Starting phenix.real_space_refine on Tue Dec 31 03:13:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pey_13361/12_2024/7pey_13361.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pey_13361/12_2024/7pey_13361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pey_13361/12_2024/7pey_13361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pey_13361/12_2024/7pey_13361.map" model { file = "/net/cci-nas-00/data/ceres_data/7pey_13361/12_2024/7pey_13361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pey_13361/12_2024/7pey_13361.cif" } resolution = 4.5 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 342 5.49 5 S 10 5.16 5 C 7159 2.51 5 N 2464 2.21 5 O 3124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13099 Number of models: 1 Model: "" Number of chains: 10 Chain: "K" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "L" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "M" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "N" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "O" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "P" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "Q" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "R" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "J" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3532 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "I" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3479 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Time building chain proxies: 7.62, per 1000 atoms: 0.58 Number of scatterers: 13099 At special positions: 0 Unit cell: (150.15, 130.2, 116.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 342 15.00 O 3124 8.00 N 2464 7.00 C 7159 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 911.7 milliseconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 72.0% alpha, 2.1% beta 166 base pairs and 301 stacking pairs defined. Time for finding SS restraints: 6.33 Creating SS restraints... Processing helix chain 'K' and resid 44 through 57 Processing helix chain 'K' and resid 63 through 79 removed outlier: 3.700A pdb=" N PHE K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE K 78 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 removed outlier: 3.819A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 29 removed outlier: 4.055A pdb=" N GLN L 27 " --> pdb=" O ASP L 24 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE L 29 " --> pdb=" O ILE L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 50 through 76 Processing helix chain 'L' and resid 82 through 93 Processing helix chain 'M' and resid 16 through 21 Processing helix chain 'M' and resid 26 through 36 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.079A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 89 Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'M' and resid 112 through 116 Processing helix chain 'N' and resid 37 through 49 removed outlier: 3.869A pdb=" N VAL N 41 " --> pdb=" O TYR N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 84 Processing helix chain 'N' and resid 90 through 102 removed outlier: 3.531A pdb=" N ILE N 94 " --> pdb=" O THR N 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 123 Processing helix chain 'O' and resid 44 through 57 Processing helix chain 'O' and resid 63 through 77 Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 131 removed outlier: 3.580A pdb=" N ILE O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 29 Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 49 through 76 removed outlier: 4.023A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP P 68 " --> pdb=" O ASN P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 93 removed outlier: 3.503A pdb=" N VAL P 86 " --> pdb=" O THR P 82 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN P 93 " --> pdb=" O ALA P 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 22 Processing helix chain 'Q' and resid 26 through 36 Processing helix chain 'Q' and resid 45 through 73 removed outlier: 4.238A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 89 Processing helix chain 'Q' and resid 90 through 97 Processing helix chain 'Q' and resid 112 through 116 Processing helix chain 'R' and resid 37 through 49 Processing helix chain 'R' and resid 55 