Starting phenix.real_space_refine on Sat Mar 16 19:14:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pew_13359/03_2024/7pew_13359.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pew_13359/03_2024/7pew_13359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pew_13359/03_2024/7pew_13359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pew_13359/03_2024/7pew_13359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pew_13359/03_2024/7pew_13359.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pew_13359/03_2024/7pew_13359.pdb" } resolution = 4.6 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= 0.008 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 352 5.49 5 S 10 5.16 5 C 7254 2.51 5 N 2504 2.21 5 O 3184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 76": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13304 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" 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: "B" 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: "C" 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: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 3636 Classifications: {'DNA': 176} Link IDs: {'rna3p': 175} Chain: "I" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 3580 Classifications: {'DNA': 176} Link IDs: {'rna3p': 175} Time building chain proxies: 6.92, per 1000 atoms: 0.52 Number of scatterers: 13304 At special positions: 0 Unit cell: (131.25, 163.8, 117.6, 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 352 15.00 O 3184 8.00 N 2504 7.00 C 7254 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.71 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 35 helices and 9 sheets defined 71.9% alpha, 2.6% beta 173 base pairs and 310 stacking pairs defined. Time for finding SS restraints: 6.58 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.690A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.623A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.583A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.119A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.291A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.500A pdb=" N VAL D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.664A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.254A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.216A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.641A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.733A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.602A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.917A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.228A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.026A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 407 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 448 hydrogen bonds 896 hydrogen bond angles 0 basepair planarities 173 basepair parallelities 310 stacking parallelities Total time for adding SS restraints: 4.87 Time building geometry restraints manager: 8.07 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: 2350 1.33 - 1.46: 5344 1.46 - 1.58: 5846 1.58 - 1.70: 702 1.70 - 1.83: 20 Bond restraints: 14262 Sorted by residual: bond pdb=" CG GLU D 113 " pdb=" CD GLU D 113 " ideal model delta sigma weight residual 1.516 1.458 0.058 2.50e-02 1.60e+03 5.29e+00 bond pdb=" C3' DC I 12 " pdb=" O3' DC I 12 " ideal model delta sigma weight residual 1.422 1.486 -0.064 3.00e-02 1.11e+03 4.60e+00 bond pdb=" C3' DG I 140 " pdb=" O3' DG I 140 " ideal model delta sigma weight residual 1.422 1.482 -0.060 3.00e-02 1.11e+03 4.00e+00 bond pdb=" C3' DG I 28 " pdb=" O3' DG I 28 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.40e+00 bond pdb=" CD GLU D 113 " pdb=" OE1 GLU D 113 " ideal model delta sigma weight residual 1.249 1.215 0.034 1.90e-02 2.77e+03 3.25e+00 ... (remaining 14257 not shown) Histogram of bond angle deviations from ideal: 97.70 - 104.69: 1425 104.69 - 111.69: 7393 111.69 - 118.68: 3992 118.68 - 125.68: 6814 125.68 - 132.67: 1150 