Starting phenix.real_space_refine on Fri Sep 27 08:50:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfx_13383/09_2024/7pfx_13383.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfx_13383/09_2024/7pfx_13383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfx_13383/09_2024/7pfx_13383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfx_13383/09_2024/7pfx_13383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfx_13383/09_2024/7pfx_13383.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pfx_13383/09_2024/7pfx_13383.cif" } resolution = 4.3 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= 0.007 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 354 5.49 5 S 10 5.16 5 C 7612 2.51 5 N 2606 2.21 5 O 3298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13880 Number of models: 1 Model: "" Number of chains: 11 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: "I" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 3610 Classifications: {'DNA': 177} Link IDs: {'rna3p': 176} Chain: "J" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 3647 Classifications: {'DNA': 177} Link IDs: {'rna3p': 176} Chain: "S" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 8.37, per 1000 atoms: 0.60 Number of scatterers: 13880 At special positions: 0 Unit cell: (149.1, 91.35, 122.85, 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 354 15.00 O 3298 8.00 N 2606 7.00 C 7612 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: 3.50 Conformation dependent library (CDL) restraints added in 931.5 milliseconds 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 11 sheets defined 69.4% alpha, 3.1% beta 177 base pairs and 311 stacking pairs defined. Time for finding SS restraints: 7.38 Creating SS restraints... Processing helix chain 'K' and resid 44 through 57 Processing helix chain 'K' and resid 63 through 77 removed outlier: 3.593A pdb=" N PHE K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 removed outlier: 3.521A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 76 removed outlier: 4.039A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) 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 37 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.346A 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 'N' and resid 37 through 49 Processing helix chain 'N' and resid 55 through 84 Processing helix chain 'N' and resid 90 through 102 Processing helix chain 'N' and resid 104 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: 3.583A 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: 4.088A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP P 68 " --> pdb=" O ASN P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 93 removed outlier: 3.652A pdb=" N VAL P 86 " --> pdb=" O THR P 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 22 Processing helix chain 'Q' and resid 26 through 37 Processing helix chain 'Q' and resid 45 through 73 removed outlier: 4.207A 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 103 through 124 Processing helix chain 'S' and resid 38 through 51 removed outlier: 4.088A pdb=" N LEU S 42 " --> pdb=" O PRO S 38 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER S 50 " --> pdb=" O ALA S 46 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS S 51 " --> pdb=" O VAL S 47 " (cutoff:3.500A) Processing helix chain 'S' and resid 58 through 69 Processing helix chain 'S' and resid 75 through 89 