through 84 Processing helix chain 'R' and resid 90 through 102 Processing helix chain 'R' and resid 104 through 123 removed outlier: 4.156A pdb=" N LYS R 108 " --> pdb=" O GLY R 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 83 through 84 removed outlier: 6.447A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'L' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.475A pdb=" N ARG M 42 " --> pdb=" O ILE N 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'M' and resid 101 through 102 removed outlier: 7.080A pdb=" N THR M 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.669A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.151A pdb=" N ARG Q 42 " --> pdb=" O ILE R 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 400 hydrogen bonds defined for protein. 1179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 429 hydrogen bonds 858 hydrogen bond angles 0 basepair planarities 166 basepair parallelities 301 stacking parallelities Total time for adding SS restraints: 6.83 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2792 1.33 - 1.46: 4997 1.46 - 1.58: 5541 1.58 - 1.70: 682 1.70 - 1.83: 20 Bond restraints: 14032 Sorted by residual: bond pdb=" N GLU O 94 " pdb=" CA GLU O 94 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.10e+00 bond pdb=" N LEU O 92 " pdb=" CA LEU O 92 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.47e+00 bond pdb=" N GLN O 93 " pdb=" CA GLN O 93 " ideal model delta sigma weight residual 1.459 1.482 -0.022 1.18e-02 7.18e+03 3.63e+00 bond pdb=" C3' DG I 494 " pdb=" O3' DG I 494 " ideal model delta sigma weight residual 1.422 1.479 -0.057 3.00e-02 1.11e+03 3.59e+00 bond pdb=" C3' DG I 382 " pdb=" O3' DG I 382 " ideal model delta sigma weight residual 1.422 1.479 -0.057 3.00e-02 1.11e+03 3.56e+00 ... (remaining 14027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 19868 2.31 - 4.61: 476 4.61 - 6.92: 57 6.92 - 9.23: 14 9.23 - 11.54: 4 Bond angle restraints: 20419 Sorted by residual: angle pdb=" CB LYS R 46 " pdb=" CG LYS R 46 " pdb=" CD LYS R 46 " ideal model delta sigma weight residual 111.30 122.28 -10.98 2.30e+00 1.89e-01 2.28e+01 angle pdb=" C GLN O 93 " pdb=" CA GLN O 93 " pdb=" CB GLN O 93 " ideal model delta sigma weight residual 110.95 118.24 -7.29 1.55e+00 4.16e-01 2.21e+01 angle pdb=" N GLU K 50 " pdb=" CA GLU K 50 " pdb=" CB GLU K 50 " ideal model delta sigma weight residual 110.40 117.72 -7.32 1.63e+00 3.76e-01 2.02e+01 angle pdb=" N ILE M 79 " pdb=" CA ILE M 79 " pdb=" C ILE M 79 " ideal model delta sigma weight residual 108.45 103.39 5.06 1.20e+00 6.94e-01 1.78e+01 angle pdb=" N LEU O 92 " pdb=" CA LEU O 92 " pdb=" C LEU O 92 " ideal model delta sigma weight residual 111.28 106.73 4.55 1.09e+00 8.42e-01 1.74e+01 ... (remaining 20414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 5768 36.00 - 72.00: 1741 72.00 - 107.99: 22 107.99 - 143.99: 3 143.99 - 179.99: 2 Dihedral angle restraints: 7536 sinusoidal: 5314 harmonic: 2222 Sorted by residual: dihedral pdb=" CA ILE L 50 " pdb=" C ILE L 50 " pdb=" N TYR L 51 " pdb=" CA TYR L 51 " ideal model delta harmonic sigma weight residual 180.00 -156.36 -23.64 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA PRO N 103 " pdb=" C PRO N 103 " pdb=" N GLY N 104 " pdb=" CA GLY N 104 " ideal model delta harmonic sigma weight residual 180.00 157.20 22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ASP N 51 " pdb=" C ASP N 51 " pdb=" N THR N 52 " pdb=" CA THR N 52 " ideal model delta harmonic sigma weight residual 180.00 -159.05 -20.95 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 7533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1730 0.049 - 0.098: 486 0.098 - 0.148: 90 0.148 - 0.197: 8 0.197 - 0.246: 6 Chirality restraints: 2320 Sorted by residual: chirality pdb=" CG LEU M 23 " pdb=" CB LEU M 23 " pdb=" CD1 LEU M 23 " pdb=" CD2 LEU M 23 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA LEU O 92 " pdb=" N LEU O 92 " pdb=" C LEU O 92 " pdb=" CB LEU O 92 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB VAL O 101 " pdb=" CA VAL O 101 " pdb=" CG1 VAL O 101 " pdb=" CG2 VAL O 101 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2317 not shown) Planarity restraints: 1398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS L 75 " -0.035 