Starting phenix.real_space_refine on Thu Dec 7 16:17:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7h_23212/12_2023/7l7h_23212.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7h_23212/12_2023/7l7h_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_23212/12_2023/7l7h_23212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7h_23212/12_2023/7l7h_23212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7h_23212/12_2023/7l7h_23212.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7h_23212/12_2023/7l7h_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-1.21rc1-5172/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: 1.66, per 1000 atoms: 0.68 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: 0.98 Conformation dependent library (CDL) restraints added in 484.0 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: 0.21 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: 1.04 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 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: 0.130 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: 11.430 Find NCS groups from input model: 0.210 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.210 ------------------------------------------------------------------------------- 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 : 0.278 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 94 average time/residue: 0.1596 time to fit residues: 17.2996 Evaluate side-chains 62 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.275 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0253 time to fit residues: 0.7316 ------------------------------------------------------------------------------- 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: 0.2980 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- 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 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.2987 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= 0.236 Angle : 0.883 8.496 3309 Z= 0.484 Chirality : 0.056 0.155 447 Planarity : 0.003 0.014 408 Dihedral : 7.531 25.386 352 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.21 % Favored : 76.79 % Rotamer: Outliers : 8.63 % Allowed : 28.63 % Favored : 62.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.35 (0.34), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (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 71 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 49 time to evaluate : 0.302 Fit side-chains outliers start: 22 outliers final: 19 residues processed: 64 average time/residue: 0.1254 time to fit residues: 9.7148 Evaluate side-chains 62 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 43 time to evaluate : 0.282 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0265 time to fit residues: 1.2233 ------------------------------------------------------------------------------- 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: 10.0000 chunk 24 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.5863 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2438 Z= 0.236 Angle : 0.816 5.488 3309 Z= 0.449 Chirality : 0.055 0.143 447 Planarity : 0.003 0.015 408 Dihedral : 7.163 22.037 352 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 28.57 % Favored : 71.43 % Rotamer: Outliers : 4.71 % Allowed : 33.33 % 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: -5.18 (0.36), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.94 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 50 TYR 0.020 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 57 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 0.266 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 56 average time/residue: 0.1242 time to fit residues: 8.4565 Evaluate side-chains 49 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.273 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0259 time to fit residues: 0.7076 ------------------------------------------------------------------------------- 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: 0.8980 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 29 optimal weight: 0.0170 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 25 optimal weight: 30.0000 chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 overall best weight: 1.9620 ------------------------------------------------------------------------------- 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** F 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 moved from start: 0.3920 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= 0.169 Angle : 0.705 5.144 3309 Z= 0.389 Chirality : 0.053 0.134 447 Planarity : 0.002 0.014 408 Dihedral : 6.105 17.689 352 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.54 % Favored : 79.46 % Rotamer: Outliers : 8.24 % Allowed : 29.80 % 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: -4.81 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 TYR 0.016 0.002 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 70 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 49 time to evaluate : 0.269 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 66 average time/residue: 0.1091 time to fit residues: 8.7839 Evaluate side-chains 51 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 38 time to evaluate : 0.260 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0270 time to fit residues: 0.9396 ------------------------------------------------------------------------------- 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: 0.0000 chunk 12 optimal weight: 0.4980 chunk 26 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 0.0670 chunk 27 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.1124 ------------------------------------------------------------------------------- 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** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5772 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2438 Z= 0.151 Angle : 0.685 7.888 3309 Z= 0.373 Chirality : 0.054 0.172 447 Planarity : 0.002 0.011 408 Dihedral : 5.338 16.821 352 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.05 % Favored : 80.95 % Rotamer: Outliers : 4.31 % Allowed : 29.02 % Favored : 66.67 % 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: -4.54 (0.38), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 50 TYR 0.013 0.002 TYR B 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 54 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.289 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 50 average time/residue: 0.1408 time to fit residues: 8.3897 Evaluate side-chains 42 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.298 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0291 time to fit residues: 0.6433 ------------------------------------------------------------------------------- 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: 0.9980 chunk 30 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5782 moved from start: 0.4514 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= 0.163 Angle : 0.692 6.795 3309 Z= 0.376 Chirality : 0.053 0.143 447 Planarity : 0.002 0.011 408 Dihedral : 5.436 15.717 352 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.35 % Favored : 80.65 % Rotamer: Outliers : 3.53 % Allowed : 32.94 % Favored : 63.53 % 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: -4.36 (0.39), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 TYR 0.014 0.002 TYR B 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 53 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.281 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 52 average time/residue: 0.1313 time to fit residues: 8.2476 Evaluate side-chains 41 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.274 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0311 time to fit residues: 0.6058 ------------------------------------------------------------------------------- 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: 7.9990 chunk 26 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 0.0870 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 0.0670 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5711 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2438 Z= 0.157 Angle : 0.669 6.596 3309 Z= 0.366 Chirality : 0.053 0.148 447 Planarity : 0.003 0.023 408 Dihedral : 4.839 15.339 352 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.15 % Favored : 81.85 % Rotamer: Outliers : 1.96 % Allowed : 34.90 % 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: -4.07 (0.40), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 TYR 0.012 0.001 TYR B 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 51 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.258 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 0.1408 time to fit residues: 8.3469 Evaluate side-chains 44 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.281 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0261 time to fit residues: 0.4553 ------------------------------------------------------------------------------- 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: 10.0000 chunk 2 optimal weight: 0.5980 chunk 24 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 12 optimal weight: 0.0050 chunk 22 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5713 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2438 Z= 0.161 Angle : 0.676 6.115 3309 Z= 0.373 Chirality : 0.052 0.149 447 Planarity : 0.003 0.019 408 Dihedral : 4.734 15.106 352 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.26 % Favored : 82.74 % Rotamer: Outliers : 0.78 % Allowed : 37.25 % 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: -3.84 (0.42), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 50 TYR 0.015 0.002 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 41 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.275 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 40 average time/residue: 0.1451 time to fit residues: 7.0940 Evaluate side-chains 40 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.266 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0286 time to fit residues: 0.4532 ------------------------------------------------------------------------------- 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: 5.9990 chunk 28 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5819 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2438 Z= 0.245 Angle : 0.778 5.660 3309 Z= 0.431 Chirality : 0.055 0.135 447 Planarity : 0.003 0.014 408 Dihedral : 6.231 19.492 352 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.89 % Favored : 74.11 % Rotamer: Outliers : 3.14 % Allowed : 36.08 % Favored : 60.78 % 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: -4.00 (0.40), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 50 TYR 0.021 0.003 TYR C 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 56 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.255 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 52 average time/residue: 0.1246 time to fit residues: 7.9656 Evaluate side-chains 54 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.439 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0332 time to fit residues: 0.8186 ------------------------------------------------------------------------------- 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: 0.0870 chunk 20 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2438 Z= 0.294 Angle : 0.864 5.963 3309 Z= 0.479 Chirality : 0.057 0.179 447 Planarity : 0.004 0.021 408 Dihedral : 7.141 22.997 352 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.38 % Favored : 72.62 % Rotamer: Outliers : 1.18 % Allowed : 35.69 % 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: -4.31 (0.39), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS E 50 TYR 0.027 0.004 TYR C 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 45 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.284 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 43 average time/residue: 0.1376 time to fit residues: 7.1458 Evaluate side-chains 44 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.248 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0254 time to fit residues: 0.4102 ------------------------------------------------------------------------------- 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: 10.0000 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 0.4980 chunk 12 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 overall best weight: 3.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4100 r_free = 0.4100 target = 0.099528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.087563 restraints weight = 6211.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.089255 restraints weight = 3946.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.090428 restraints weight = 2791.332| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.4863 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= 0.260 Angle : 0.827 6.120 3309 Z= 0.458 Chirality : 0.056 0.137 447 Planarity : 0.003 0.013 408 Dihedral : 6.809 22.635 352 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.68 % Favored : 72.32 % Rotamer: Outliers : 1.96 % Allowed : 38.04 % Favored : 60.00 % 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: -4.33 (0.39), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 50 TYR 0.022 0.004 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 965.88 seconds wall clock time: 18 minutes 17.43 seconds (1097.43 seconds total)