Processing sheet with id=AA1, first strand: chain 'K' and resid 83 through 84 removed outlier: 6.889A 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: 7.225A 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 77 through 78 Processing sheet with id=AA6, first strand: chain 'M' and resid 100 through 101 Processing sheet with id=AA7, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.737A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.157A pdb=" N ARG Q 42 " --> pdb=" O ILE R 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'Q' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'S' and resid 56 through 57 436 hydrogen bonds defined for protein. 1293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 456 hydrogen bonds 912 hydrogen bond angles 0 basepair planarities 177 basepair parallelities 311 stacking parallelities Total time for adding SS restraints: 7.46 Time building geometry restraints manager: 4.06 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: 2630 1.33 - 1.45: 5120 1.45 - 1.57: 6370 1.57 - 1.69: 706 1.69 - 1.82: 20 Bond restraints: 14846 Sorted by residual: bond pdb=" C3' DC I 455 " pdb=" O3' DC I 455 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.77e+00 bond pdb=" CG GLU O 97 " pdb=" CD GLU O 97 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.09e+00 bond pdb=" C3' DG J 331 " pdb=" O3' DG J 331 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 2.96e+00 bond pdb=" C3' DG J 253 " pdb=" O3' DG J 253 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.77e+00 bond pdb=" CG GLU P 63 " pdb=" CD GLU P 63 " ideal model delta sigma weight residual 1.516 1.475 0.041 2.50e-02 1.60e+03 2.65e+00 ... (remaining 14841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 21361 3.09 - 6.18: 175 6.18 - 9.27: 23 9.27 - 12.37: 3 12.37 - 15.46: 1 Bond angle restraints: 21563 Sorted by residual: angle pdb=" N GLU L 63 " pdb=" CA GLU L 63 " pdb=" CB GLU L 63 " ideal model delta sigma weight residual 110.28 118.62 -8.34 1.55e+00 4.16e-01 2.90e+01 angle pdb=" N GLU P 63 " pdb=" CA GLU P 63 " pdb=" CB GLU P 63 " ideal model delta sigma weight residual 110.28 118.19 -7.91 1.55e+00 4.16e-01 2.61e+01 angle pdb=" N GLU O 97 " pdb=" CA GLU O 97 " pdb=" CB GLU O 97 " ideal model delta sigma weight residual 110.40 117.75 -7.35 1.63e+00 3.76e-01 2.03e+01 angle pdb=" CA LEU L 62 " pdb=" CB LEU L 62 " pdb=" CG LEU L 62 " ideal model delta sigma weight residual 116.30 131.76 -15.46 3.50e+00 8.16e-02 1.95e+01 angle pdb=" N GLU O 94 " pdb=" CA GLU O 94 " pdb=" CB GLU O 94 " ideal model delta sigma weight residual 110.22 116.63 -6.41 1.54e+00 4.22e-01 1.73e+01 ... (remaining 21558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 6045 35.87 - 71.74: 1922 71.74 - 107.60: 34 107.60 - 143.47: 3 143.47 - 179.34: 3 Dihedral angle restraints: 8007 sinusoidal: 5576 harmonic: 2431 Sorted by residual: dihedral pdb=" CA ILE P 50 " pdb=" C ILE P 50 " pdb=" N TYR P 51 " pdb=" CA TYR P 51 " ideal model delta harmonic sigma weight residual -180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA PRO R 103 " pdb=" C PRO R 103 " pdb=" N GLY R 104 " pdb=" CA GLY R 104 " ideal model delta harmonic sigma weight residual 180.00 156.27 23.73 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA PHE O 84 " pdb=" C PHE O 84 " pdb=" N GLN O 85 " pdb=" CA GLN O 85 " ideal model delta harmonic sigma weight residual 180.00 158.41 21.59 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 