Starting phenix.real_space_refine on Sat Mar 16 04:38:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxz_35083/03_2024/8hxz_35083_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxz_35083/03_2024/8hxz_35083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxz_35083/03_2024/8hxz_35083.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxz_35083/03_2024/8hxz_35083.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxz_35083/03_2024/8hxz_35083_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxz_35083/03_2024/8hxz_35083_updated.pdb" } resolution = 3.4 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 328 5.49 5 S 16 5.16 5 C 7628 2.51 5 N 2563 2.21 5 O 3205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13740 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 837 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3345 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "J" Number of atoms: 3379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3379 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "M" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 915 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain breaks: 1 Time building chain proxies: 6.99, per 1000 atoms: 0.51 Number of scatterers: 13740 At special positions: 0 Unit cell: (75.6, 119.7, 142.8, 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 16 16.00 P 328 15.00 O 3205 8.00 N 2563 7.00 C 7628 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: 7.51 Conformation dependent library (CDL) restraints added in 1.6 seconds 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1644 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 2 sheets defined 59.3% alpha, 3.2% beta 164 base pairs and 294 stacking pairs defined. Time for finding SS restraints: 7.99 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 86 through 113 removed outlier: 3.571A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 48 through 76 removed outlier: 4.002A pdb=" N TYR B 51 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU B 52 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 62 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 65 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS B 75 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.292A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 102 through 120 removed outlier: 4.272A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 76 Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 48 through 76 removed outlier: 4.007A pdb=" N TYR F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU F 52 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU F 53 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE F 66 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU F 74 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 35 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.065A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 81 removed outlier: 3.791A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 97 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.944A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 88 No H-bonds generated for 'chain 'M' and resid 86 through 88' Processing helix chain 'M' and resid 102 through 130 Processing sheet with id= A, first strand: chain 'M' and resid 97 through 99 removed outlier: 6.564A pdb=" N PHE M 78 " --> pdb=" O LEU M 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'M' and resid 29 through 32 380 hydrogen bonds defined for protein. 1002 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 416 hydrogen bonds 832 hydrogen bond angles 0 basepair planarities 164 basepair parallelities 294 stacking parallelities Total time for adding SS restraints: 6.09 Time building geometry restraints manager: 7.97 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: 2322 1.33 - 1.45: 5135 1.45 - 1.58: 6519 1.58 - 1.70: 654 1.70 - 1.82: 30 Bond restraints: 14660 Sorted by residual: bond pdb=" CA ASN G 73 " pdb=" C ASN G 73 " ideal model delta sigma weight residual 1.523 1.571 -0.048 1.41e-02 5.03e+03 1.16e+01 bond pdb=" CA HIS M 18 " pdb=" C HIS M 18 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.34e-02 5.57e+03 1.00e+01 bond pdb=" SG ML3 A 36 " pdb=" CD ML3 A 36 " ideal model delta sigma weight residual 1.815 1.755 0.060 2.00e-02 2.50e+03 8.99e+00 bond pdb=" CB ML3 A 36 " pdb=" SG ML3 A 36 " ideal model delta sigma weight residual 1.817 1.766 0.051 2.00e-02 2.50e+03 6.46e+00 bond pdb=" CA PHE M 17 " pdb=" C PHE M 17 " ideal model delta sigma weight residual 1.527 1.496 0.031 1.35e-02 5.49e+03 