Rotamer Outliers : 5.88 % 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: -4.86 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.28), residues: 336 *********************** 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 56 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 41 time to evaluate : 0.320 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 53 average time/residue: 0.1253 time to fit residues: 8.1877 Evaluate side-chains 47 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.298 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0261 time to fit residues: 0.8194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 2438 Z= 0.308 Angle : 0.861 6.116 3309 Z= 0.478 Chirality : 0.058 0.138 447 Planarity : 0.004 0.016 408 Dihedral : 7.653 19.269 352 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 30.95 % Favored : 69.05 % Rotamer Outliers : 7.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.13 (0.36), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.27), residues: 336 *********************** 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 64 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 45 time to evaluate : 0.294 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 60 average time/residue: 0.1359 time to fit residues: 9.6703 Evaluate side-chains 54 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.228 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0230 time to fit residues: 0.8408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5987 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 2438 Z= 0.236 Angle : 0.802 8.606 3309 Z= 0.436 Chirality : 0.057 0.185 447 Planarity : 0.003 0.013 408 Dihedral : 6.958 19.329 352 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.19 % Favored : 73.81 % Rotamer Outliers : 7.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.36), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.28), residues: 336 *********************** 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 66 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 47 time to evaluate : 0.271 Fit side-chains outliers start: 19 outliers final: 16 residues processed: 63 average time/residue: 0.1240 time to fit residues: 9.4160 Evaluate side-chains 59 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 0.304 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0282 time to fit residues: 1.1091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 0.0060 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 moved from start: 0.4241 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= 0.207 Angle : 0.767 7.844 3309 Z= 0.420 Chirality : 0.055 0.139 447 Planarity : 0.003 0.014 408 Dihedral : 6.493 18.850 352 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.68 % Favored : 72.32 % Rotamer Outliers : 4.31 % 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: -4.90 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.28), residues: 336 *********************** 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 59 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.289 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 57 average time/residue: 0.1273 time to fit residues: 8.7704 Evaluate side-chains 53 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.293 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0252 time to fit residues: 0.7239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 17 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN D 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5903 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 2438 Z= 0.186 Angle : 0.736 7.052 3309 Z= 0.405 Chirality : 0.054 0.147 447 Planarity : 0.003 0.022 408 Dihedral : 5.788 17.623 352 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.32 % Favored : 77.68 % Rotamer Outliers : 1.57 % 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: -4.62 (0.38), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.29), residues: 336 *********************** 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 54 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.481 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 53 average time/residue: 0.2092 time to fit residues: 13.7245 Evaluate side-chains 46 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.415 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0464 time to fit residues: 0.7488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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: 0.5907 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 2438 Z= 0.190 Angle : 0.739 6.686 3309 Z= 0.407 Chirality : 0.054 0.148 447 Planarity : 0.003 0.019 408 Dihedral : 5.796 17.773 352 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.70 % Favored : 75.30 % Rotamer Outliers : 1.57 % 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: -4.44 (0.39), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.29), residues: 336 *********************** 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 48 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.240 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 46 average time/residue: 0.1416 time to fit residues: 7.8209 Evaluate side-chains 44 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.300 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0374 time to fit residues: 0.5984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 18 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 2 optimal weight: 0.0870 chunk 19 optimal weight: 0.3980 overall best weight: 2.8562 ------------------------------------------------------------------------------- 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: 0.5934 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 2438 Z= 0.221 Angle : 0.783 6.546 3309 Z= 0.432 Chirality : 0.054 0.140 447 Planarity : 0.003 0.019 408 Dihedral : 6.305 19.257 352 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.79 % Favored : 73.21 % Rotamer Outliers : 2.35 % 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: -4.49 (0.39), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.29), residues: 336 *********************** 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 53 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.283 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 50 average time/residue: 0.1353 time to fit residues: 8.1118 Evaluate side-chains 49 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.285 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0250 time to fit residues: 0.6148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 0.3980 chunk 20 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 23 optimal weight: 0.0060 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 overall best weight: 2.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5933 moved from start: 0.4844 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= 0.231 Angle : 0.812 7.743 3309 Z= 0.446 Chirality : 0.055 0.141 447 Planarity : 0.003 0.021 408 Dihedral : 6.398 19.219 352 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.49 % Favored : 73.51 % Rotamer Outliers : 0.39 % 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: -4.43 (0.39), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.30), residues: 336 ********************** 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 46 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.313 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.1506 time to fit residues: 8.3248 Evaluate side-chains 44 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.293 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 1 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 29 optimal weight: 0.0770 chunk 17 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 overall best weight: 4.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.107099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.096144 restraints weight = 6454.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.097743 restraints weight = 3983.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.098843 restraints weight = 2787.000| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 2438 Z= 0.298 Angle : 0.886 6.462 3309 Z= 0.489 Chirality : 0.058 0.141 447 Planarity : 0.004 0.017 408 Dihedral : 7.316 21.948 352 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 32.14 % Favored : 67.86 % Rotamer Outliers : 1.96 % 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: -4.69 (0.38), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.29), residues: 336 =============================================================================== Job complete usr+sys time: 940.62 seconds wall clock time: 18 minutes 11.32 seconds (1091.32 seconds total)