8004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1884 0.051 - 0.102: 484 0.102 - 0.153: 74 0.153 - 0.205: 11 0.205 - 0.256: 3 Chirality restraints: 2456 Sorted by residual: chirality pdb=" CG LEU Q 23 " pdb=" CB LEU Q 23 " pdb=" CD1 LEU Q 23 " pdb=" CD2 LEU Q 23 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA PHE O 104 " pdb=" N PHE O 104 " pdb=" C PHE O 104 " pdb=" CB PHE O 104 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA GLU L 63 " pdb=" N GLU L 63 " pdb=" C GLU L 63 " pdb=" CB GLU L 63 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2453 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS L 59 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.43e+00 pdb=" C LYS L 59 " 0.047 2.00e-02 2.50e+03 pdb=" O LYS L 59 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL L 60 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE M 79 " -0.045 5.00e-02 4.00e+02 6.81e-02 7.41e+00 pdb=" N PRO M 80 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO M 80 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO M 80 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 60 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.64e+00 pdb=" C VAL L 60 " 0.041 2.00e-02 2.50e+03 pdb=" O VAL L 60 " -0.016 2.00e-02 2.50e+03 pdb=" N PHE L 61 " -0.014 2.00e-02 2.50e+03 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2510 2.77 - 3.30: 12738 3.30 - 3.83: 30793 3.83 - 4.37: 34366 4.37 - 4.90: 46793 Nonbonded interactions: 127200 Sorted by model distance: nonbonded pdb=" O GLN O 93 " pdb=" OG SER O 96 " model vdw 2.234 3.040 nonbonded pdb=" OG SER M 40 " pdb=" O ARG M 42 " model vdw 2.258 3.040 nonbonded pdb=" O VAL N 111 " pdb=" OG1 THR N 115 " model vdw 2.266 3.040 nonbonded pdb=" O THR Q 16 " pdb=" OG SER Q 19 " model vdw 2.302 3.040 nonbonded pdb=" NE2 HIS K 113 " pdb=" OD1 ASP O 123 " model vdw 2.302 3.120 ... (remaining 127195 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 39.940 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 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 0.058 14846 Z= 0.321 Angle : 0.880 15.456 21563 Z= 0.506 Chirality : 0.047 0.256 2456 Planarity : 0.006 0.068 1498 Dihedral : 30.285 179.340 6441 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: 0.30 (0.27), residues: 825 helix: 0.59 (0.20), residues: 567 sheet: -1.82 (1.57), residues: 10 loop : -0.37 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS K 113 PHE 0.040 0.003 PHE O 104 TYR 0.022 0.003 TYR N 37 ARG 0.005 0.001 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 104 PHE cc_start: 0.9476 (m-80) cc_final: 0.9199 (m-80) REVERT: K 120 MET cc_start: 0.8002 (tpp) cc_final: 0.7489 (tpp) REVERT: M 61 GLU cc_start: 0.9314 (pp20) cc_final: 0.9027 (pp20) REVERT: N 37 TYR cc_start: 0.9261 (m-10) cc_final: 0.8909 (m-10) REVERT: N 102 LEU cc_start: 0.8944 (tp) cc_final: 0.8666 (tp) REVERT: N 105 GLU cc_start: 0.9568 (tp30) cc_final: 0.9323 (tp30) REVERT: O 59 GLU cc_start: 0.9536 (tp30) cc_final: 0.9273 (pm20) REVERT: O 67 PHE cc_start: 0.9295 (t80) cc_final: 0.9068 (t80) REVERT: O 104 PHE cc_start: 0.9014 (m-80) cc_final: 0.8755 (m-10) REVERT: O 105 GLU cc_start: 0.9086 (mp0) cc_final: 0.8846 (mp0) REVERT: P 74 GLU cc_start: 0.9363 (pp20) cc_final: 0.9108 (pp20) REVERT: Q 56 GLU cc_start: 0.8992 (tt0) cc_final: 0.8516 (mt-10) REVERT: Q 64 GLU cc_start: 0.9578 (mm-30) cc_final: 0.9360 (mm-30) REVERT: Q 95 LYS cc_start: 0.9136 (pptt) cc_final: 0.8496 (mmtt) REVERT: R 102 LEU cc_start: 0.9445 (mm) cc_final: 0.8887 (tp) REVERT: R 109 HIS cc_start: 0.9717 (m-70) cc_final: 0.9455 (m170) REVERT: R 113 GLU cc_start: 0.9655 (mm-30) cc_final: 0.9451 (mt-10) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2470 time to fit residues: 42.6807 Evaluate side-chains 80 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 68 ASN R 109 HIS ** S 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 14846 Z= 0.333 Angle : 0.679 6.542 21563 Z= 0.408 Chirality : 0.037 0.164 2456 Planarity : 0.005 0.054 1498 Dihedral : 33.766 176.441 4789 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.29 % Allowed : 5.34 % Favored : 94.37 % 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 (0.28), residues: 825 helix: 1.48 (0.21), residues: 586 sheet: -2.48 (1.41), residues: 10 loop : -0.18 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS R 109 PHE 0.020 0.002 PHE P 100 TYR 0.015 0.002 TYR N 37 ARG 0.006 0.001 ARG Q 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.962 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 94 GLU cc_start: 0.9533 (tp30) cc_final: 0.9294 (tp30) REVERT: K 104 PHE cc_start: 0.9577 (m-80) cc_final: 0.9150 (m-80) REVERT: K 105 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.9107 (mm-30) REVERT: K 120 MET cc_start: 0.8105 (tpp) cc_final: 0.7743 (tpp) REVERT: N 37 TYR cc_start: 0.9357 (m-10) cc_final: 0.9118 (m-10) REVERT: N 62 MET cc_start: 0.9353 (mmp) cc_final: 0.9074 (mmp) REVERT: N 71 GLU cc_start: 0.9362 (mm-30) cc_final: 0.9105 (mm-30) REVERT: N 105 GLU cc_start: 0.9618 (tp30) cc_final: 0.9376 (tp30) REVERT: O 59 GLU cc_start: 0.9549 (tp30) cc_final: 0.9148 (pm20) REVERT: O 67 PHE cc_start: 0.9323 (t80) cc_final: 0.9074 (t80) REVERT: O 104 PHE cc_start: 0.9257 (m-80) cc_final: 0.9044 (m-80) REVERT: O 106 ASP cc_start: 0.9512 (m-30) cc_final: 0.9281 (m-30) REVERT: O 120 MET cc_start: 0.7123 (mtt) cc_final: 0.6870 (mtt) REVERT: Q 56 GLU cc_start: 0.9060 (tt0) cc_final: 0.8648 (tt0) REVERT: Q 95 LYS cc_start: 0.9222 (pptt) cc_final: 0.8574 (tptt) REVERT: R 109 HIS cc_start: 0.9478 (m90) cc_final: 0.9258 (m90) REVERT: R 113 GLU cc_start: 0.9664 (mm-30) cc_final: 0.9404 (mm-30) outliers start: 2 outliers final: 0 residues processed: 95 average time/residue: 0.2718 time to fit residues: 37.6819 Evaluate side-chains 67 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14846 Z= 0.260 Angle : 0.639 7.028 21563 Z= 0.384 Chirality : 0.035 0.148 2456 Planarity : 0.005 0.062 1498 Dihedral : 33.729 178.575 4789 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.14 % Allowed : 3.46 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.29), residues: 825 helix: 1.73 (0.21), residues: 588 sheet: -2.88 (1.42), residues: 10 loop : 0.02 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS L 75 PHE 0.015 0.002 PHE P 100 TYR 0.020 0.002 TYR R 42 ARG 0.004 0.000 ARG M 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 1.028 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 104 PHE cc_start: 0.9567 (m-80) cc_final: 0.9162 (m-80) REVERT: K 105 GLU cc_start: 0.9266 (mp0) cc_final: 0.9018 (mp0) REVERT: K 120 MET cc_start: 0.8285 (tpp) cc_final: 0.7933 (tpp) REVERT: N 37 TYR cc_start: 0.9325 (m-10) cc_final: 0.9119 (m-10) REVERT: N 62 MET cc_start: 0.9388 (mmp) cc_final: 0.9080 (mmm) REVERT: N 71 GLU cc_start: 0.9354 (mm-30) cc_final: 0.8978 (pp20) REVERT: N 102 LEU