2.00e-02 2.50e+03 2.80e-02 1.18e+01 pdb=" CG HIS L 75 " 0.052 2.00e-02 2.50e+03 pdb=" ND1 HIS L 75 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS L 75 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS L 75 " -0.024 2.00e-02 2.50e+03 pdb=" NE2 HIS L 75 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 83 " -0.027 2.00e-02 2.50e+03 2.18e-02 9.48e+00 pdb=" CG TYR R 83 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR R 83 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR R 83 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR R 83 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR R 83 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR R 83 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR R 83 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 100 " -0.014 2.00e-02 2.50e+03 2.22e-02 8.60e+00 pdb=" CG PHE P 100 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE P 100 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE P 100 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE P 100 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE P 100 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE P 100 " 0.000 2.00e-02 2.50e+03 ... (remaining 1395 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1084 2.72 - 3.27: 11922 3.27 - 3.81: 28286 3.81 - 4.36: 32152 4.36 - 4.90: 44433 Nonbonded interactions: 117877 Sorted by model distance: nonbonded pdb=" OH TYR Q 39 " pdb=" OE1 GLU R 71 " model vdw 2.177 3.040 nonbonded pdb=" OG SER M 40 " pdb=" O ARG M 42 " model vdw 2.197 3.040 nonbonded pdb=" O LEU O 61 " pdb=" NH2 ARG P 36 " model vdw 2.283 3.120 nonbonded pdb=" OD2 ASP K 106 " pdb=" NH2 ARG K 131 " model vdw 2.288 3.120 nonbonded pdb=" O LEU M 85 " pdb=" ND2 ASN M 89 " model vdw 2.291 3.120 ... (remaining 117872 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'P' } ncs_group { reference = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'R' } 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 36.290 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 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 : 0.006 0.057 14032 Z= 0.333 Angle : 0.895 11.536 20419 Z= 0.510 Chirality : 0.047 0.246 2320 Planarity : 0.007 0.062 1398 Dihedral : 29.812 179.988 6104 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -0.09 (0.28), residues: 752 helix: 0.19 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -0.36 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.002 HIS L 75 PHE 0.050 0.003 PHE P 100 TYR 0.053 0.003 TYR R 83 ARG 0.015 0.001 ARG M 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 GLU cc_start: 0.9460 (pm20) cc_final: 0.9031 (pm20) REVERT: K 85 GLN cc_start: 0.9086 (mt0) cc_final: 0.8802 (mt0) REVERT: K 90 MET cc_start: 0.9440 (mmp) cc_final: 0.9203 (mmp) REVERT: K 120 MET cc_start: 0.8702 (mtm) cc_final: 0.8213 (mtt) REVERT: L 75 HIS cc_start: 0.9443 (t70) cc_final: 0.8943 (t70) REVERT: M 36 LYS cc_start: 0.9401 (mppt) cc_final: 0.9053 (mmtm) REVERT: M 64 GLU cc_start: 0.9578 (mm-30) cc_final: 0.9301 (mm-30) REVERT: M 79 ILE cc_start: 0.9590 (tp) cc_final: 0.9318 (pt) REVERT: N 96 THR cc_start: 0.9683 (m) cc_final: 0.9463 (m) REVERT: N 99 ARG cc_start: 0.9334 (mtp85) cc_final: 0.8543 (ttm110) REVERT: N 102 LEU cc_start: 0.8854 (tp) cc_final: 0.8421 (tt) REVERT: O 86 SER cc_start: 0.9826 (t) cc_final: 0.9545 (t) REVERT: O 90 MET cc_start: 0.9660 (mmp) cc_final: 0.9173 (mmm) REVERT: O 120 MET cc_start: 0.8299 (mtt) cc_final: 0.8035 (mtt) REVERT: O 125 GLN cc_start: 0.9400 (mt0) cc_final: 0.9195 (mt0) REVERT: P 72 TYR cc_start: 0.9560 (m-80) cc_final: 0.9259 (m-80) REVERT: Q 87 ILE cc_start: 0.9480 (mm) cc_final: 0.9159 (mm) REVERT: Q 90 ASP cc_start: 0.8905 (t70) cc_final: 0.8392 (t0) REVERT: R 93 GLU cc_start: 0.9067 (mp0) cc_final: 0.8802 (mp0) REVERT: R 113 GLU cc_start: 0.9357 (mm-30) cc_final: 0.9000 (mm-30) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2929 time to fit residues: 72.7943 Evaluate side-chains 116 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 55 GLN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN M 104 GLN N 109 HIS O 55 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14032 Z= 0.262 Angle : 0.631 7.096 20419 Z= 0.377 Chirality : 0.035 0.129 2320 Planarity : 0.005 