5.27e+00 ... (remaining 14655 not shown) Histogram of bond angle deviations from ideal: 96.08 - 103.66: 948 103.66 - 111.24: 7019 111.24 - 118.82: 5139 118.82 - 126.40: 7066 126.40 - 133.98: 1024 Bond angle restraints: 21196 Sorted by residual: angle pdb=" N HIS M 18 " pdb=" CA HIS M 18 " pdb=" C HIS M 18 " ideal model delta sigma weight residual 110.80 96.08 14.72 2.13e+00 2.20e-01 4.78e+01 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 112.64 120.58 -7.94 1.21e+00 6.83e-01 4.30e+01 angle pdb=" N GLU F 63 " pdb=" CA GLU F 63 " pdb=" CB GLU F 63 " ideal model delta sigma weight residual 110.28 119.35 -9.07 1.55e+00 4.16e-01 3.43e+01 angle pdb=" N VAL D 95 " pdb=" CA VAL D 95 " pdb=" C VAL D 95 " ideal model delta sigma weight residual 110.62 104.73 5.89 1.02e+00 9.61e-01 3.34e+01 angle pdb=" CA ASN G 73 " pdb=" C ASN G 73 " pdb=" N LYS G 74 " ideal model delta sigma weight residual 118.32 110.98 7.34 1.35e+00 5.49e-01 2.95e+01 ... (remaining 21191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 6308 35.86 - 71.73: 1647 71.73 - 107.59: 32 107.59 - 143.45: 1 143.45 - 179.32: 4 Dihedral angle restraints: 7992 sinusoidal: 5444 harmonic: 2548 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 150.91 29.09 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LYS F 79 " pdb=" C LYS F 79 " pdb=" N THR F 80 " pdb=" CA THR F 80 " ideal model delta harmonic sigma weight residual 180.00 151.03 28.97 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA LYS H 31 " pdb=" C LYS H 31 " pdb=" N GLU H 32 " pdb=" CA GLU H 32 " ideal model delta harmonic sigma weight residual -180.00 -155.05 -24.95 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 7989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2054 0.067 - 0.134: 287 0.134 - 0.200: 43 0.200 - 0.267: 5 0.267 - 0.334: 2 Chirality restraints: 2391 Sorted by residual: chirality pdb=" CG LEU E 70 " pdb=" CB LEU E 70 " pdb=" CD1 LEU E 70 " pdb=" CD2 LEU E 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB THR D 112 " pdb=" CA THR D 112 " pdb=" OG1 THR D 112 " pdb=" CG2 THR D 112 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 2388 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.055 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO G 80 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.050 5.00e-02 4.00e+02 7.55e-02 9.13e+00 pdb=" N PRO C 80 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 88 " -0.011 2.00e-02 2.50e+03 2.02e-02 8.16e+00 pdb=" CG TYR B 88 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR B 88 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 88 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR B 88 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR B 88 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR B 88 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 88 " -0.006 2.00e-02 2.50e+03 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3379 2.82 - 3.34: 13070 3.34 - 3.86: 29161 3.86 - 4.38: 32358 4.38 - 4.90: 44151 Nonbonded interactions: 122119 Sorted by model distance: nonbonded pdb=" NZ LYS F 79 " pdb=" OP1 DG I 101 " model vdw 2.303 2.520 nonbonded pdb=" N THR H 87 " pdb=" OE2 GLU H 90 " model vdw 2.318 2.520 nonbonded pdb=" O ILE F 50 " pdb=" OG1 THR F 54 " model vdw 2.325 2.440 nonbonded pdb=" NH2 ARG A 42 " pdb=" OP1 DA I 69 " model vdw 2.329 2.520 nonbonded pdb=" NZ LYS G 15 " pdb=" OG SER G 19 " model vdw 2.337 2.520 ... (remaining 122114 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 37 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = (chain 'H' and resid 28 through 121) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.300 Check model and map are aligned: 0.180 Set scattering table: 0.140 Process input model: 46.570 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 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 : 0.005 0.067 14660 Z= 0.318 Angle : 0.983 14.720 21196 Z= 0.556 Chirality : 0.050 0.334 2391 Planarity : 0.007 0.084 1543 Dihedral : 29.122 179.316 6348 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.26), residues: 856 helix: -0.86 (0.20), residues: 541 sheet: -0.52 (0.90), residues: 30 loop : -1.15 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 84 HIS 0.014 0.002 HIS B 75 PHE 0.016 0.003 PHE G 25 TYR 0.042 0.004 TYR B 88 ARG 0.012 0.001 ARG H 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 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: 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 97 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8504 (mt-10) REVERT: B 35 ARG cc_start: 0.9274 (mtp-110) cc_final: 0.8911 (mtp-110) REVERT: B 59 LYS cc_start: 0.9445 (tmmt) cc_final: 0.9058 (ttpp) REVERT: B 63 GLU cc_start: 0.8892 (pp20) cc_final: 0.8632 (pp20) REVERT: B 91 LYS cc_start: 0.9644 (tppp) cc_final: 0.9255 (tppp) REVERT: C 36 LYS cc_start: 0.9435 (mmpt) cc_final: 0.9075 (mmmt) REVERT: C 104 GLN cc_start: 0.9084 (mp10) cc_final: 0.8819 (mp10) REVERT: C 111 ILE cc_start: 0.8572 (mm) cc_final: 0.8360 (mm) REVERT: C 112 GLN cc_start: 0.8565 (mp10) cc_final: 0.7286 (mp10) REVERT: D 80 TYR cc_start: 0.8716 (m-80) cc_final: 0.8444 (m-80) REVERT: D 102 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8953 (tp30) REVERT: E 108 ASN cc_start: 0.9229 (t0) cc_final: 0.8490 (t0) REVERT: E 109 LEU cc_start: 0.9619 (mm) cc_final: 0.9137 (mm) REVERT: F 25 ASN cc_start: 0.9414 (m-40) cc_final: 0.9196 (m110) REVERT: F 27 GLN cc_start: 0.9121 (mp10) cc_final: 0.8764 (mp10) REVERT: F 59 LYS cc_start: 0.9376 (ptmm) cc_final: 0.9167 (ptmm) REVERT: F 63 GLU cc_start: 0.9306 (pm20) cc_final: 0.9068 (pm20) REVERT: F 88 TYR cc_start: 0.8692 (m-10) cc_final: 0.7946 (m-10) REVERT: F 93 GLN cc_start: 0.8450 (tm-30) cc_final: 0.7910 (tm-30) REVERT: G 56 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8276 (mm-30) REVERT: G 92 GLU cc_start: 0.8359 (tt0) cc_final: 0.8066 (tt0) REVERT: G 112 GLN cc_start: 0.9081 (mp10) cc_final: 0.8685 (mp10) REVERT: H 65 ASP cc_start: 0.9349 (t0) cc_final: 0.9049 (t0) REVERT: H 92 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8623 (tm-30) REVERT: H 97 LEU cc_start: 0.9180 (tt) cc_final: 0.8896 (tt) REVERT: H 103 LEU cc_start: 0.9451 (mt) cc_final: 0.8816 (mt) REVERT: M 89 ASP cc_start: 0.7249 (m-30) cc_final: 0.7028 (m-30) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.3457 time to fit residues: 119.3010 Evaluate side-chains 189 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 46 optimal weight: 0.4980 chunk 90 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN M 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 14660 Z= 0.311 Angle : 0.720 9.120 21196 Z= 0.418 Chirality : 0.038 0.181 2391 Planarity : 0.006 0.070 1543 Dihedral : 32.303 177.681 4579 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.01 % Allowed : 12.57 % Favored : 84.43 % 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: -0.59 (0.27), residues: 856 helix: 0.02 (0.21), residues: 544 sheet: -1.05 (1.44), residues: 15 loop : -0.95 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 31 HIS 0.008 0.002 HIS F 75 PHE 0.021 0.002 PHE A 84 TYR 0.049 0.003 TYR B 88 ARG 0.005 0.001 ARG H 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 204 time to evaluate : 1.072 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: symmetry clash REVERT: A 108 ASN cc_start: 0.9538 (t0) cc_final: 0.8989 (t0) REVERT: A 119 ILE cc_start: 0.9410 (pt) cc_final: 0.9098 (pt) REVERT: A 120 MET cc_start: 0.8746 (mmm) cc_final: 0.8238 (mmm) REVERT: B 35 ARG cc_start: 0.9436 (mtp-110) cc_final: 0.9028 (mtp-110) REVERT: B 59 LYS cc_start: 0.9449 (tmmt) cc_final: 0.9142 (ttpp) REVERT: C 36 LYS cc_start: 0.9564 (mmpt) cc_final: 0.9325 (mtmm) REVERT: C 104 GLN cc_start: 0.9107 (mp10) cc_final: 0.8807 (mp10) REVERT: C 112 GLN cc_start: 0.8404 (mp10) cc_final: 0.7641 (mp10) REVERT: D 73 GLU cc_start: 0.9074 (tp30) cc_final: 0.8781 (tp30) REVERT: D 102 GLU cc_start: 0.9356 (mm-30) cc_final: 0.9009 (tp30) REVERT: E 84 PHE cc_start: 0.9035 (m-80) cc_final: 0.8773 (m-80) REVERT: E 108 ASN cc_start: 0.9370 (t0) cc_final: 0.8745 (t0) REVERT: F 25 ASN cc_start: 0.9358 (m-40) cc_final: 0.9088 (m110) REVERT: F 27 GLN cc_start: 0.9134 (mp10) cc_final: 0.8786 (mp10) REVERT: G 56 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8353 (mm-30) REVERT: G 61 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8743 (mm-30) REVERT: G 77 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7343 (tpp80) REVERT: G 112 GLN cc_start: 0.9057 (mp10) cc_final: 0.8479 (mp10) REVERT: H 65 ASP cc_start: 0.9405 (t0) cc_final: 0.9109 (t0) REVERT: H 80 TYR cc_start: 0.8733 (m-80) cc_final: 0.8061 (m-80) REVERT: H 92 GLN cc_start: 0.9289 (tm130) cc_final: 0.8989 (tm-30) outliers start: 22 outliers final: 15 residues processed: 215 average time/residue: 0.3297 time to fit residues: 94.8613 Evaluate side-chains 188 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 172 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain M residue 28 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 8.9990 chunk 71 optimal weight: 0.2980 chunk 29 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 overall best weight: 3.