Bond angle restraints: 20774 Sorted by residual: angle pdb=" N GLU D 113 " pdb=" CA GLU D 113 " pdb=" CB GLU D 113 " ideal model delta sigma weight residual 110.28 118.47 -8.19 1.55e+00 4.16e-01 2.79e+01 angle pdb=" N GLU A 105 " pdb=" CA GLU A 105 " pdb=" CB GLU A 105 " ideal model delta sigma weight residual 110.28 118.46 -8.18 1.55e+00 4.16e-01 2.79e+01 angle pdb=" N GLU G 64 " pdb=" CA GLU G 64 " pdb=" CB GLU G 64 " ideal model delta sigma weight residual 110.16 117.31 -7.15 1.48e+00 4.57e-01 2.33e+01 angle pdb=" N GLU E 50 " pdb=" CA GLU E 50 " pdb=" CB GLU E 50 " ideal model delta sigma weight residual 110.28 117.42 -7.14 1.55e+00 4.16e-01 2.12e+01 angle pdb=" N GLN D 95 " pdb=" CA GLN D 95 " pdb=" CB GLN D 95 " ideal model delta sigma weight residual 110.12 116.69 -6.57 1.47e+00 4.63e-01 2.00e+01 ... (remaining 20769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 5814 35.97 - 71.94: 1791 71.94 - 107.90: 26 107.90 - 143.87: 2 143.87 - 179.84: 3 Dihedral angle restraints: 7636 sinusoidal: 5414 harmonic: 2222 Sorted by residual: dihedral pdb=" CA ARG B 23 " pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta harmonic sigma weight residual -180.00 -156.56 -23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ARG H 33 " pdb=" C ARG H 33 " pdb=" N LYS H 34 " pdb=" CA LYS H 34 " ideal model delta harmonic sigma weight residual 180.00 157.97 22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA GLU E 59 " pdb=" C GLU E 59 " pdb=" N LEU E 60 " pdb=" CA LEU E 60 " ideal model delta harmonic sigma weight residual 180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 7633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1790 0.050 - 0.100: 451 0.100 - 0.150: 96 0.150 - 0.200: 19 0.200 - 0.251: 4 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CB THR B 54 " pdb=" CA THR B 54 " pdb=" OG1 THR B 54 " pdb=" CG2 THR B 54 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA GLU A 94 " pdb=" N GLU A 94 " pdb=" C GLU A 94 " pdb=" CB GLU A 94 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA PHE A 104 " pdb=" N PHE A 104 " pdb=" C PHE A 104 " pdb=" CB PHE A 104 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2357 not shown) Planarity restraints: 1408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 60 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C ALA G 60 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA G 60 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU G 61 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 113 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" CD GLU D 113 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU D 113 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU D 113 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 106 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" CG ASP E 106 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASP E 106 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP E 106 " -0.013 2.00e-02 2.50e+03 ... (remaining 1405 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2643 2.78 - 3.31: 12088 3.31 - 3.84: 29169 3.84 - 4.37: 32242 4.37 - 4.90: 44010 Nonbonded interactions: 120152 Sorted by model distance: nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.249 2.520 nonbonded pdb=" O LYS H 116 " pdb=" OG1 THR H 119 " model vdw 2.274 2.440 nonbonded pdb=" O GLN A 93 " pdb=" OG SER A 96 " model vdw 2.279 2.440 nonbonded pdb=" NE2 HIS A 113 " pdb=" OD1 ASP E 123 " model vdw 2.282 2.520 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.291 2.440 ... (remaining 120147 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 1.300 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: 6.200 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 43.710 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 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 0.064 14262 Z= 0.335 Angle : 0.912 11.014 20774 Z= 0.518 Chirality : 0.048 0.251 2360 Planarity : 0.007 0.075 1408 Dihedral : 30.189 179.839 6204 