0.088 1398 Dihedral : 32.458 179.070 4580 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.63 % Allowed : 3.14 % Favored : 96.23 % 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: 1.41 (0.30), residues: 752 helix: 1.35 (0.22), residues: 540 sheet: None (None), residues: 0 loop : 0.04 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS M 31 PHE 0.025 0.002 PHE O 104 TYR 0.023 0.002 TYR R 83 ARG 0.004 0.000 ARG N 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 150 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 54 TYR cc_start: 0.9465 (m-80) cc_final: 0.8906 (m-80) REVERT: K 59 GLU cc_start: 0.8871 (pm20) cc_final: 0.8597 (pm20) REVERT: K 85 GLN cc_start: 0.9227 (mt0) cc_final: 0.8881 (mt0) REVERT: K 90 MET cc_start: 0.9347 (mmp) cc_final: 0.8957 (mmp) REVERT: K 94 GLU cc_start: 0.9533 (mm-30) cc_final: 0.9278 (mm-30) REVERT: K 120 MET cc_start: 0.8657 (mtm) cc_final: 0.8274 (mtt) REVERT: L 100 PHE cc_start: 0.8412 (m-80) cc_final: 0.8183 (m-80) REVERT: M 36 LYS cc_start: 0.9268 (mppt) cc_final: 0.8851 (mmtm) REVERT: M 38 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.7858 (t0) REVERT: M 41 GLU cc_start: 0.8983 (mp0) cc_final: 0.7967 (tp30) REVERT: M 64 GLU cc_start: 0.9597 (mm-30) cc_final: 0.9397 (mm-30) REVERT: M 101 THR cc_start: 0.8862 (m) cc_final: 0.8550 (p) REVERT: N 45 LEU cc_start: 0.9323 (pp) cc_final: 0.8946 (pp) REVERT: N 71 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8637 (mm-30) REVERT: N 102 LEU cc_start: 0.8568 (tp) cc_final: 0.8293 (tp) REVERT: O 67 PHE cc_start: 0.9170 (t80) cc_final: 0.8826 (t80) REVERT: O 86 SER cc_start: 0.9798 (t) cc_final: 0.9585 (p) REVERT: O 93 GLN cc_start: 0.9546 (pt0) cc_final: 0.9291 (pt0) REVERT: O 104 PHE cc_start: 0.9170 (m-80) cc_final: 0.8713 (m-80) REVERT: O 120 MET cc_start: 0.8321 (mtt) cc_final: 0.8001 (mtt) REVERT: P 72 TYR cc_start: 0.9538 (m-80) cc_final: 0.9281 (m-80) REVERT: Q 38 ASN cc_start: 0.8780 (m-40) cc_final: 0.8493 (p0) REVERT: R 76 GLU cc_start: 0.9344 (tp30) cc_final: 0.9086 (mt-10) REVERT: R 83 TYR cc_start: 0.8890 (m-10) cc_final: 0.8586 (m-10) REVERT: R 101 LEU cc_start: 0.9492 (tt) cc_final: 0.9048 (tt) REVERT: R 113 GLU cc_start: 0.9412 (mm-30) cc_final: 0.9058 (mm-30) outliers start: 4 outliers final: 2 residues processed: 152 average time/residue: 0.2321 time to fit residues: 52.7027 Evaluate side-chains 115 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 HIS N 109 HIS Q 73 ASN R 47 GLN R 109 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 14032 Z= 0.434 Angle : 0.753 8.095 20419 Z= 0.441 Chirality : 0.041 0.196 2320 Planarity : 0.006 0.060 1398 Dihedral : 33.223 173.242 4580 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.16 % Allowed : 5.50 % Favored : 94.34 % 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: 1.03 (0.29), residues: 752 helix: 1.15 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.38 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS P 75 PHE 0.022 0.003 PHE K 104 TYR 0.020 0.002 TYR M 39 ARG 0.006 0.001 ARG O 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: K 54 TYR cc_start: 0.9518 (m-80) cc_final: 0.9039 (m-80) REVERT: K 85 GLN cc_start: 0.9211 (mt0) cc_final: 0.8690 (mt0) REVERT: K 90 MET cc_start: 0.9368 (mmp) cc_final: 0.8920 (mmp) REVERT: K 94 GLU cc_start: 0.9571 (mm-30) cc_final: 0.9276 (mm-30) REVERT: K 120 MET cc_start: 0.8666 (mtm) cc_final: 0.8183 (mtt) REVERT: L 63 GLU cc_start: 0.9305 (mt-10) cc_final: 0.9089 (mt-10) REVERT: M 41 GLU cc_start: 0.9070 (mp0) cc_final: 0.8463 (tp30) REVERT: N 47 GLN cc_start: 0.9371 (mm-40) cc_final: 0.9107 (mm110) REVERT: N 71 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8709 (mm-30) REVERT: N 102 LEU cc_start: 0.8629 (tp) cc_final: 0.8292 (tp) REVERT: N 105 GLU cc_start: 0.9632 (mp0) cc_final: 0.9416 (pm20) REVERT: N 109 HIS cc_start: 0.9741 (m90) cc_final: 0.9428 (m170) REVERT: O 86 SER cc_start: 0.9808 (t) cc_final: 0.9605 (p) REVERT: O 93 GLN cc_start: 0.9599 (pt0) cc_final: 0.9248 (pt0) REVERT: O 104 PHE cc_start: 0.9430 (m-80) cc_final: 0.9002 (m-80) REVERT: O 106 ASP cc_start: 0.9403 (m-30) cc_final: 0.9196 (m-30) REVERT: O 120 MET cc_start: 0.8027 (mtt) cc_final: 0.7610 (mtt) REVERT: P 72 TYR cc_start: 0.9500 (m-80) cc_final: 0.9143 (m-80) REVERT: R 62 MET cc_start: 0.9376 (mmp) cc_final: 0.9131 (mmp) REVERT: R 113 GLU cc_start: 0.9397 (mm-30) cc_final: 0.9058 (mm-30) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.2343 time to fit residues: 44.2154 Evaluate side-chains 94 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14032 Z= 0.295 Angle : 0.651 6.396 20419 Z= 0.389 Chirality : 0.036 0.159 2320 Planarity : 0.005 0.058 1398 Dihedral : 33.012 178.901 4580 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: 1.42 (0.30), residues: 752 helix: 1.51 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.45 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS P 75 PHE 0.025 0.002 PHE K 104 TYR 0.034 0.002 TYR R 83 ARG 0.005 0.000 ARG Q 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 54 TYR cc_start: 0.9527 (m-80) cc_final: 0.9085 (m-80) REVERT: K 85 GLN cc_start: 0.9143 (mt0) cc_final: 0.8488 (mt0) REVERT: K 90 MET cc_start: 0.9355 (mmp) cc_final: 0.8950 (mmp) REVERT: K 94 GLU cc_start: 0.9484 (mm-30) cc_final: 0.9248 (mm-30) REVERT: K 120 MET cc_start: 0.8744 (mtm) cc_final: 0.8162 (mtt) REVERT: M 41 GLU cc_start: 0.9030 (mp0) cc_final: 0.8502 (tp30) REVERT: M 90 ASP cc_start: 0.6981 (t0) cc_final: 0.6435 (t70) REVERT: M 102 ILE cc_start: 0.8537 (mm) cc_final: 0.8334 (tp) REVERT: N 47 GLN cc_start: 0.9348 (mm-40) cc_final: 0.9077 (mm110) REVERT: N 71 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8704 (mm-30) REVERT: N 102 LEU cc_start: 0.8711 (tp) cc_final: 0.8358 (tp) REVERT: N 109 HIS cc_start: 0.9775 (m90) cc_final: 0.9479 (m-70) REVERT: O 86 SER cc_start: 0.9820 (t) cc_final: 0.9582 (p) REVERT: O 90 MET cc_start: 0.9560 (mmp) cc_final: 0.9182 (mmp) REVERT: O 93 GLN cc_start: 0.9641 (pt0) cc_final: 0.9202 (pt0) REVERT: O 104 PHE cc_start: 0.9416 (m-80) cc_final: 0.8967 (m-80) REVERT: O 106 ASP cc_start: 0.9375 (m-30) cc_final: 0.9155 (m-30) REVERT: P 72 TYR cc_start: 0.9459 (m-80) cc_final: 0.9091 (m-80) REVERT: R 71 GLU cc_start: 0.9532 (mm-30) cc_final: 0.9232 (mm-30) REVERT: R 73 ILE cc_start: 0.9659 (mm) cc_final: 0.9412 (mm) REVERT: R 76 GLU cc_start: 0.9356 (tp30) cc_final: 0.8837 (mt-10) REVERT: R 101 LEU cc_start: 0.9414 (tt) cc_final: 0.8912 (tt) REVERT: R 113 GLU cc_start: 0.9370 (mm-30) cc_final: 0.9088 (mm-30) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2442 time to fit residues: 49.6018 Evaluate side-chains 106 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 0.2980 chunk 34 optimal weight: 6.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 93 GLN ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14032 Z= 0.250 Angle : 0.622 8.440 20419 Z= 0.371 Chirality : 0.035 0.147 2320 Planarity : 0.004 0.060 1398 Dihedral : 32.859 177.339 4580 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.47 % Allowed : 1.89 % Favored : 97.64 % 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: 1.75 (0.30), residues: 752 helix: 1.77 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS O 39 PHE 0.018 0.002 PHE R 65 TYR 0.038 0.002 TYR R 83 ARG 0.003 0.000 ARG Q 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 54 TYR cc_start: 0.9520 (m-10) cc_final: 0.9048 (m-80) REVERT: K 85 GLN cc_start: 0.9099 (mt0) cc_final: 0.8436 (mt0) REVERT: K 90 MET cc_start: 0.9344 (mmp) cc_final: 0.8943 (mmp) REVERT: K 94 GLU cc_start: 0.9575 (mm-30) cc_final: 0.9275 (mm-30) REVERT: K 104 PHE cc_start: 0.9624 (m-10) cc_final: 0.9362 (m-10) REVERT: K 120 MET cc_start: 0.8728 (mtm) cc_final: 0.8114 (mtt) REVERT: K 123 ASP cc_start: 0.9742 (m-30) cc_final: 0.9524 (m-30) REVERT: L 44 LYS cc_start: 0.8770 (pptt) cc_final: 0.8545 (pptt) REVERT: M 36 LYS cc_start: 0.9429 (mptt) cc_final: 0.9149 (mmtm) REVERT: M 41 GLU cc_start: 0.8938 (mp0) cc_final: 0.8487 (tp30) REVERT: M 79 ILE cc_start: 0.9494 (tp) cc_final: 0.9220 (pt) REVERT: M 90 ASP cc_start: 0.6955 (t0) cc_final: 0.6511 (t0) REVERT: N 47 GLN cc_start: 0.9386 (mm-40) cc_final: 0.9136 (mm-40) REVERT: N 71 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8670 (mm-30) REVERT: N 102 LEU cc_start: 0.8782 (tp) cc_final: 0.8430 (tp) REVERT: N 105 GLU cc_start: 0.9524 (pm20) cc_final: 0.9139 (pm20) REVERT: N 109 HIS cc_start: 0.9747 (m90) cc_final: 0.9365 (m-70) REVERT: O 86 SER cc_start: 0.9826 (t) cc_final: 0.9596 (p) REVERT: O 94 GLU cc_start: 