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14660 Z= 0.270 Angle : 0.696 9.541 21196 Z= 0.402 Chirality : 0.038 0.187 2391 Planarity : 0.005 0.058 1543 Dihedral : 32.125 179.729 4579 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.19 % Allowed : 17.08 % Favored : 80.74 % 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: -0.34 (0.28), residues: 856 helix: 0.18 (0.22), residues: 548 sheet: -0.66 (1.00), residues: 29 loop : -0.75 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 31 HIS 0.005 0.001 HIS F 75 PHE 0.013 0.002 PHE A 84 TYR 0.055 0.002 TYR B 88 ARG 0.005 0.001 ARG M 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 193 time to evaluate : 0.996 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 108 ASN cc_start: 0.9551 (t0) cc_final: 0.8954 (t0) REVERT: B 88 TYR cc_start: 0.8802 (m-10) cc_final: 0.8589 (m-80) REVERT: C 25 PHE cc_start: 0.9053 (m-10) cc_final: 0.8575 (m-10) REVERT: C 36 LYS cc_start: 0.9593 (mmpt) cc_final: 0.9385 (mtmm) REVERT: C 104 GLN cc_start: 0.9150 (mp10) cc_final: 0.8819 (mp10) REVERT: D 80 TYR cc_start: 0.8523 (m-80) cc_final: 0.8234 (m-80) REVERT: D 102 GLU cc_start: 0.9386 (mm-30) cc_final: 0.9049 (tp30) REVERT: E 84 PHE cc_start: 0.9069 (m-80) cc_final: 0.8830 (m-80) REVERT: E 97 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8068 (mt-10) REVERT: F 27 GLN cc_start: 0.9113 (mp10) cc_final: 0.8836 (mp10) REVERT: F 64 ASN cc_start: 0.9566 (m-40) cc_final: 0.9333 (m-40) REVERT: G 56 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8299 (mm-30) REVERT: G 61 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8687 (mm-30) REVERT: G 72 ASP cc_start: 0.9119 (m-30) cc_final: 0.8719 (p0) REVERT: G 89 ASN cc_start: 0.9514 (m-40) cc_final: 0.9089 (p0) REVERT: G 112 GLN cc_start: 0.8941 (mp10) cc_final: 0.8311 (mp10) REVERT: H 65 ASP cc_start: 0.9429 (t0) cc_final: 0.9112 (t0) REVERT: H 80 TYR cc_start: 0.8709 (m-80) cc_final: 0.8267 (m-80) REVERT: H 92 GLN cc_start: 0.9342 (tm130) cc_final: 0.9015 (tm-30) REVERT: H 96 ARG cc_start: 0.8938 (ptm-80) cc_final: 0.8280 (ttp80) outliers start: 16 outliers final: 10 residues processed: 199 average time/residue: 0.3321 time to fit residues: 88.7270 Evaluate side-chains 181 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14660 Z= 0.229 Angle : 0.678 10.709 21196 Z= 0.391 Chirality : 0.036 0.196 2391 Planarity : 0.005 0.054 1543 Dihedral : 31.864 178.754 4579 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.91 % Allowed : 20.77 % Favored : 77.32 % 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: -0.08 (0.28), residues: 856 helix: 0.33 (0.22), residues: 551 sheet: -1.81 (1.26), residues: 15 loop : -0.46 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 31 HIS 0.003 0.001 HIS F 75 PHE 0.011 0.001 PHE A 84 TYR 0.033 0.002 TYR H 80 ARG 0.010 0.001 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 205 time to evaluate : 1.146 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 108 ASN cc_start: 0.9544 (t0) cc_final: 0.8917 (t0) REVERT: A 119 ILE cc_start: 0.9401 (pt) cc_final: 0.9119 (pt) REVERT: A 120 MET cc_start: 0.8720 (mmm) cc_final: 0.7885 (mmm) REVERT: A 122 LYS cc_start: 0.9321 (mmtm) cc_final: 0.9093 (ptpp) REVERT: B 91 LYS cc_start: 0.9651 (tppp) cc_final: 0.9144 (tppp) REVERT: C 36 LYS cc_start: 0.9605 (mmpt) cc_final: 0.9404 (mtmm) REVERT: C 104 GLN cc_start: 0.9099 (mp10) cc_final: 0.8802 (mp10) REVERT: C 112 GLN cc_start: 0.8422 (mp10) cc_final: 0.7544 (mp10) REVERT: D 102 GLU cc_start: 0.9328 (mm-30) cc_final: 0.8996 (tp30) REVERT: E 84 PHE cc_start: 0.9050 (m-80) cc_final: 0.8833 (m-80) REVERT: E 108 ASN cc_start: 0.9520 (t0) cc_final: 0.9193 (t0) REVERT: F 27 GLN cc_start: 0.9109 (mp10) cc_final: 0.8898 (mp10) REVERT: F 64 ASN cc_start: 0.9569 (m-40) cc_final: 0.9310 (m110) REVERT: G 61 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8691 (mm-30) REVERT: G 72 ASP cc_start: 0.9104 (m-30) cc_final: 0.8748 (p0) REVERT: G 89 ASN cc_start: 0.9504 (m110) cc_final: 0.9139 (p0) REVERT: G 92 GLU cc_start: 0.8974 (tt0) cc_final: 0.8696 (tt0) REVERT: G 104 GLN cc_start: 0.9109 (mp10) cc_final: 0.8363 (mp10) REVERT: G 112 GLN cc_start: 0.8884 (mp10) cc_final: 0.8217 (mp10) REVERT: H 65 ASP cc_start: 0.9335 (t0) cc_final: 0.9056 (t0) REVERT: H 69 ARG cc_start: 0.9523 (mtm-85) cc_final: 0.9301 (mtm-85) REVERT: H 92 GLN cc_start: 0.9368 (tm130) cc_final: 0.8993 (tm-30) REVERT: H 96 ARG cc_start: 0.9022 (ptm-80) cc_final: 0.8300 (ttp80) outliers start: 14 outliers final: 10 residues processed: 209 average time/residue: 0.3342 time to fit residues: 92.8423 Evaluate side-chains 188 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 178 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 14660 Z= 0.369 Angle : 0.740 15.119 21196 Z= 0.424 Chirality : 0.039 0.201 2391 Planarity : 0.005 0.047 1543 Dihedral : 32.105 178.616 4579 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 23.