Starting phenix.real_space_refine on Sun Apr 7 23:45:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wz9_21971/04_2024/6wz9_21971.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wz9_21971/04_2024/6wz9_21971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wz9_21971/04_2024/6wz9_21971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wz9_21971/04_2024/6wz9_21971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wz9_21971/04_2024/6wz9_21971.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wz9_21971/04_2024/6wz9_21971.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 296 5.49 5 S 12 5.16 5 C 6569 2.51 5 N 2233 2.21 5 O 2816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11926 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 786 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "D" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "H" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3050 Classifications: {'DNA': 148} Link IDs: {'rna3p': 147} Chain: "J" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3018 Classifications: {'DNA': 148} Link IDs: {'rna3p': 147} Time building chain proxies: 6.85, per 1000 atoms: 0.57 Number of scatterers: 11926 At special positions: 0 Unit cell: (124.02, 95.4, 116.6, 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 12 16.00 P 296 15.00 O 2816 8.00 N 2233 7.00 C 6569 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: 6.21 Conformation dependent library (CDL) restraints added in 1.1 seconds 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 74.8% alpha, 3.3% beta 148 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 6.20 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.189A 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 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.738A 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 17 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.265A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.920A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.580A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) 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: 3.764A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.331A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.875A 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: 6.540A 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: 7.297A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.757A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.195A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 411 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 380 hydrogen bonds 760 hydrogen bond angles 0 basepair planarities 148 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 4.95 Time building geometry restraints manager: 6.48 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: 2091 1.33 - 1.45: 4337 1.45 - 1.57: 5701 1.57 - 1.69: 590 1.69 - 1.81: 22 Bond restraints: 12741 Sorted by residual: bond pdb=" C LEU D 98 " pdb=" N LEU D 99 " ideal model delta sigma weight residual 1.339 1.263 0.076 5.57e-02 3.22e+02 1.87e+00 bond pdb=" C3' DG I -37 " pdb=" O3' DG I -37 " ideal model delta sigma weight residual 1.422 1.383 0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" C3' DG I -6 " pdb=" O3' DG I -6 " ideal model delta sigma weight residual 1.422 1.386 0.036 3.00e-02 1.11e+03 1.46e+00 bond pdb=" CG LEU H 42 " pdb=" CD2 LEU H 42 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.46e+00 ... (remaining 12736 not shown) Histogram of bond angle deviations from ideal: 98.06 - 104.96: 1240 104.96 - 111.87: 6868 111.87 - 118.77: 3346 118.77 - 125.68: 6064 125.68 - 132.58: 966 Bond angle restraints: 18484 Sorted by residual: angle pdb=" CB MET B 84 " pdb=" CG MET B 84 " pdb=" SD MET B 84 " ideal model delta sigma weight residual 112.70 121.17 -8.47 3.00e+00 1.11e-01 7.98e+00 angle pdb=" N PRO D 100 " pdb=" CA PRO D 100 " pdb=" C PRO D 100 " ideal model delta sigma weight residual 110.21 114.73 -4.52 1.64e+00 3.72e-01 7.60e+00 angle pdb=" N LYS A 64 " pdb=" CA LYS A 64 " pdb=" C LYS A 64 " ideal model delta sigma weight residual 111.07 113.91 -2.84 1.07e+00 8.73e-01 7.03e+00 angle pdb=" CA LEU G 85 " pdb=" CB LEU G 85 " pdb=" CG LEU G 85 " ideal model delta sigma weight residual 116.30 125.38 -9.08 3.50e+00 8.16e-02 6.73e+00 angle pdb=" CA ILE H 51 " pdb=" CB ILE H 51 " pdb=" CG1 ILE H 51 " ideal model delta sigma weight residual 110.40 114.80 -4.40 1.70e+00 3.46e-01 6.70e+00 ... (remaining 18479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.12: 5262 33.12 - 66.24: 1589 66.24 - 99.36: 31 99.36 - 132.48: 0 132.48 - 165.60: 2 Dihedral angle restraints: 6884 sinusoidal: 4740 harmonic: 2144 Sorted by residual: dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 54.40 165.60 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 80.53 139.47 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual 180.00 162.47 17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 6881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1287 0.034 - 0.069: 594 0.069 - 0.103: 178 0.103 - 0.138: 43 0.138 - 0.172: 8 Chirality restraints: 2110 Sorted by residual: chirality pdb=" CA LYS B 79 " pdb=" N LYS B 79 " pdb=" C LYS B 79 " pdb=" CB LYS B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.42e-01 chirality pdb=" CA ILE D 86 " pdb=" N ILE D 86 " pdb=" C ILE D 86 " pdb=" CB ILE D 86 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" CA ILE H 