0.9377 (mp0) cc_final: 0.9129 (mp0) REVERT: O 100 LEU cc_start: 0.9763 (mt) cc_final: 0.9555 (mt) REVERT: O 104 PHE cc_start: 0.9458 (m-80) cc_final: 0.8870 (m-80) REVERT: P 58 LEU cc_start: 0.9755 (tt) cc_final: 0.9490 (pp) REVERT: R 113 GLU cc_start: 0.9381 (mm-30) cc_final: 0.9057 (mm-30) outliers start: 3 outliers final: 1 residues processed: 143 average time/residue: 0.2746 time to fit residues: 55.9854 Evaluate side-chains 110 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14032 Z= 0.233 Angle : 0.615 6.660 20419 Z= 0.368 Chirality : 0.035 0.166 2320 Planarity : 0.004 0.059 1398 Dihedral : 32.719 178.735 4580 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.30), residues: 752 helix: 1.77 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.51 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS O 39 PHE 0.021 0.002 PHE K 67 TYR 0.033 0.002 TYR R 83 ARG 0.005 0.000 ARG N 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 54 TYR cc_start: 0.9494 (m-10) cc_final: 0.8955 (m-80) REVERT: K 85 GLN cc_start: 0.9094 (mt0) cc_final: 0.8508 (mt0) REVERT: K 90 MET cc_start: 0.9212 (mmp) cc_final: 0.8832 (mmp) REVERT: K 94 GLU cc_start: 0.9503 (mm-30) cc_final: 0.9192 (mm-30) REVERT: K 104 PHE cc_start: 0.9597 (m-10) cc_final: 0.9320 (m-10) REVERT: K 120 MET cc_start: 0.8716 (mtm) cc_final: 0.8009 (mtt) REVERT: L 63 GLU cc_start: 0.9330 (mt-10) cc_final: 0.9105 (mt-10) REVERT: M 36 LYS cc_start: 0.9384 (mptt) cc_final: 0.9089 (mmtm) REVERT: M 41 GLU cc_start: 0.8859 (mp0) cc_final: 0.8519 (tp30) REVERT: M 64 GLU cc_start: 0.9449 (mm-30) cc_final: 0.9167 (mm-30) REVERT: M 79 ILE cc_start: 0.9500 (tp) cc_final: 0.9232 (pt) REVERT: M 90 ASP cc_start: 0.6710 (t0) cc_final: 0.6191 (t0) REVERT: N 47 GLN cc_start: 0.9331 (mm-40) cc_final: 0.9039 (mm-40) REVERT: N 59 MET cc_start: 0.9118 (tpp) cc_final: 0.8853 (tpt) REVERT: N 71 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8656 (mm-30) REVERT: N 102 LEU cc_start: 0.8769 (tp) cc_final: 0.8445 (tp) REVERT: N 105 GLU cc_start: 0.9522 (pm20) cc_final: 0.9214 (pm20) REVERT: N 109 HIS cc_start: 0.9761 (m90) cc_final: 0.9390 (m-70) REVERT: O 86 SER cc_start: 0.9826 (t) cc_final: 0.9602 (p) REVERT: O 90 MET cc_start: 0.9396 (mmp) cc_final: 0.9151 (mmm) REVERT: O 93 GLN cc_start: 0.9344 (pt0) cc_final: 0.9103 (pp30) REVERT: O 104 PHE cc_start: 0.9438 (m-80) cc_final: 0.8919 (m-80) REVERT: O 120 MET cc_start: 0.8089 (mtt) cc_final: 0.7740 (mtt) REVERT: R 113 GLU cc_start: 0.9392 (mm-30) cc_final: 0.9062 (mm-30) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2492 time to fit residues: 52.5463 Evaluate side-chains 117 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 73 ASN ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 14032 Z= 0.333 Angle : 0.666 7.495 20419 Z= 0.396 Chirality : 0.037 0.174 2320 Planarity : 0.005 0.056 1398 Dihedral : 32.920 177.355 4580 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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: 1.48 (0.30), residues: 752 helix: 1.57 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.50 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS P 75 PHE 0.033 0.002 PHE K 67 TYR 0.028 0.002 TYR M 50 ARG 0.004 0.001 ARG Q 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 54 TYR cc_start: 0.9516 (m-10) cc_final: 0.8971 (m-80) REVERT: K 85 GLN cc_start: 0.9039 (mt0) cc_final: 0.8435 (mt0) REVERT: K 90 MET cc_start: 0.9175 (mmp) cc_final: 0.8877 (mmp) REVERT: K 94 GLU cc_start: 0.9584 (mm-30) cc_final: 0.9236 (mm-30) REVERT: K 120 MET cc_start: 0.8733 (mtm) cc_final: 0.8039 (mtt) REVERT: K 123 ASP cc_start: 0.9741 (m-30) cc_final: 0.9519 (m-30) REVERT: M 36 LYS cc_start: 0.9338 (mptt) cc_final: 0.9041 (mmtm) REVERT: M 41 GLU cc_start: 0.8848 (mp0) cc_final: 0.8604 (tp30) REVERT: M 90 ASP cc_start: 0.6706 (t0) cc_final: 0.6312 (t70) REVERT: N 47 GLN cc_start: 0.9344 (mm-40) cc_final: 0.9078 (mm110) REVERT: N 71 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8676 (mm-30) REVERT: N 102 LEU cc_start: 0.8840 (tp) cc_final: 0.8476 (tp) REVERT: N 105 GLU cc_start: 0.9576 (pm20) cc_final: 0.9328 (pm20) REVERT: N 109 HIS cc_start: 0.9736 (m90) cc_final: 0.9390 (m-70) REVERT: O 94 GLU cc_start: 0.9543 (mp0) cc_final: 0.9261 (mp0) REVERT: O 104 PHE cc_start: 