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.96 % Allowed : 21.86 % Favored : 74.18 % 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: -0.19 (0.28), residues: 856 helix: 0.27 (0.22), residues: 552 sheet: -1.75 (1.30), residues: 15 loop : -0.58 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP M 88 HIS 0.004 0.001 HIS M 80 PHE 0.011 0.002 PHE A 104 TYR 0.059 0.003 TYR B 88 ARG 0.005 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 182 time to evaluate : 0.899 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 108 ASN cc_start: 0.9552 (t0) cc_final: 0.8990 (t0) REVERT: A 125 GLN cc_start: 0.9268 (mt0) cc_final: 0.9068 (mp10) REVERT: C 104 GLN cc_start: 0.9086 (mp10) cc_final: 0.8830 (mp10) REVERT: C 112 GLN cc_start: 0.8343 (mp10) cc_final: 0.7569 (mp10) REVERT: D 59 MET cc_start: 0.9203 (mmm) cc_final: 0.8989 (mmm) REVERT: D 73 GLU cc_start: 0.8824 (tp30) cc_final: 0.8059 (tp30) REVERT: D 76 ARG cc_start: 0.9175 (ttp-110) cc_final: 0.8626 (ttp-110) REVERT: D 102 GLU cc_start: 0.9352 (mm-30) cc_final: 0.9030 (tp30) REVERT: D 105 LYS cc_start: 0.9445 (mmtt) cc_final: 0.9208 (ptpp) REVERT: E 79 LYS cc_start: 0.9249 (tptp) cc_final: 0.9005 (tptp) REVERT: E 108 ASN cc_start: 0.9553 (t0) cc_final: 0.9266 (t0) REVERT: F 64 ASN cc_start: 0.9535 (m-40) cc_final: 0.9268 (m110) REVERT: F 88 TYR cc_start: 0.9115 (m-10) cc_final: 0.8731 (m-10) REVERT: G 56 GLU cc_start: 0.9218 (tp30) cc_final: 0.8533 (mm-30) REVERT: G 61 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8802 (mm-30) REVERT: G 72 ASP cc_start: 0.9226 (m-30) cc_final: 0.8826 (p0) REVERT: G 92 GLU cc_start: 0.9085 (tt0) cc_final: 0.8788 (tt0) REVERT: G 104 GLN cc_start: 0.8991 (mp10) cc_final: 0.8469 (mp10) REVERT: G 112 GLN cc_start: 0.8957 (mp10) cc_final: 0.8355 (mp10) REVERT: H 56 MET cc_start: 0.9240 (tpt) cc_final: 0.9035 (tpt) REVERT: H 65 ASP cc_start: 0.9408 (t0) cc_final: 0.9124 (t0) REVERT: H 80 TYR cc_start: 0.8392 (m-10) cc_final: 0.8108 (m-80) REVERT: H 92 GLN cc_start: 0.9439 (OUTLIER) cc_final: 0.9066 (tm-30) outliers start: 29 outliers final: 16 residues processed: 199 average time/residue: 0.3182 time to fit residues: 85.8197 Evaluate side-chains 189 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 92 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 108 optimal weight: 0.0170 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN H 92 GLN ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14660 Z= 0.261 Angle : 0.718 11.587 21196 Z= 0.408 Chirality : 0.038 0.206 2391 Planarity : 0.005 0.049 1543 Dihedral : 31.978 179.031 4579 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.14 % Allowed : 23.91 % Favored : 72.95 % 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: -0.04 (0.29), residues: 856 helix: 0.36 (0.22), residues: 551 sheet: -1.82 (1.31), residues: 15 loop : -0.47 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 88 HIS 0.003 0.001 HIS B 75 PHE 0.011 0.001 PHE E 84 TYR 0.062 0.002 TYR B 88 ARG 0.007 0.001 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 199 time to evaluate : 1.105 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: A 108 ASN cc_start: 0.9575 (t0) cc_final: 0.9038 (t0) REVERT: A 122 LYS cc_start: 0.9368 (mmtm) cc_final: 0.9081 (ptpp) REVERT: B 98 TYR cc_start: 0.9120 (m-10) cc_final: 0.8796 (m-10) REVERT: C 38 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.8150 (t0) REVERT: C 104 GLN cc_start: 0.9077 (mp10) cc_final: 0.8744 (mp10) REVERT: C 112 GLN cc_start: 0.8269 (mp10) cc_final: 0.7371 (mp10) REVERT: D 31 LYS cc_start: 0.8567 (mmtm) cc_final: 0.8335 (mmtm) REVERT: D 73 GLU cc_start: 0.8842 (tp30) cc_final: 0.8106 (tp30) REVERT: D 76 ARG cc_start: 0.9136 (ttp-110) cc_final: 0.8601 (ttp-110) REVERT: D 102 GLU cc_start: 0.9314 (mm-30) cc_final: 0.8922 (tp30) REVERT: E 50 GLU cc_start: 0.9352 (OUTLIER) cc_final: 0.9132 (pp20) REVERT: E 79 LYS cc_start: 0.9312 (tptp) cc_final: 0.9003 (tptp) REVERT: E 108 ASN cc_start: 0.9538 (t0) cc_final: 0.9284 (t0) REVERT: F 59 LYS cc_start: 0.9488 (ptmm) cc_final: 0.9080 (tmmt) REVERT: F 63 GLU cc_start: 0.9366 (pm20) cc_final: 0.9040 (pm20) REVERT: F 64 ASN cc_start: 0.9556 (m-40) cc_final: 0.9353 (m110) REVERT: F 91 LYS cc_start: 0.9518 (ttpt) cc_final: 0.9073 (ttpt) REVERT: G 61 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8791 (mm-30) REVERT: G 72 ASP cc_start: 0.9209 (m-30) cc_final: 0.8868 (p0) REVERT: G 92 GLU cc_start: 0.9013 (tt0) cc_final: 0.8748 (tt0) REVERT: G 104 GLN cc_start: 0.8982 (mp10) cc_final: 0.8683 (mp10) REVERT: G 112 GLN cc_start: 0.9012 (mp10) cc_final: 0.8413 (mp10) REVERT: H 59 MET cc_start: 0.9150 (mmm) cc_final: 0.8912 (mmm) REVERT: H 65 ASP cc_start: 0.9349 (t0) cc_final: 0.9023 (t0) REVERT: H 80 TYR cc_start: 0.8512 (m-10) cc_final: 0.7544 (m-80) REVERT: H 92 GLN cc_start: 0.9408 (tm-30) cc_final: 0.9028 (tm-30) REVERT: M 89 ASP cc_start: 0.7235 (m-30) cc_final: 0.7016 (m-30) outliers start: 23 outliers final: 17 residues processed: 212 average time/residue: 0.3359 time to fit residues: 96.2280 Evaluate side-chains 196 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 177 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain M residue 123 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 81 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14660 Z= 0.254 Angle : 0.719 15.020 21196 Z= 0.406 Chirality : 0.037 0.200 2391 Planarity : 0.005 0.047 1543 Dihedral : 31.871 179.811 4579 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.42 % Allowed : 25.14 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.29), residues: 856 helix: 0.36 (0.22), residues: 554 sheet: -1.78 (1.31), residues: 15 loop : -0.48 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 88 HIS 0.004 0.001 HIS D 79 PHE 0.010 0.001 PHE F 61 TYR 0.035 0.002 TYR B 88 ARG 0.008 0.001 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 193 time to evaluate : 1.090 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 67 PHE cc_start: 0.9238 (t80) cc_final: 0.9033 (t80) REVERT: A 108 ASN cc_start: 0.9573 (t0) cc_final: 0.9036 (t0) REVERT: A 115 LYS cc_start: 0.9332 (mmmm) cc_final: 0.9108 (mmmt) REVERT: A 122 LYS cc_start: 0.9363 (mmtm) cc_final: 0.9069 (ptpp) REVERT: A 125 GLN cc_start: 0.9262 (mt0) cc_final: 0.8971 (mt0) REVERT: B 39 ARG cc_start: 0.9439 (OUTLIER) cc_final: 0.9228 (mmt-90) REVERT: B 98 TYR cc_start: 0.9135 (m-10) cc_final: 0.8671 (m-10) REVERT: C 25 PHE cc_start: 0.9070 (m-10) cc_final: 0.8639 (m-10) REVERT: C 38 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7877 (t0) REVERT: C 104 GLN cc_start: 0.9032 (mp10) cc_final: 0.8787 (mp10) REVERT: C 112 GLN cc_start: 0.8249 (mp10) cc_final: 0.7376 (mp10) REVERT: D 73 GLU cc_start: 0.8725 (tp30) cc_final: 0.8000 (tp30) REVERT: D 76 ARG cc_start: 0.9126 (ttp-110) cc_final: 0.8666 (ttp-110) REVERT: D 102 GLU cc_start: 0.9300 (mm-30) cc_final: 0.8917 (tp30) REVERT: E 50 GLU cc_start: 0.9351 (OUTLIER) cc_final: 0.9132 (pp20) REVERT: E 79 LYS cc_start: 0.9352 (tptp) cc_final: 0.8993 (tptp) REVERT: E 108 ASN cc_start: 0.9549 (t0) cc_final: 0.9298 (t0) REVERT: F 27 GLN cc_start: 0.9129 (mp10) cc_final: 0.8854 (mp10) REVERT: F 59 LYS cc_start: 0.9427 (ptmm) cc_final: 0.9040 (tmmt) REVERT: F 63 GLU cc_start: 0.9251 (pm20) cc_final: 0.8996 (pm20) REVERT: F 64 ASN cc_start: 0.9562 (m-40) cc_final: 0.9350 (m110) REVERT: F 88 TYR cc_start: 0.9081 (m-80) cc_final: 0.8326 (m-80) REVERT: F 91 LYS cc_start: 0.9623 (ttpt) cc_final: 0.9322 (pttm) REVERT: G 61 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8794 (mm-30) REVERT: G 72 ASP cc_start: 0.9221 (m-30) cc_final: 0.8885 (p0) REVERT: G 89 ASN cc_start: 0.9597 (m110) cc_final: 0.9308 (p0) REVERT: G 104 GLN cc_start: 0.8863 (mp10) cc_final: 0.8575 (mp10) REVERT: G 112 GLN cc_start: 0.9060 (mp10) cc_final: 0.8431 (mp10) REVERT: H 56 MET cc_start: 0.9257 (tpt) cc_final: 0.9019 (tpt) REVERT: H 65 ASP cc_start: 0.9340 (t0) cc_final: 0.9036 (t70) REVERT: H 92 GLN cc_start: 0.9484 (tm-30) cc_final: 0.9154 (tm-30) outliers start: 25 outliers final: 18 residues processed: 206 average time/residue: 0.3192 time to fit residues: 88.9261 Evaluate side-chains 211 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 190 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain M residue 123 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 0.0970 chunk 87 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 107 optimal weight: 30.0000 chunk 97 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14660 Z= 0.306 Angle : 0.750 15.877 21196 Z= 0.422 Chirality : 0.038 0.198 2391 Planarity : 0.005 0.049 1543 Dihedral : 31.973 179.872 4579 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.73 % Allowed : 26.09 % Favored : 71.17 % 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: -0.10 (0.28), residues: 856 helix: 0.33 (0.22), residues: 553 sheet: -1.67 (1.37), residues: 15 loop : -0.54 