86 " pdb=" N ILE H 86 " pdb=" C ILE H 86 " pdb=" CB ILE H 86 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 2107 not shown) Planarity restraints: 1312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO A 43 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 47 " -0.029 2.00e-02 2.50e+03 1.22e-02 4.09e+00 pdb=" N9 DA I 47 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 47 " 0.008 2.00e-02 2.50e+03 pdb=" N7 DA I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 47 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 47 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DA I 47 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 47 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA I 47 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 47 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 42 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO E 43 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " 0.027 5.00e-02 4.00e+02 ... (remaining 1309 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 71 2.59 - 3.17: 9062 3.17 - 3.75: 22466 3.75 - 4.32: 31511 4.32 - 4.90: 43549 Nonbonded interactions: 106659 Sorted by model distance: nonbonded pdb=" OG1 THR H 29 " pdb=" OP1 DT J 30 " model vdw 2.015 2.440 nonbonded pdb=" NZ LYS F 59 " pdb=" OE2 GLU F 63 " model vdw 2.151 2.520 nonbonded pdb=" NH2 ARG C 20 " pdb=" OP1 DG I -42 " model vdw 2.186 2.520 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.253 2.440 nonbonded pdb=" OE1 GLU A 105 " pdb=" NH2 ARG E 129 " model vdw 2.298 2.520 ... (remaining 106654 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' and resid 16 through 116) selection = (chain 'G' and resid 16 through 116) } 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 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: 6.700 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: 24.150 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 41.580 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 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 0.076 12741 Z= 0.339 Angle : 0.743 11.165 18484 Z= 0.457 Chirality : 0.043 0.172 2110 Planarity : 0.005 0.052 1312 Dihedral : 28.895 165.603 5500 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.27 % Allowed : 4.55 % Favored : 93.18 % 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: 0.07 (0.28), residues: 722 helix: 0.56 (0.20), residues: 546 sheet: None (None), residues: 0 loop : -1.33 (0.38), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.003 HIS E 113 PHE 0.020 0.003 PHE H 67 TYR 0.019 0.002 TYR H 37 ARG 0.008 0.001 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 154 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.5531 (mmm) cc_final: 0.5156 (mmm) REVERT: B 91 LYS cc_start: 0.7915 (ttmm) cc_final: 0.7648 (ttmt) REVERT: C 108 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7236 (mt) REVERT: D 31 LYS cc_start: 0.7140 (mmtt) cc_final: 0.6879 (tppt) REVERT: F 68 ASP cc_start: 0.7377 (m-30) cc_final: 0.6858 (m-30) REVERT: H 68 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7425 (mt-10) outliers start: 14 outliers final: 3 residues processed: 161 average time/residue: 1.8616 time to fit residues: 316.6438 Evaluate side-chains 105 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN C 31 HIS C 38 ASN D 81 ASN E 39 HIS E 108 ASN E 125 GLN F 93 GLN G 31 HIS G 89 ASN G 110 ASN H 44 GLN H 64 ASN H 81 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12741 Z= 0.227 Angle : 0.596 8.502 18484 Z= 0.357 Chirality : 0.035 0.132 2110 Planarity : 0.005 0.047 1312 Dihedral : 31.223 165.062 4063 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.71 % Allowed : 13.80 % Favored : 81.49 % 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: 1.71 (0.29), residues: 722 helix: 1.83 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.98 (0.39), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 82 PHE 0.020 0.002 PHE A 67 TYR 0.010 0.002 TYR H 118 ARG 0.007 0.001 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6019 (OUTLIER) cc_final: 0.5635 (tm-30) REVERT: B 91 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7615 (ttmt) REVERT: B 92 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6361 (ptm160) REVERT: D 31 LYS cc_start: 0.6923 (mmtt) cc_final: 0.6708 (tppt) REVERT: F 68 ASP cc_start: 0.7414 (m-30) cc_final: 0.6906 (m-30) REVERT: H 68 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: H 90 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6928 (mp0) REVERT: H 113 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6850 (tmtt) outliers start: 29 outliers final: 11 residues processed: 129 average time/residue: 1.8207 time to fit residues: 248.6820 Evaluate side-chains 111 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 25 ASN B 75 HIS B 93 GLN D 81 ASN E 125 GLN H 44 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12741 Z= 0.284 Angle : 0.623 8.606 18484 Z= 0.369 Chirality : 0.037 0.136 2110 Planarity : 0.005 0.043 1312 Dihedral : 31.395 163.519 4061 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 6.17 % Allowed : 15.58 % Favored : 78.25 % 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: 1.83 (0.30), residues: 722 helix: 1.85 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.82 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS C 82 PHE 0.021 0.002 PHE A 67 TYR 0.012 0.002 TYR H 118 ARG 0.005 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 109 