cc_start: 0.8624 (tp) cc_final: 0.8256 (tp) REVERT: N 105 GLU cc_start: 0.9622 (tp30) cc_final: 0.9411 (tp30) REVERT: O 59 GLU cc_start: 0.9554 (tp30) cc_final: 0.9154 (pm20) REVERT: O 104 PHE cc_start: 0.9269 (m-10) cc_final: 0.8986 (m-80) REVERT: O 106 ASP cc_start: 0.9504 (m-30) cc_final: 0.9300 (m-30) REVERT: Q 56 GLU cc_start: 0.9217 (tt0) cc_final: 0.8595 (mt-10) REVERT: R 109 HIS cc_start: 0.9552 (m90) cc_final: 0.9333 (m90) REVERT: R 113 GLU cc_start: 0.9653 (mm-30) cc_final: 0.9383 (mm-30) outliers start: 1 outliers final: 1 residues processed: 94 average time/residue: 0.2606 time to fit residues: 36.1997 Evaluate side-chains 75 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 104 GLN ** N 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 GLN ** S 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 14846 Z= 0.375 Angle : 0.704 8.329 21563 Z= 0.417 Chirality : 0.038 0.169 2456 Planarity : 0.005 0.063 1498 Dihedral : 33.960 178.349 4789 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % 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 (0.28), residues: 825 helix: 1.70 (0.21), residues: 574 sheet: -3.55 (1.29), residues: 10 loop : 0.13 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS L 75 PHE 0.012 0.002 PHE L 100 TYR 0.017 0.002 TYR R 40 ARG 0.010 0.001 ARG M 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.044 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 94 GLU cc_start: 0.9549 (tp30) cc_final: 0.9302 (tp30) REVERT: K 104 PHE cc_start: 0.9574 (m-80) cc_final: 0.9268 (m-80) REVERT: K 120 MET cc_start: 0.8391 (tpp) cc_final: 0.8019 (tpp) REVERT: N 37 TYR cc_start: 0.9407 (m-10) cc_final: 0.9116 (m-10) REVERT: N 62 MET cc_start: 0.9421 (mmp) cc_final: 0.9128 (mmm) REVERT: N 71 GLU cc_start: 0.9395 (mm-30) cc_final: 0.9015 (pp20) REVERT: N 105 GLU cc_start: 0.9633 (tp30) cc_final: 0.9405 (tp30) REVERT: O 104 PHE cc_start: 0.9400 (m-10) cc_final: 0.8990 (m-80) REVERT: O 105 GLU cc_start: 0.9242 (mp0) cc_final: 0.8943 (mm-30) REVERT: P 74 GLU cc_start: 0.9328 (pp20) cc_final: 0.9111 (pp20) REVERT: Q 56 GLU cc_start: 0.9174 (tt0) cc_final: 0.8811 (tt0) REVERT: R 113 GLU cc_start: 0.9648 (mm-30) cc_final: 0.9393 (mm-30) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2574 time to fit residues: 34.6770 Evaluate side-chains 69 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 68 GLN ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN P 27 GLN ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 14846 Z= 0.413 Angle : 0.738 8.534 21563 Z= 0.437 Chirality : 0.040 0.174 2456 Planarity : 0.006 0.061 1498 Dihedral : 34.306 179.359 4789 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 23.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.29 % Allowed : 2.74 % Favored : 96.97 % 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 (0.28), residues: 825 helix: 1.34 (0.21), residues: 574 sheet: -3.66 (1.40), residues: 10 loop : 0.02 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS N 49 PHE 0.014 0.002 PHE K 104 TYR 0.019 0.002 TYR P 98 ARG 0.008 0.001 ARG L 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 1.052 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 94 GLU cc_start: 0.9538 (tp30) cc_final: 0.9294 (tp30) REVERT: K 104 PHE cc_start: 0.9617 (m-80) cc_final: 0.9313 (m-80) REVERT: N 62 MET cc_start: 0.9340 (mmp) cc_final: 0.9043 (mmm) REVERT: N 71 GLU cc_start: 0.9446 (mm-30) cc_final: 0.9125 (mm-30) REVERT: N 82 HIS cc_start: 0.9777 (t-90) cc_final: 0.9573 (t-90) REVERT: N 105 GLU cc_start: 0.9650 (tp30) cc_final: 0.9419 (tp30) REVERT: P 66 ILE cc_start: 0.9829 (tp) cc_final: 0.9589 (pt) REVERT: Q 56 GLU cc_start: 0.9204 (tt0) cc_final: 0.8886 (tt0) REVERT: R 113 GLU cc_start: 0.9653 (mm-30) cc_final: 0.9419 (mm-30) outliers start: 2 outliers final: 1 residues processed: 89 average time/residue: 0.2674 time to fit residues: 35.0944 Evaluate side-chains 65 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14846 Z= 0.236 Angle : 0.644 6.326 21563 Z= 0.384 Chirality : 0.036 0.156 2456 Planarity : 0.004 0.060 1498 Dihedral : 33.953 179.811 4789 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.14 % Allowed : 2.02 % Favored : 97.84 % 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: 1.96 (0.29), residues: 825 helix: 1.93 (0.21), residues: 574 sheet: -3.51 (1.44), residues: 10 loop : 0.07 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 49 PHE 0.012 0.001 PHE K 104 TYR 0.010 0.001 TYR R 121 ARG 0.005 0.000 ARG O 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 1.117 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 94 GLU cc_start: 0.9538 (tp30) cc_final: 0.9226 (tp30) REVERT: K 104 PHE cc_start: 0.9554 (m-80) cc_final: 0.9243 (m-80) REVERT: K 120 MET cc_start: 0.9250 (tpt) cc_final: 0.8943 (tpp) REVERT: N 37 TYR cc_start: 0.9314 (m-10) cc_final: 0.9029 (m-10) REVERT: N 62 MET cc_start: 0.9389 (mmp) cc_final: 0.9115 (mmm) REVERT: N 71 GLU cc_start: 0.9396 (mm-30) cc_final: 0.8999 (pp20) REVERT: N 82 HIS cc_start: 0.9731 (t-90) cc_final: 0.9492 (t-90) REVERT: N 102 LEU cc_start: 0.8616 (tp) cc_final: 0.8181 (tp) REVERT: N 105 GLU cc_start: 0.9653 (tp30) cc_final: 0.9450 (tp30) REVERT: O 81 ASP cc_start: 0.9662 (m-30) cc_final: 0.9426 (t70) REVERT: O 104 PHE cc_start: 0.9364 (m-10) cc_final: 0.9047 (m-80) REVERT: P 74 GLU cc_start: 0.9369 (pp20) cc_final: 0.9147 (pp20) REVERT: Q 61 GLU cc_start: 0.9401 (pp20) cc_final: 0.9043 (pp20) REVERT: R 109 HIS cc_start: 0.9542 (m90) cc_final: 0.9321 (m90) REVERT: R 113 GLU cc_start: 0.9644 (mm-30) cc_final: 0.9439 (mm-30) outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.2387 time to fit residues: 35.8678 Evaluate side-chains 73 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 14846 Z= 0.319 Angle : 0.675 6.607 21563 Z= 0.402 Chirality : 0.037 0.170 2456 Planarity : 0.005 0.066 1498 Dihedral : 33.974 179.180 4789 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: 1.73 (0.29), residues: 825 helix: 1.78 (0.21), residues: 572 sheet: -3.69 (1.36), residues: 10 loop : -0.06 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS L 75 PHE 0.013 0.002 PHE R 65 TYR 0.013 0.001 TYR R 121 ARG 0.004 0.000 ARG O 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 94 GLU cc_start: 0.9530 (tp30) cc_final: 0.9229 (tp30) REVERT: K 104 PHE cc_start: 0.9564 (m-80) cc_final: 0.9255 (m-80) REVERT: K 105 GLU cc_start: 0.9238 (mp0) cc_final: 0.9002 (mp0) REVERT: N 71 GLU cc_start: 0.9418 (mm-30) cc_final: 0.9035 (pp20) REVERT: N 82 HIS cc_start: 0.9741 (t-90) cc_final: 0.9510 (t-90) REVERT: N 105 GLU cc_start: 0.9645 (tp30) cc_final: 0.9431 (tp30) REVERT: O 81 ASP cc_start: 0.9711 (m-30) cc_final: 0.9490 (t70) REVERT: O 104 PHE cc_start: 0.9315 (m-10) cc_final: 0.8989 (m-80) REVERT: O 105 GLU cc_start: 0.9215 (mp0) cc_final: 0.8979 (mp0) REVERT: O 106 ASP cc_start: 0.9541 (m-30) cc_final: 0.9316 (m-30) REVERT: P 66 ILE cc_start: 0.9807 (tp) cc_final: 0.9590 (pt) REVERT: P 74 GLU cc_start: 0.9366 (pp20) cc_final: 0.9089 (pp20) REVERT: Q 73 ASN cc_start: 0.9044 (m-40) cc_final: 0.8736 (m110) REVERT: R 109 HIS cc_start: 0.9542 (m90) cc_final: 0.9299 (m90) REVERT: R 113 GLU cc_start: 0.9646 (mm-30) cc_final: 0.9418 (mm-30) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2324 time to fit residues: 32.5995 Evaluate side-chains 68 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14846 Z= 0.237 Angle : 0.643 6.684 21563 Z= 0.383 Chirality : 0.036 0.161 2456 Planarity : 0.004 0.065 1498 Dihedral : 33.773 179.497 4789 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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: 1.90 (0.29), residues: 825 helix: 1.93 (0.21), residues: 572 sheet: -3.48 (1.40), residues: 10 loop : -0.06 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 49 PHE 0.011 0.001 PHE M 25 TYR 0.009 0.001 TYR R 37 ARG 0.003 0.000 ARG O 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 94 GLU cc_start: 0.9538 (tp30) cc_final: 0.9225 (tp30) REVERT: K 104 PHE cc_start: 0.9541 (m-80) cc_final: 0.9231 (m-80) REVERT: K 105 GLU cc_start: 0.9240 (mp0) cc_final: 0.9011 (mp0) REVERT: K 120 MET cc_start: 0.9213 (tpt) cc_final: 0.8884 (tpp) REVERT: N 71 GLU cc_start: 0.9396 (mm-30) cc_final: 0.9006 (pp20) REVERT: N 82 HIS cc_start: 0.9736 (t-90) cc_final: 0.9489 (t-90) REVERT: N 102 LEU cc_start: 0.8723 (tp) cc_final: 0.8285 (tp) REVERT: O 59 GLU cc_start: 0.9555 (tp30) cc_final: 0.9225 (pm20) REVERT: O 104 PHE cc_start: 0.9308 (m-10) cc_final: 0.8962 (m-80) REVERT: O 105 GLU cc_start: 0.9186 (mp0) cc_final: 0.8913 (mp0) REVERT: O 106 ASP cc_start: 0.9522 (m-30) cc_final: 0.9295 (m-30) REVERT: P 66 ILE cc_start: 0.9806 (tp) cc_final: 0.9574 (pt) REVERT: P 74 GLU cc_start: 0.9246 (pp20) cc_final: 0.9030 (pp20) REVERT: Q 61 GLU cc_start: 0.9387 (pp20) cc_final: 0.9035 (pp20) REVERT: Q 79 ILE cc_start: 0.9643 (tp) cc_final: 0.9433 (tp) REVERT: Q 95 LYS cc_start: 0.9015 (pptt) cc_final: 0.8175 (tptt) REVERT: R 102 LEU cc_start: 0.9263 (mm) cc_final: 0.8822 (mp) REVERT: R 109 HIS cc_start: 0.9541 (m90) cc_final: 0.9308 (m90) REVERT: R 113 GLU cc_start: 0.9649 (mm-30) cc_final: 0.9424 (mm-30) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2313 time to fit residues: 33.7789 Evaluate side-chains 73 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 107 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14846 Z= 0.317 Angle : 0.680 7.991 21563 Z= 0.404 Chirality : 0.037 0.192 2456 Planarity : 0.005 0.061 1498 Dihedral : 33.884 178.895 4789 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.29), residues: 825 helix: 1.71 (0.21), residues: 572 sheet: -3.53 (1.43), residues: 10 loop : -0.06 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS Q 82 PHE 0.013 0.002 PHE R 65 TYR 0.020 0.002 TYR R 40 ARG 0.013 0.001 ARG Q 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 94 GLU cc_start: 0.9536 (tp30) cc_final: 0.9243 (tp30) REVERT: K 104 PHE cc_start: 0.9539 (m-80) cc_final: 0.9260 (m-80) REVERT: N 62 MET cc_start: 0.9497 (mmp) cc_final: 0.9287 (mmm) REVERT: N 71 GLU cc_start: 0.9428 (mm-30) cc_final: 0.9032 (pp20) REVERT: N 82 HIS cc_start: 0.9754 (t-90) cc_final: 0.9503 (t-90) REVERT: O 104 PHE cc_start: 0.9345 (m-10) cc_final: 0.9099 (m-80) REVERT: P 66 ILE cc_start: 0.9800 (tp) cc_final: 0.9591 (pt) REVERT: R 102 LEU cc_start: 0.9265 (mm) cc_final: 