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: -0.20 (0.27), residues: 752 helix: 0.18 (0.21), residues: 520 sheet: None (None), residues: 0 loop : -0.58 (0.35), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS H 109 PHE 0.024 0.003 PHE G 25 TYR 0.035 0.003 TYR D 37 ARG 0.009 0.001 ARG F 92 *********************** 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 170 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9384 (mpp) cc_final: 0.8851 (mpp) REVERT: A 104 PHE cc_start: 0.9170 (m-80) cc_final: 0.8786 (m-80) REVERT: A 105 GLU cc_start: 0.9474 (pm20) cc_final: 0.9228 (pm20) REVERT: A 106 ASP cc_start: 0.9444 (m-30) cc_final: 0.9074 (m-30) REVERT: A 120 MET cc_start: 0.8366 (mtt) cc_final: 0.8082 (mpp) REVERT: B 59 LYS cc_start: 0.9594 (tmtt) cc_final: 0.9373 (tptt) REVERT: C 25 PHE cc_start: 0.8185 (m-10) cc_final: 0.7745 (m-10) REVERT: D 34 LYS cc_start: 0.8280 (mmmm) cc_final: 0.7645 (tmmt) REVERT: E 50 GLU cc_start: 0.9493 (mp0) cc_final: 0.8860 (pm20) REVERT: E 51 ILE cc_start: 0.9570 (mt) cc_final: 0.9256 (mt) REVERT: E 54 TYR cc_start: 0.9506 (m-80) cc_final: 0.9088 (m-80) REVERT: E 59 GLU cc_start: 0.9092 (mp0) cc_final: 0.8764 (pm20) REVERT: E 90 MET cc_start: 0.9429 (mmp) cc_final: 0.9138 (mmp) REVERT: E 93 GLN cc_start: 0.9125 (tm-30) cc_final: 0.8047 (tm-30) REVERT: E 94 GLU cc_start: 0.9403 (tp30) cc_final: 0.9097 (tp30) REVERT: E 104 PHE cc_start: 0.9622 (m-10) cc_final: 0.9333 (m-80) REVERT: E 105 GLU cc_start: 0.9401 (pp20) cc_final: 0.9194 (pp20) REVERT: E 120 MET cc_start: 0.8744 (mtm) cc_final: 0.8271 (mtt) REVERT: E 123 ASP cc_start: 0.9563 (m-30) cc_final: 0.9310 (m-30) REVERT: F 24 ASP cc_start: 0.9237 (t0) cc_final: 0.9014 (t0) REVERT: F 59 LYS cc_start: 0.9663 (tttp) cc_final: 0.9225 (tppp) REVERT: F 60 VAL cc_start: 0.9651 (t) cc_final: 0.9438 (p) REVERT: F 62 LEU cc_start: 0.9793 (mt) cc_final: 0.9407 (pp) REVERT: F 63 GLU cc_start: 0.9680 (mt-10) cc_final: 0.9299 (mt-10) REVERT: G 102 ILE cc_start: 0.8328 (mm) cc_final: 0.8102 (mm) REVERT: H 47 GLN cc_start: 0.9202 (mp10) cc_final: 0.8942 (mp10) REVERT: H 105 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8309 (tm-30) REVERT: H 109 HIS cc_start: 0.9391 (m90) cc_final: 0.8441 (m90) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2664 time to fit residues: 64.0974 Evaluate side-chains 120 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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: 20.0000 chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 14262 Z= 0.341 Angle : 0.671 10.188 20774 Z= 0.399 Chirality : 0.037 0.149 2360 Planarity : 0.005 0.052 1408 Dihedral : 33.065 178.475 4680 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.16 % Allowed : 5.19 % Favored : 94.65 % 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: 1.19 (0.29), residues: 752 helix: 1.23 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -0.15 (0.37), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS D 109 PHE 0.019 0.002 PHE E 67 TYR 0.013 0.002 TYR D 37 ARG 0.009 0.001 ARG C 42 *********************** 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 141 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.034 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: A 90 MET cc_start: 0.9356 (mpp) cc_final: 0.9122 (mpp) REVERT: A 104 PHE cc_start: 0.9435 (m-80) cc_final: 0.9117 (m-80) REVERT: A 106 ASP cc_start: 0.9393 (m-30) cc_final: 0.9153 (m-30) REVERT: A 120 MET cc_start: 0.8061 (mtt) cc_final: 0.6992 (mpp) REVERT: B 59 LYS cc_start: 0.9647 (tmtt) cc_final: 0.9435 (tptt) REVERT: B 74 GLU cc_start: 0.9766 (tm-30) cc_final: 0.9489 (tm-30) REVERT: C 50 TYR cc_start: 0.9257 (t80) cc_final: 0.8787 (t80) REVERT: D 109 HIS cc_start: 0.9419 (m90) cc_final: 0.8972 (m-70) REVERT: E 50 GLU cc_start: 0.9485 (mp0) cc_final: 0.9225 (pt0) REVERT: E 59 GLU cc_start: 0.9185 (mp0) cc_final: 0.8852 (pm20) REVERT: E 90 MET cc_start: 0.9476 (mmp) cc_final: 0.9183 (mmp) REVERT: E 93 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8440 (tm-30) REVERT: E 