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 88 HIS 0.003 0.001 HIS M 80 PHE 0.012 0.002 PHE A 84 TYR 0.039 0.002 TYR B 88 ARG 0.005 0.001 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 190 time to evaluate : 1.025 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: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9565 (t0) cc_final: 0.9014 (t0) REVERT: A 115 LYS cc_start: 0.9385 (mmmm) cc_final: 0.9164 (mmmt) REVERT: A 122 LYS cc_start: 0.9378 (mmtm) cc_final: 0.9082 (ptpp) REVERT: A 125 GLN cc_start: 0.9264 (mt0) cc_final: 0.8971 (mt0) REVERT: B 39 ARG cc_start: 0.9472 (OUTLIER) cc_final: 0.9153 (mmt-90) REVERT: B 98 TYR cc_start: 0.9146 (m-10) cc_final: 0.8805 (m-10) REVERT: C 104 GLN cc_start: 0.9048 (mp10) cc_final: 0.8777 (mp10) REVERT: C 112 GLN cc_start: 0.8105 (mp10) cc_final: 0.7289 (mp10) REVERT: D 73 GLU cc_start: 0.8785 (tp30) cc_final: 0.8170 (tp30) REVERT: D 76 ARG cc_start: 0.9170 (ttp-110) cc_final: 0.8751 (ttp-110) REVERT: D 102 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8913 (tp30) REVERT: E 50 GLU cc_start: 0.9326 (OUTLIER) cc_final: 0.9121 (pp20) REVERT: E 84 PHE cc_start: 0.9230 (m-80) cc_final: 0.8837 (m-80) REVERT: E 108 ASN cc_start: 0.9551 (t0) cc_final: 0.9286 (t0) REVERT: F 63 GLU cc_start: 0.9191 (pm20) cc_final: 0.8924 (pm20) REVERT: F 64 ASN cc_start: 0.9544 (m-40) cc_final: 0.9312 (m110) REVERT: F 88 TYR cc_start: 0.9087 (m-80) cc_final: 0.7948 (m-80) REVERT: F 91 LYS cc_start: 0.9622 (ttpt) cc_final: 0.9119 (ptpt) REVERT: G 61 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8842 (mm-30) REVERT: G 89 ASN cc_start: 0.9629 (m110) cc_final: 0.9394 (p0) REVERT: G 104 GLN cc_start: 0.8802 (mp10) cc_final: 0.8210 (mp10) REVERT: G 112 GLN cc_start: 0.9247 (mp10) cc_final: 0.8657 (mp10) REVERT: H 65 ASP cc_start: 0.9364 (t0) cc_final: 0.9013 (t0) REVERT: H 92 GLN cc_start: 0.9514 (tm-30) cc_final: 0.9005 (tm-30) outliers start: 20 outliers final: 16 residues processed: 200 average time/residue: 0.3047 time to fit residues: 82.4693 Evaluate side-chains 198 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 180 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 30.0000 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14660 Z= 0.288 Angle : 0.752 16.568 21196 Z= 0.422 Chirality : 0.038 0.200 2391 Planarity : 0.005 0.048 1543 Dihedral : 31.955 178.673 4579 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.42 % Allowed : 26.09 % Favored : 70.49 % 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: -0.14 (0.28), residues: 856 helix: 0.31 (0.22), residues: 553 sheet: -1.94 (1.29), residues: 15 loop : -0.56 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 88 HIS 0.008 0.001 HIS D 79 PHE 0.010 0.002 PHE A 84 TYR 0.047 0.003 TYR B 88 ARG 0.005 0.001 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 200 time to evaluate : 1.037 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 67 PHE cc_start: 0.9319 (t80) cc_final: 0.9071 (t80) REVERT: A 108 ASN cc_start: 0.9585 (t0) cc_final: 0.9049 (t0) REVERT: A 115 LYS cc_start: 0.9435 (mmmm) cc_final: 0.9209 (mmmt) REVERT: A 122 LYS cc_start: 0.9382 (mmtm) cc_final: 0.9088 (ptpp) REVERT: A 125 GLN cc_start: 0.9258 (mt0) cc_final: 0.8957 (mt0) REVERT: B 98 TYR cc_start: 0.9106 (m-10) cc_final: 0.8624 (m-10) REVERT: C 41 GLU cc_start: 0.8677 (pm20) cc_final: 0.8291 (pm20) REVERT: C 104 GLN cc_start: 0.9026 (mp10) cc_final: 0.8748 (mp10) REVERT: C 112 GLN cc_start: 0.8057 (mp10) cc_final: 0.7060 (mp10) REVERT: D 73 GLU cc_start: 0.8755 (tp30) cc_final: 0.8154 (tp30) REVERT: D 76 ARG cc_start: 0.9184 (ttp-110) cc_final: 0.8745 (ttp-110) REVERT: D 102 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8911 (tp30) REVERT: E 60 LEU cc_start: 0.9467 (mm) cc_final: 0.9248 (mt) REVERT: E 76 GLN cc_start: 0.9158 (tp-100) cc_final: 0.8837 (tp-100) REVERT: E 84 PHE cc_start: 0.9261 (m-80) cc_final: 0.8901 (m-80) REVERT: E 97 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7529 (mt-10) REVERT: E 108 ASN cc_start: 0.9534 (t0) cc_final: 0.9143 (t0) REVERT: F 27 GLN cc_start: 0.9116 (mp10) cc_final: 0.8856 (mp10) REVERT: F 31 LYS cc_start: 0.9423 (tmtt) cc_final: 0.9182 (tptp) REVERT: F 64 ASN cc_start: 0.9543 (m-40) cc_final: 0.9296 (m110) REVERT: F 88 TYR cc_start: 0.9036 (m-80) cc_final: 0.8381 (m-80) REVERT: F 91 LYS cc_start: 0.9628 (ttpt) cc_final: 0.9222 (ttpt) REVERT: G 38 ASN cc_start: 0.8078 (t0) cc_final: 0.7712 (t0) REVERT: G 61 GLU cc_start: 0.9311 (mm-30) cc_final: 0.8849 (mm-30) REVERT: G 89 ASN cc_start: 0.9633 (m110) cc_final: 0.9416 (p0) REVERT: G 112 GLN cc_start: 0.9244 (mp10) cc_final: 0.8635 (mp10) REVERT: H 65 ASP cc_start: 0.9350 (t0) cc_final: 0.9058 (t70) REVERT: H 76 ARG cc_start: 0.9282 (mtm110) cc_final: 0.9049 (ptp-110) REVERT: H 80 TYR cc_start: 0.8401 (m-10) cc_final: 0.6872 (m-10) REVERT: H 92 GLN cc_start: 0.9501 (tm-30) cc_final: 0.8972 (tm-30) REVERT: M 89 ASP cc_start: 0.7799 (m-30) cc_final: 0.7529 (m-30) outliers start: 25 outliers final: 16 residues processed: 213 average time/residue: 0.3147 time to fit residues: 91.3995 Evaluate side-chains 202 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 186 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 73 optimal weight: 30.0000 chunk 98 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14660 Z= 0.336 Angle : 0.800 17.110 21196 Z= 0.445 Chirality : 0.039 0.226 2391 Planarity : 0.005 0.044 1543 Dihedral : 32.065 178.964 4579 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.73 % Allowed : 27.46 % Favored : 69.81 % 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 (0.29), residues: 856 helix: 0.23 (0.22), residues: 552 sheet: -1.93 (1.28), residues: 15 loop : -0.50 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 88 HIS 0.005 0.001 HIS D 79 PHE 0.014 0.002 PHE F 61 TYR 0.062 0.003 TYR B 88 ARG 0.007 0.001 ARG F 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 193 time to evaluate : 1.090 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 108 ASN cc_start: 0.9564 (t0) cc_final: 0.9022 (t0) REVERT: A 115 LYS cc_start: 0.9412 (mmmm) cc_final: 0.9205 (mmmt) REVERT: A 122 LYS cc_start: 0.9389 (mmtm) cc_final: 0.9103 (ptpp) REVERT: A 125 GLN cc_start: 0.9256 (mt0) cc_final: 0.8962 (mt0) REVERT: B 39 ARG cc_start: 0.9496 (OUTLIER) cc_final: 0.9176 (mmt-90) REVERT: B 98 TYR cc_start: 0.9118 (m-10) cc_final: 0.8790 (m-10) REVERT: C 25 PHE cc_start: 0.9153 (m-10) cc_final: 0.8773 (m-10) REVERT: C 38 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7411 (t0) REVERT: C 41 GLU cc_start: 0.8678 (pm20) cc_final: 0.8295 (pm20) REVERT: C 104 GLN cc_start: 0.9033 (mp10) cc_final: 0.8757 (mp10) REVERT: C 112 GLN cc_start: 0.7920 (mp10) cc_final: 0.7427 (mp10) REVERT: D 73 GLU cc_start: 0.8747 (tp30) cc_final: 0.8100 (tp30) REVERT: D 76 ARG cc_start: 0.9142 (ttp-110) cc_final: 0.8739 (ttp-110) REVERT: D 102 GLU cc_start: 0.9307 (mm-30) cc_final: 0.8909 (tp30) REVERT: E 60 LEU cc_start: 0.9467 (mm) cc_final: 0.9242 (mt) REVERT: E 76 GLN cc_start: 0.9185 (tp-100) cc_final: 0.8878 (tp-100) REVERT: E 84 PHE cc_start: 0.9304 (m-80) cc_final: 0.8966 (m-80) REVERT: E 97 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7507 (mt-10) REVERT: E 108 ASN cc_start: 0.9527 (t0) cc_final: 0.9224 (t0) REVERT: F 31 LYS cc_start: 0.9425 (tmtt) cc_final: 0.9126 (tptp) REVERT: F 88 TYR cc_start: 0.9036 (m-80) cc_final: 0.8473 (m-80) REVERT: F 91 LYS cc_start: 0.9628 (ttpt) cc_final: 0.9216 (ttpt) REVERT: G 38 ASN cc_start: 0.8083 (t0) cc_final: 0.7545 (t0) REVERT: G 41 GLU cc_start: 0.9385 (pm20) cc_final: 0.9124 (pm20) REVERT: G 61 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8892 (mm-30) REVERT: G 64 GLU cc_start: 0.9335 (pp20) cc_final: 0.9118 (pp20) REVERT: G 112 GLN cc_start: 0.9233 (mp10) cc_final: 0.8625 (mp10) REVERT: H 65 ASP cc_start: 0.9300 (t0) cc_final: 0.8994 (t0) REVERT: H 80 TYR cc_start: 0.8470 (m-10) cc_final: 0.7177 (m-10) REVERT: H 92 GLN cc_start: 0.9516 (tm-30) cc_final: 0.9226 (tm-30) REVERT: M 89 ASP cc_start: 0.7864 (m-30) cc_final: 0.7508 (m-30) outliers start: 20 outliers final: 17 residues processed: 205 average time/residue: 0.3155 time to fit residues: 87.7276 Evaluate side-chains 202 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 183 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.050382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.037135 restraints weight = 125981.425| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.76 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14660 Z= 0.239 Angle : 0.782 17.124 21196 Z= 0.430 Chirality : 0.038 0.213 2391 Planarity : 0.005 0.049 1543 Dihedral : 31.785 178.670 4579 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.19 % Allowed : 28.55 % Favored : 69.26 % 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: -0.14 (0.29), residues: 856 helix: 0.26 (0.22), residues: 551 sheet: -1.83 (1.29), residues: 15 loop : -0.43 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 88 HIS 0.004 0.001 HIS D 79 PHE 0.014 0.002 PHE F 61 TYR 0.040 0.003 TYR D 80 ARG 0.010 0.000 ARG G 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2694.38 seconds wall clock time: 49 minutes 27.26 seconds (2967.26 seconds total)