0.9016 (mp) REVERT: R 109 HIS cc_start: 0.9551 (m90) cc_final: 0.9336 (m90) REVERT: R 113 GLU cc_start: 0.9654 (mm-30) cc_final: 0.9445 (mm-30) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2378 time to fit residues: 32.4797 Evaluate side-chains 64 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 112 optimal weight: 0.0770 chunk 103 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 54 optimal weight: 0.0050 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.7556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14846 Z= 0.198 Angle : 0.640 7.037 21563 Z= 0.378 Chirality : 0.036 0.182 2456 Planarity : 0.004 0.064 1498 Dihedral : 33.638 178.861 4789 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 1.87 (0.29), residues: 825 helix: 1.90 (0.21), residues: 572 sheet: -3.28 (1.48), residues: 10 loop : -0.09 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS Q 82 PHE 0.017 0.002 PHE Q 25 TYR 0.010 0.001 TYR R 37 ARG 0.003 0.000 ARG Q 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 94 GLU cc_start: 0.9539 (tp30) cc_final: 0.9221 (tp30) REVERT: K 104 PHE cc_start: 0.9454 (m-80) cc_final: 0.9156 (m-80) REVERT: K 120 MET cc_start: 0.9205 (tpt) cc_final: 0.8829 (tpp) REVERT: N 71 GLU cc_start: 0.9382 (mm-30) cc_final: 0.8999 (pp20) REVERT: N 82 HIS cc_start: 0.9706 (t-90) cc_final: 0.9479 (t-90) REVERT: N 102 LEU cc_start: 0.8634 (tp) cc_final: 0.8237 (tp) REVERT: O 59 GLU cc_start: 0.9577 (tp30) cc_final: 0.9185 (pm20) REVERT: O 104 PHE cc_start: 0.9315 (m-10) cc_final: 0.9060 (m-80) REVERT: O 106 ASP cc_start: 0.9525 (m-30) cc_final: 0.9318 (m-30) REVERT: P 66 ILE cc_start: 0.9793 (tp) cc_final: 0.9554 (pt) REVERT: P 74 GLU cc_start: 0.9274 (pp20) cc_final: 0.9061 (pp20) REVERT: Q 61 GLU cc_start: 0.9386 (pp20) cc_final: 0.9013 (pp20) REVERT: Q 95 LYS cc_start: 0.8974 (pptt) cc_final: 0.8070 (tptt) REVERT: R 102 LEU cc_start: 0.9272 (mm) cc_final: 0.8912 (mp) REVERT: R 105 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8709 (tm-30) REVERT: R 109 HIS cc_start: 0.9527 (m90) cc_final: 0.9271 (m170) REVERT: R 113 GLU cc_start: 0.9652 (mm-30) cc_final: 0.9424 (mm-30) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2320 time to fit residues: 34.7145 Evaluate side-chains 69 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 63 ASN ** 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 = 0.2824 r_free = 0.2824 target = 0.024423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.019854 restraints weight = 251101.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.020497 restraints weight = 117644.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.020943 restraints weight = 70092.720| |-----------------------------------------------------------------------------| r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 14846 Z= 0.294 Angle : 0.664 7.137 21563 Z= 0.395 Chirality : 0.036 0.175 2456 Planarity : 0.005 0.065 1498 Dihedral : 33.767 178.223 4789 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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 (0.29), residues: 825 helix: 1.80 (0.21), residues: 572 sheet: -3.41 (1.50), residues: 10 loop : -0.09 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS L 75 PHE 0.015 0.002 PHE Q 25 TYR 0.018 0.002 TYR R 121 ARG 0.005 0.000 ARG N 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1847.82 seconds wall clock time: 34 minutes 32.60 seconds (2072.60 seconds total)