94 GLU cc_start: 0.9066 (tp30) cc_final: 0.8315 (tp30) REVERT: E 97 GLU cc_start: 0.9099 (pt0) cc_final: 0.8495 (pp20) REVERT: E 104 PHE cc_start: 0.9588 (m-10) cc_final: 0.9335 (m-10) REVERT: E 105 GLU cc_start: 0.9209 (pp20) cc_final: 0.9003 (pp20) REVERT: E 106 ASP cc_start: 0.8834 (m-30) cc_final: 0.8338 (m-30) REVERT: E 120 MET cc_start: 0.8680 (mtm) cc_final: 0.7961 (mtt) REVERT: E 123 ASP cc_start: 0.9379 (m-30) cc_final: 0.8769 (m-30) REVERT: F 60 VAL cc_start: 0.9672 (t) cc_final: 0.9201 (t) REVERT: F 63 GLU cc_start: 0.9697 (mt-10) cc_final: 0.9480 (mt-10) REVERT: F 74 GLU cc_start: 0.9321 (pp20) cc_final: 0.9097 (pp20) REVERT: G 102 ILE cc_start: 0.8430 (mm) cc_final: 0.8175 (mm) REVERT: H 95 GLN cc_start: 0.9418 (pt0) cc_final: 0.9156 (pt0) outliers start: 1 outliers final: 1 residues processed: 141 average time/residue: 0.2693 time to fit residues: 53.8764 Evaluate side-chains 103 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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: 4.9990 chunk 29 optimal weight: 0.0980 chunk 80 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 14262 Z= 0.302 Angle : 0.653 9.324 20774 Z= 0.388 Chirality : 0.036 0.148 2360 Planarity : 0.005 0.048 1408 Dihedral : 32.901 179.361 4680 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % 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: 1.33 (0.29), residues: 752 helix: 1.37 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.22 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 109 PHE 0.015 0.002 PHE D 65 TYR 0.015 0.002 TYR D 40 ARG 0.008 0.001 ARG C 42 *********************** 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 135 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.032 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: A 90 MET cc_start: 0.9430 (mpp) cc_final: 0.9057 (mmm) REVERT: A 97 GLU cc_start: 0.9261 (pm20) cc_final: 0.8839 (pm20) REVERT: A 104 PHE cc_start: 0.9448 (m-80) cc_final: 0.9202 (m-80) REVERT: A 120 MET cc_start: 0.7755 (mtt) cc_final: 0.7073 (mtt) REVERT: B 59 LYS cc_start: 0.9684 (tmtt) cc_final: 0.9475 (tptt) REVERT: B 74 GLU cc_start: 0.9782 (tm-30) cc_final: 0.9515 (tm-30) REVERT: B 85 ASP cc_start: 0.8474 (m-30) cc_final: 0.8255 (m-30) REVERT: E 59 GLU cc_start: 0.9093 (mp0) cc_final: 0.8715 (pm20) REVERT: E 90 MET cc_start: 0.9466 (mmp) cc_final: 0.9146 (mmp) REVERT: E 104 PHE cc_start: 0.9525 (m-10) cc_final: 0.9307 (m-80) REVERT: E 105 GLU cc_start: 0.9202 (pp20) cc_final: 0.8973 (pp20) REVERT: E 106 ASP cc_start: 0.8807 (m-30) cc_final: 0.8312 (m-30) REVERT: E 120 MET cc_start: 0.8572 (mtm) cc_final: 0.7884 (mtt) REVERT: F 74 GLU cc_start: 0.9347 (pp20) cc_final: 0.9136 (pp20) REVERT: G 64 GLU cc_start: 0.9170 (mp0) cc_final: 0.8882 (mp0) REVERT: G 72 ASP cc_start: 0.9368 (m-30) cc_final: 0.9149 (m-30) REVERT: G 92 GLU cc_start: 0.8536 (mt-10) cc_final: 0.7746 (mt-10) REVERT: H 95 GLN cc_start: 0.9412 (pt0) cc_final: 0.9158 (pt0) REVERT: H 108 LYS cc_start: 0.9449 (mtmm) cc_final: 0.9196 (ptpp) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2613 time to fit residues: 50.3992 Evaluate side-chains 97 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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: 6.9990 chunk 72 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN C 112 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 14262 Z= 0.423 Angle : 0.733 11.466 20774 Z= 0.429 Chirality : 0.039 0.164 2360 Planarity : 0.005 0.055 1408 Dihedral : 33.239 177.986 4680 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 26.