0.9480 (m-80) cc_final: 0.8946 (m-80) REVERT: O 120 MET cc_start: 0.8051 (mtt) cc_final: 0.7661 (mtt) REVERT: P 72 TYR cc_start: 0.9637 (m-80) cc_final: 0.9289 (m-80) REVERT: P 91 LYS cc_start: 0.9471 (tmmt) cc_final: 0.9097 (pttm) REVERT: R 62 MET cc_start: 0.9318 (mmp) cc_final: 0.9086 (mmp) REVERT: R 73 ILE cc_start: 0.9689 (mm) cc_final: 0.9408 (mm) REVERT: R 76 GLU cc_start: 0.9286 (tp30) cc_final: 0.8935 (mt-10) REVERT: R 101 LEU cc_start: 0.9475 (tt) cc_final: 0.8748 (tt) REVERT: R 113 GLU cc_start: 0.9411 (mm-30) cc_final: 0.9069 (mm-30) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2371 time to fit residues: 47.3241 Evaluate side-chains 102 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14032 Z= 0.184 Angle : 0.617 7.255 20419 Z= 0.366 Chirality : 0.036 0.189 2320 Planarity : 0.004 0.058 1398 Dihedral : 32.568 179.155 4580 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 1.67 (0.30), residues: 752 helix: 1.70 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.42 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS L 75 PHE 0.024 0.002 PHE K 67 TYR 0.020 0.002 TYR M 50 ARG 0.003 0.000 ARG O 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 54 TYR cc_start: 0.9441 (m-10) cc_final: 0.8857 (m-80) REVERT: K 77 ASP cc_start: 0.9621 (t0) cc_final: 0.9315 (m-30) REVERT: K 90 MET cc_start: 0.9227 (mmp) cc_final: 0.8811 (mmp) REVERT: K 94 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9130 (mm-30) REVERT: K 120 MET cc_start: 0.8694 (mtm) cc_final: 0.8004 (mtt) REVERT: L 74 GLU cc_start: 0.9690 (tp30) cc_final: 0.9377 (mp0) REVERT: M 41 GLU cc_start: 0.8831 (mp0) cc_final: 0.8602 (tp30) REVERT: M 79 ILE cc_start: 0.9563 (tp) cc_final: 0.9310 (pt) REVERT: M 90 ASP cc_start: 0.6719 (t0) cc_final: 0.6280 (t0) REVERT: N 47 GLN cc_start: 0.9306 (mm-40) cc_final: 0.9031 (mm-40) REVERT: N 59 MET cc_start: 0.8922 (tpp) cc_final: 0.8646 (tpt) REVERT: N 71 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8638 (mm-30) REVERT: N 102 LEU cc_start: 0.8748 (tp) cc_final: 0.8379 (tp) REVERT: N 105 GLU cc_start: 0.9582 (pm20) cc_final: 0.9267 (pm20) REVERT: N 109 HIS cc_start: 0.9756 (m90) cc_final: 0.9354 (m-70) REVERT: O 86 SER cc_start: 0.9792 (p) cc_final: 0.9461 (p) REVERT: O 93 GLN cc_start: 0.9606 (pt0) cc_final: 0.9339 (pt0) REVERT: O 104 PHE cc_start: 0.9362 (m-80) cc_final: 0.8887 (m-80) REVERT: P 58 LEU cc_start: 0.9799 (tt) cc_final: 0.9503 (pp) REVERT: P 72 TYR cc_start: 0.9612 (m-80) cc_final: 0.9252 (m-80) REVERT: P 91 LYS cc_start: 0.9436 (tmmt) cc_final: 0.8975 (pttm) REVERT: Q 25 PHE cc_start: 0.8560 (m-10) cc_final: 0.8329 (m-10) REVERT: R 59 MET cc_start: 0.8476 (tpt) cc_final: 0.8231 (tpt) REVERT: R 83 TYR cc_start: 0.8646 (m-80) cc_final: 0.8256 (m-80) REVERT: R 113 GLU cc_start: 0.9392 (mm-30) cc_final: 0.9030 (mm-30) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2488 time to fit residues: 54.7735 Evaluate side-chains 116 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 14032 Z= 0.402 Angle : 0.710 8.655 20419 Z= 0.420 Chirality : 0.039 0.210 2320 Planarity : 0.005 0.052 1398 Dihedral : 32.973 176.346 4580 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 1.27 (0.30), residues: 752 helix: 1.37 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.40 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS L 75 PHE 0.013 0.002 PHE P 61 TYR 0.029 0.003 TYR M 50 ARG 0.004 0.001 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 54 TYR cc_start: 0.9536 (m-10) cc_final: 0.8941 (m-80) REVERT: K 85 GLN cc_start: 0.9263 (mt0) cc_final: 0.8871 (mt0) REVERT: K 90 MET cc_start: 0.9165 (mmp) cc_final: 0.8861 (mmp) REVERT: K 94 GLU cc_start: 0.9641 (mm-30) cc_final: 0.9278 (mm-30) REVERT: K 120 MET cc_start: 0.8652 (mtm) cc_final: 0.7945 (mtt) REVERT: L 63 GLU cc_start: 0.9346 (mt-10) cc_final: 0.9136 (mp0) REVERT: M 36 LYS cc_start: 0.9432 (mptt) cc_final: 0.9208 (mmtm) REVERT: M 90 ASP cc_start: 0.6657 (t0) cc_final: 0.6263 (t70) REVERT: N 30 LYS cc_start: 0.5554 (tptt) cc_final: 0.5346 (tptp) REVERT: N 47 GLN cc_start: 0.9298 (mm-40) cc_final: 0.9028 (mm-40) REVERT: N 59 MET cc_start: 0.9024 (tpp) cc_final: 0.8735 (tpt) REVERT: N 71 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8683 (mm-30) REVERT: N 102 LEU cc_start: 0.8959 (tp) cc_final: 0.8540 (tp) REVERT: N 105 GLU cc_start: 0.9594 (pm20) cc_final: 0.9332 (pm20) REVERT: N 109 HIS cc_start: 0.9785 (m90) cc_final: 0.9482 (m-70) REVERT: O 86 SER cc_start: 0.9834 (p) cc_final: 0.9567 (p) REVERT: O 90 MET cc_start: 0.9686 (mpp) cc_final: 0.9396 (mpp) REVERT: O 104 PHE cc_start: 0.9518 (m-80) cc_final: 0.8992 (m-80) REVERT: O 120 MET cc_start: 0.8546 (mtt) cc_final: 0.8274 (mtt) REVERT: P 91 LYS cc_start: 0.9483 (tmmt) cc_final: 0.9016 (pttm) REVERT: R 113 GLU cc_start: 0.9410 (mm-30) cc_final: 0.9045 (mm-30) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2497 time to fit residues: 49.8234 Evaluate side-chains 108 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 105 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 27 GLN Q 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.5653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14032 Z= 0.188 Angle : 0.629 6.746 20419 Z= 0.373 Chirality : 0.036 0.222 2320 Planarity : 0.004 0.057 1398 Dihedral : 32.519 179.187 4580 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 1.58 (0.30), residues: 752 helix: 1.62 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.36 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS L 75 PHE 0.011 0.001 PHE O 104 TYR 0.018 0.002 TYR M 50 ARG 0.004 0.000 ARG M 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 54 TYR cc_start: 0.9452 (m-10) cc_final: 0.9034 (m-80) REVERT: K 85 GLN cc_start: 0.9243 (mt0) cc_final: 0.8752 (mt0) REVERT: K 90 MET cc_start: 0.9241 (mmp) cc_final: 0.8877 (mmp) REVERT: K 94 GLU cc_start: 0.9478 (mm-30) cc_final: 0.9165 (mm-30) REVERT: K 120 MET cc_start: 0.8694 (mtm) cc_final: 0.8030 (mtt) REVERT: L 63 GLU cc_start: 0.9326 (mt-10) cc_final: 0.9092 (mp0) REVERT: L 74 GLU cc_start: 0.9696 (tp30) cc_final: 0.9293 (mt-10) REVERT: L 75 HIS cc_start: 0.9508 (t70) cc_final: 0.9295 (t70) REVERT: M 79 ILE cc_start: 0.9536 (tp) cc_final: 0.9241 (pt) REVERT: M 90 ASP cc_start: 0.6701 (t0) cc_final: 0.6278 (t0) REVERT: N 47 GLN cc_start: 0.9262 (mm-40) cc_final: 0.8965 (mm110) REVERT: N 59 MET cc_start: 0.8982 (tpp) cc_final: 0.8696 (tpt) REVERT: N 71 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8651 (mm-30) REVERT: N 99 ARG cc_start: 0.9279 (mtp85) cc_final: 0.9078 (mtp-110) REVERT: N 102 LEU cc_start: 0.8772 (tp) cc_final: 0.8377 (tp) REVERT: N 105 GLU cc_start: 0.9535 (pm20) cc_final: 0.9217 (pm20) REVERT: N 109 HIS cc_start: 0.9800 (m90) cc_final: 0.9504 (m-70) REVERT: O 93 GLN cc_start: 0.9414 (pt0) cc_final: 0.9189 (pt0) REVERT: O 97 GLU cc_start: 0.9274 (pm20) cc_final: 0.8942 (pm20) REVERT: O 104 PHE cc_start: 0.9421 (m-80) cc_final: 0.8924 (m-80) REVERT: O 120 MET cc_start: 0.8493 (mtt) cc_final: 0.8290 (mtt) REVERT: P 72 TYR cc_start: 0.9654 (m-80) cc_final: 0.9280 (m-80) REVERT: P 91 LYS cc_start: 0.9444 (tmmt) cc_final: 0.8992 (pttm) REVERT: R 83 TYR cc_start: 0.8676 (m-80) cc_final: 0.8278 (m-80) REVERT: R 113 GLU cc_start: 0.9385 (mm-30) cc_final: 0.9029 (mm-30) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2614 time to fit residues: 56.1039 Evaluate side-chains 121 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 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 = 0.2832 r_free = 0.2832 target = 0.027412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.020376 restraints weight = 178406.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.021135 restraints weight = 85848.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.021650 restraints weight = 52304.157| |-----------------------------------------------------------------------------| r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.5836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14032 Z= 0.300 Angle : 0.655 6.937 20419 Z= 0.389 Chirality : 0.037 0.213 2320 Planarity : 0.005 0.052 1398 Dihedral : 32.688 177.275 4580 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 1.58 (0.30), residues: 752 helix: 1.60 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.32 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS L 75 PHE 0.031 0.003 PHE K 104 TYR 0.025 0.002 TYR M 50 ARG 0.003 0.000 ARG L 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1968.42 seconds wall clock time: 37 minutes 44.71 seconds (2264.71 seconds total)