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % 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: 0.96 (0.29), residues: 752 helix: 1.12 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -0.33 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS D 109 PHE 0.016 0.002 PHE A 104 TYR 0.016 0.002 TYR D 40 ARG 0.011 0.001 ARG C 42 *********************** 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 121 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.995 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: A 97 GLU cc_start: 0.9189 (pm20) cc_final: 0.8713 (pm20) REVERT: A 104 PHE cc_start: 0.9479 (m-80) cc_final: 0.9242 (m-80) REVERT: A 120 MET cc_start: 0.7661 (mtt) cc_final: 0.6969 (mtt) REVERT: B 63 GLU cc_start: 0.9507 (tt0) cc_final: 0.9011 (tm-30) REVERT: B 74 GLU cc_start: 0.9815 (tm-30) cc_final: 0.9539 (tm-30) REVERT: C 101 THR cc_start: 0.8398 (p) cc_final: 0.8166 (p) REVERT: E 50 GLU cc_start: 0.9462 (mp0) cc_final: 0.9211 (mt-10) REVERT: E 90 MET cc_start: 0.9472 (mmp) cc_final: 0.9141 (mmm) REVERT: E 105 GLU cc_start: 0.9192 (pp20) cc_final: 0.8973 (pp20) REVERT: E 106 ASP cc_start: 0.8812 (m-30) cc_final: 0.8324 (m-30) REVERT: E 120 MET cc_start: 0.8550 (mtm) cc_final: 0.7822 (mtt) REVERT: F 44 LYS cc_start: 0.8526 (pptt) cc_final: 0.8176 (tmtt) REVERT: G 64 GLU cc_start: 0.9176 (mp0) cc_final: 0.8918 (mp0) REVERT: H 47 GLN cc_start: 0.9452 (tm-30) cc_final: 0.9222 (tm-30) REVERT: H 95 GLN cc_start: 0.9362 (pt0) cc_final: 0.9111 (pt0) REVERT: H 108 LYS cc_start: 0.9478 (mtmm) cc_final: 0.9089 (ptpp) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2518 time to fit residues: 44.2098 Evaluate side-chains 96 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14262 Z= 0.203 Angle : 0.622 7.306 20774 Z= 0.369 Chirality : 0.035 0.152 2360 Planarity : 0.004 0.055 1408 Dihedral : 32.854 179.267 4680 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.31 % Allowed : 2.83 % Favored : 96.86 % 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: 1.52 (0.30), residues: 752 helix: 1.52 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.20 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.020 0.002 PHE E 104 TYR 0.009 0.001 TYR D 40 ARG 0.005 0.000 ARG C 42 *********************** 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 140 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 0.964 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: A 90 MET cc_start: 0.9384 (mpp) cc_final: 0.8987 (mmm) REVERT: A 104 PHE cc_start: 0.9383 (m-80) cc_final: 0.9034 (m-80) REVERT: A 120 MET cc_start: 0.7920 (mtt) cc_final: 0.7098 (mtt) REVERT: A 123 ASP cc_start: 0.9408 (m-30) cc_final: 0.8973 (m-30) REVERT: B 74 GLU cc_start: 0.9804 (tm-30) cc_final: 0.9492 (tm-30) REVERT: B 85 ASP cc_start: 0.8465 (m-30) cc_final: 0.8229 (m-30) REVERT: C 101 THR cc_start: 0.8516 (p) cc_final: 0.8287 (p) REVERT: E 50 GLU cc_start: 0.9488 (mp0) cc_final: 0.9235 (mp0) REVERT: E 59 GLU cc_start: 0.9046 (mp0) cc_final: 0.8532 (pm20) REVERT: E 90 MET cc_start: 0.9433 (mmp) cc_final: 0.9130 (mmp) REVERT: E 94 GLU cc_start: 0.9260 (tp30) cc_final: 0.8892 (tp30) REVERT: E 104 PHE cc_start: 0.9454 (m-10) cc_final: 0.9254 (m-80) REVERT: E 105 GLU cc_start: 0.9119 (pp20) cc_final: 0.8798 (pp20) REVERT: E 106 ASP cc_start: 0.8727 (m-30) cc_final: 0.8232 (m-30) REVERT: E 120 MET cc_start: 0.8445 (mtm) cc_final: 0.7726 (mtt) REVERT: F 60 VAL cc_start: 0.9654 (t) cc_final: 0.9201 (t) REVERT: F 74 GLU cc_start: 0.9325 (pp20) cc_final: 0.9102 (pp20) REVERT: F 75 HIS cc_start: 0.8959 (t70) cc_final: 0.8684 (t70) REVERT: F 79 LYS cc_start: 0.9493 (tptp) cc_final: 0.9291 (tttt) REVERT: G 36 LYS cc_start: 0.9573 (mmtm) cc_final: 0.9365 (mmtm) REVERT: G 92 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7835 (mt-10) REVERT: H 47 GLN cc_start: 0.9474 (tm-30) cc_final: 0.9243 (tm-30) REVERT: H 95 GLN cc_start: 0.9367 (pt0) cc_final: 0.9067 (pt0) REVERT: H 108 LYS cc_start: 0.9436 (mtmm) cc_final: 0.9132 (ptpp) outliers start: 2 outliers final: 1 residues processed: 138 average time/residue: 0.2566 time to fit residues: 50.7903 Evaluate side-chains 109 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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: 8.9990 chunk 20 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 14262 Z= 0.361 Angle : 0.686 10.025 20774 Z= 0.403 Chirality : 0.037 0.168 2360 Planarity : 0.005 0.055 1408 Dihedral : 32.964 178.400 4680 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 23.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.16 % Allowed : 1.89 % 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: 1.21 (0.30), residues: 752 helix: 1.21 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.10 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.019 0.002 PHE G 25 TYR 0.013 0.002 TYR D 40 ARG 0.009 0.001 ARG C 42 *********************** 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 123 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 0.830 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: A 90 MET cc_start: 0.9432 (mpp) cc_final: 0.9089 (mpp) REVERT: A 97 GLU cc_start: 0.8964 (pm20) cc_final: 0.8674 (pm20) REVERT: A 104 PHE cc_start: 0.9525 (m-80) cc_final: 0.9275 (m-80) REVERT: A 106 ASP cc_start: 0.9518 (m-30) cc_final: 0.9310 (m-30) REVERT: A 120 MET cc_start: 0.7743 (mtt) cc_final: 0.6982 (mtt) REVERT: B 74 GLU cc_start: 0.9823 (tm-30) cc_final: 0.9504 (tm-30) REVERT: B 85 ASP cc_start: 0.8449 (m-30) cc_final: 0.8227 (m-30) REVERT: D 109 HIS cc_start: 0.9206 (m170) cc_final: 0.8833 (m170) REVERT: E 50 GLU cc_start: 0.9454 (mp0) cc_final: 0.9238 (mp0) REVERT: E 59 GLU cc_start: 0.9117 (mp0) cc_final: 0.8591 (pm20) REVERT: E 90 MET cc_start: 0.9483 (mmp) cc_final: 0.9157 (mmp) REVERT: E 120 MET cc_start: 0.8386 (mtm) cc_final: 0.7732 (mtt) REVERT: H 45 LEU cc_start: 0.9397 (tp) cc_final: 0.9181 (tp) REVERT: H 47 GLN cc_start: 0.9467 (tm-30) cc_final: 0.9264 (tm-30) REVERT: H 95 GLN cc_start: 0.9356 (pt0) cc_final: 0.9062 (pt0) REVERT: H 108 LYS cc_start: 0.9430 (mtmm) cc_final: 0.9058 (ptpp) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.2446 time to fit residues: 43.7827 Evaluate side-chains 99 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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: 10.0000 chunk 58 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14262 Z= 0.278 Angle : 0.651 8.652 20774 Z= 0.385 Chirality : 0.036 0.177 2360 Planarity : 0.004 0.053 1408 Dihedral : 32.903 179.402 4680 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: 1.30 (0.30), residues: 752 helix: 1.28 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.09 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.015 0.002 PHE G 25 TYR 0.011 0.002 TYR D 121 ARG 0.007 0.000 ARG C 42 *********************** 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 131 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.919 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: A 90 MET cc_start: 0.9301 (mpp) cc_final: 0.8958 (mpp) REVERT: A 97 GLU cc_start: 0.8829 (pm20) cc_final: 0.8431 (pm20) REVERT: A 104 PHE cc_start: 0.9516 (m-80) cc_final: 0.9237 (m-80) REVERT: A 120 MET cc_start: 0.7765 (mtt) cc_final: 0.6971 (mtt) REVERT: B 63 GLU cc_start: 0.9425 (tt0) cc_final: 0.9005 (tm-30) REVERT: B 74 GLU cc_start: 0.9825 (tm-30) cc_final: 0.9515 (tm-30) REVERT: B 85 ASP cc_start: 0.8449 (m-30) cc_final: 0.8207 (m-30) REVERT: D 34 LYS cc_start: 0.8094 (mmmm) cc_final: 0.7442 (ttpp) REVERT: D 109 HIS cc_start: 0.9188 (m170) cc_final: 0.8808 (m170) REVERT: E 50 GLU cc_start: 0.9479 (mp0) cc_final: 0.9221 (mp0) REVERT: E 59 GLU cc_start: 0.9099 (mp0) cc_final: 0.8625 (pm20) REVERT: E 90 MET cc_start: 0.9443 (mmp) cc_final: 0.9123 (mmp) REVERT: E 97 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8944 (mt-10) REVERT: E 120 MET cc_start: 0.8366 (mtm) cc_final: 0.7723 (mtt) REVERT: F 75 HIS cc_start: 0.8965 (t70) cc_final: 0.8718 (t70) REVERT: G 36 LYS cc_start: 0.9526 (mmmt) cc_final: 0.9308 (mmtm) REVERT: G 64 GLU cc_start: 0.9177 (mp0) cc_final: 0.8928 (mp0) REVERT: G 92 GLU cc_start: 0.8642 (mt-10) cc_final: 0.7678 (tt0) REVERT: H 47 GLN cc_start: 0.9462 (tm-30) cc_final: 0.9253 (tm-30) REVERT: H 95 GLN cc_start: 0.9353 (pt0) cc_final: 0.9035 (pt0) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.2468 time to fit residues: 46.4196 Evaluate side-chains 103 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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: 8.9990 chunk 19 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14262 Z= 0.182 Angle : 0.610 6.748 20774 Z= 0.361 Chirality : 0.035 0.148 2360 Planarity : 0.004 0.054 1408 Dihedral : 32.542 179.846 4680 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: 1.59 (0.30), residues: 752 helix: 1.56 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.22 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.014 0.002 PHE G 25 TYR 0.013 0.001 TYR E 99 ARG 0.006 0.000 ARG G 20 *********************** 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 140 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.054 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: A 90 MET cc_start: 0.9338 (mpp) cc_final: 0.9076 (mpp) REVERT: A 97 GLU cc_start: 0.8722 (pm20) cc_final: 0.8296 (pm20) REVERT: A 104 PHE cc_start: 0.9370 (m-80) cc_final: 0.9040 (m-80) REVERT: A 120 MET cc_start: 0.7877 (mtt) cc_final: 0.7084 (mtt) REVERT: B 74 GLU cc_start: 0.9818 (tm-30) cc_final: 0.9516 (tm-30) REVERT: B 85 ASP cc_start: 0.8468 (m-30) cc_final: 0.8123 (m-30) REVERT: B 91 LYS cc_start: 0.9373 (tmmt) cc_final: 0.9151 (tmmt) REVERT: C 110 ASN cc_start: 0.9312 (t0) cc_final: 0.9043 (p0) REVERT: D 109 HIS cc_start: 0.9154 (m170) cc_final: 0.8854 (m170) REVERT: E 50 GLU cc_start: 0.9455 (mp0) cc_final: 0.9190 (mp0) REVERT: E 59 GLU cc_start: 0.9070 (mp0) cc_final: 0.8581 (pm20) REVERT: E 90 MET cc_start: 0.9423 (mmp) cc_final: 0.9155 (mmp) REVERT: E 94 GLU cc_start: 0.9206 (tp30) cc_final: 0.9005 (tp30) REVERT: E 97 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8805 (mt-10) REVERT: E 120 MET cc_start: 0.8318 (mtm) cc_final: 0.7705 (mtt) REVERT: E 123 ASP cc_start: 0.8895 (m-30) cc_final: 0.8449 (m-30) REVERT: F 74 GLU cc_start: 0.9234 (pp20) cc_final: 0.9000 (pp20) REVERT: F 75 HIS cc_start: 0.9136 (t-90) cc_final: 0.8864 (t70) REVERT: G 36 LYS cc_start: 0.9547 (mmmt) cc_final: 0.9069 (mmtm) REVERT: G 64 GLU cc_start: 0.9171 (mp0) cc_final: 0.8905 (mp0) REVERT: H 95 GLN cc_start: 0.9313 (pt0) cc_final: 0.9007 (pt0) REVERT: H 108 LYS cc_start: 0.9373 (mtmm) cc_final: 0.9058 (ptpp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2458 time to fit residues: 50.3942 Evaluate side-chains 109 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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: 7.9990 chunk 97 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 14262 Z= 0.325 Angle : 0.664 9.185 20774 Z= 0.390 Chirality : 0.036 0.176 2360 Planarity : 0.005 0.053 1408 Dihedral : 32.771 178.059 4680 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 22.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: 1.60 (0.30), residues: 752 helix: 1.58 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.14 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.011 0.002 PHE D 65 TYR 0.012 0.002 TYR D 40 ARG 0.009 0.001 ARG C 42 *********************** 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 130 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9523 (mp0) cc_final: 0.9257 (mp0) REVERT: A 104 PHE cc_start: 0.9528 (m-80) cc_final: 0.9208 (m-80) REVERT: A 120 MET cc_start: 0.7727 (mtt) cc_final: 0.6961 (mtt) REVERT: B 74 GLU cc_start: 0.9827 (tm-30) cc_final: 0.9503 (tm-30) REVERT: B 91 LYS cc_start: 0.9404 (tmmt) cc_final: 0.9161 (tmmt) REVERT: C 110 ASN cc_start: 0.9394 (t0) cc_final: 0.9042 (p0) REVERT: D 109 HIS cc_start: 0.9119 (m170) cc_final: 0.8715 (m170) REVERT: E 50 GLU cc_start: 0.9428 (mp0) cc_final: 0.9176 (mp0) REVERT: E 90 MET cc_start: 0.9444 (mmp) cc_final: 0.9132 (mmp) REVERT: E 97 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8894 (mt-10) REVERT: E 120 MET cc_start: 0.8334 (mtm) cc_final: 0.7901 (mtt) REVERT: E 123 ASP cc_start: 0.8982 (m-30) cc_final: 0.8552 (m-30) REVERT: F 62 LEU cc_start: 0.9838 (mt) cc_final: 0.9631 (mt) REVERT: F 63 GLU cc_start: 0.9613 (mt-10) cc_final: 0.9333 (mp0) REVERT: F 75 HIS cc_start: 0.9123 (t-90) cc_final: 0.8771 (t70) REVERT: G 36 LYS cc_start: 0.9565 (mmmt) cc_final: 0.9091 (mmtm) REVERT: G 64 GLU cc_start: 0.9196 (mp0) cc_final: 0.8981 (mp0) REVERT: G 92 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8354 (pm20) REVERT: H 95 GLN cc_start: 0.9351 (pt0) cc_final: 0.9033 (pt0) REVERT: H 108 LYS cc_start: 0.9442 (mtmm) cc_final: 0.9131 (ptpp) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2413 time to fit residues: 45.8008 Evaluate side-chains 102 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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: 7.9990 chunk 47 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 89 optimal weight: 20.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14262 Z= 0.251 Angle : 0.640 9.449 20774 Z= 0.376 Chirality : 0.035 0.182 2360 Planarity : 0.004 0.053 1408 Dihedral : 32.740 178.713 4680 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: 1.65 (0.30), residues: 752 helix: 1.65 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.21 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.013 0.002 PHE G 25 TYR 0.014 0.002 TYR D 121 ARG 0.006 0.000 ARG C 42 ********************** 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 131 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.940 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: A 90 MET cc_start: 0.9289 (mpp) cc_final: 0.8948 (mpp) REVERT: A 94 GLU cc_start: 0.9516 (mp0) cc_final: 0.9045 (mp0) REVERT: A 104 PHE cc_start: 0.9514 (m-80) cc_final: 0.9181 (m-80) REVERT: A 120 MET cc_start: 0.7784 (mtt) cc_final: 0.6979 (mtt) REVERT: B 74 GLU cc_start: 0.9824 (tm-30) cc_final: 0.9495 (tm-30) REVERT: B 91 LYS cc_start: 0.9380 (tmmt) cc_final: 0.9131 (tmmt) REVERT: C 110 ASN cc_start: 0.9365 (t0) cc_final: 0.9047 (p0) REVERT: D 109 HIS cc_start: 0.9139 (m170) cc_final: 0.8745 (m170) REVERT: E 50 GLU cc_start: 0.9419 (mp0) cc_final: 0.9149 (mp0) REVERT: E 59 GLU cc_start: 0.9107 (mp0) cc_final: 0.8603 (pm20) REVERT: E 90 MET cc_start: 0.9431 (mmp) cc_final: 0.9138 (mmp) REVERT: E 97 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8866 (mt-10) REVERT: E 120 MET cc_start: 0.8358 (mtm) cc_final: 0.7680 (mtt) REVERT: E 123 ASP cc_start: 0.8835 (m-30) cc_final: 0.8471 (m-30) REVERT: F 62 LEU cc_start: 0.9830 (mt) cc_final: 0.9624 (mt) REVERT: F 63 GLU cc_start: 0.9578 (mt-10) cc_final: 0.9281 (mp0) REVERT: F 75 HIS cc_start: 0.9155 (t-90) cc_final: 0.8803 (t70) REVERT: G 36 LYS cc_start: 0.9560 (mmmt) cc_final: 0.9084 (mmtm) REVERT: G 64 GLU cc_start: 0.9242 (mp0) cc_final: 0.8975 (mp0) REVERT: H 95 GLN cc_start: 0.9339 (pt0) cc_final: 0.9024 (pt0) REVERT: H 108 LYS cc_start: 0.9428 (mtmm) cc_final: 0.9131 (ptpp) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.2354 time to fit residues: 45.2485 Evaluate side-chains 104 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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: 3.9990 chunk 77 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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 = 0.2828 r_free = 0.2828 target = 0.029876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.023463 restraints weight = 197760.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.024280 restraints weight = 91803.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.024803 restraints weight = 52872.799| |-----------------------------------------------------------------------------| r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14262 Z= 0.262 Angle : 0.645 10.703 20774 Z= 0.378 Chirality : 0.035 0.177 2360 Planarity : 0.004 0.053 1408 Dihedral : 32.740 178.316 4680 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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: 1.56 (0.30), residues: 752 helix: 1.57 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.19 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.012 0.002 PHE G 25 TYR 0.013 0.002 TYR D 121 ARG 0.006 0.000 ARG C 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1938.05 seconds wall clock time: 36 minutes 45.66 seconds (2205.66 seconds total)