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.5530 (mmt) cc_final: 0.5074 (ttm) REVERT: C 41 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7923 (mp0) REVERT: D 31 LYS cc_start: 0.6913 (mmtt) cc_final: 0.6675 (tppt) REVERT: E 120 MET cc_start: 0.7589 (mtm) cc_final: 0.7378 (mtm) REVERT: F 31 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7111 (mtpp) REVERT: F 68 ASP cc_start: 0.7456 (m-30) cc_final: 0.6930 (m-30) REVERT: F 79 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7888 (mtmt) REVERT: H 68 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: H 90 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6977 (mp0) REVERT: H 113 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6937 (tmtt) outliers start: 38 outliers final: 20 residues processed: 128 average time/residue: 1.6341 time to fit residues: 222.6851 Evaluate side-chains 119 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 94 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 46 optimal weight: 0.2980 chunk 9 optimal weight: 0.0770 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 25 optimal weight: 0.2980 chunk 78 optimal weight: 1.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 27 GLN B 93 GLN C 24 GLN D 44 GLN E 125 GLN H 44 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12741 Z= 0.211 Angle : 0.573 8.206 18484 Z= 0.344 Chirality : 0.034 0.131 2110 Planarity : 0.004 0.044 1312 Dihedral : 31.130 164.013 4061 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 5.52 % Allowed : 18.02 % Favored : 76.46 % 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: 2.14 (0.30), residues: 722 helix: 2.14 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.85 (0.40), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 113 PHE 0.022 0.002 PHE A 67 TYR 0.010 0.001 TYR B 88 ARG 0.005 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 106 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 80 THR cc_start: 0.7755 (OUTLIER) cc_final: 0.7514 (t) REVERT: A 90 MET cc_start: 0.5583 (mmt) cc_final: 0.5088 (ttm) REVERT: A 131 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7672 (mtt180) REVERT: E 120 MET cc_start: 0.7480 (mtm) cc_final: 0.7271 (mtm) REVERT: F 68 ASP cc_start: 0.7413 (m-30) cc_final: 0.6901 (m-30) REVERT: H 68 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: H 90 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: H 113 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6880 (tmtt) outliers start: 34 outliers final: 13 residues processed: 124 average time/residue: 1.7042 time to fit residues: 224.6498 Evaluate side-chains 113 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 93 GLN C 94 ASN E 125 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 46 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12741 Z= 0.241 Angle : 0.593 8.193 18484 Z= 0.354 Chirality : 0.035 0.134 2110 Planarity : 0.004 0.043 1312 Dihedral : 31.167 162.833 4060 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 7.47 % Allowed : 17.21 % Favored : 75.32 % 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: 2.11 (0.30), residues: 722 helix: 2.13 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.91 (0.40), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS G 82 PHE 0.023 0.002 PHE A 67 TYR 0.015 0.002 TYR G 50 ARG 0.004 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 104 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 THR cc_start: 0.7747 (OUTLIER) cc_final: 0.7497 (t) REVERT: A 90 MET cc_start: 0.5596 (mmt) cc_final: 0.5099 (ttm) REVERT: A 131 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7719 (mtt180) REVERT: B 92 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.6710 (ptm160) REVERT: B 95 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7452 (mtp85) REVERT: C 29 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7000 (ttm110) REVERT: D 59 MET cc_start: 0.7713 (mmm) cc_final: 0.7462 (tpt) REVERT: F 68 ASP cc_start: 0.7430 (m-30) cc_final: 0.6845 (m-30) REVERT: F 79 LYS cc_start: 0.8098 (mtmp) cc_final: 0.7847 (mtmt) REVERT: H 90 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: H 113 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6941 (tmtt) outliers start: 46 outliers final: 20 residues processed: 130 average time/residue: 1.8408 time to fit residues: 254.0574 Evaluate side-chains 128 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 125 GLN B 93 GLN C 94 ASN E 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12741 Z= 0.294 Angle : 0.634 8.949 18484 Z= 0.374 Chirality : 0.037 0.146 2110 Planarity : 0.005 0.045 1312 Dihedral : 31.362 161.987 4057 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 6.66 % Allowed : 18.83 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.30), residues: 722 helix: 1.85 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -1.04 (0.41), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS G 82 PHE 0.025 0.002 PHE A 67 TYR 0.012 0.002 TYR B 51 ARG 0.004 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 102 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 THR cc_start: 0.7837 (OUTLIER) cc_final: 0.7574 (t) REVERT: A 90 MET cc_start: 0.5573 (mmt) cc_final: 0.5085 (ttm) REVERT: A 120 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6658 (mtt) REVERT: A 131 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7740 (mtt180) REVERT: A 133 GLU cc_start: 0.6473 (mt-10) cc_final: 0.6264 (mt-10) REVERT: B 95 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7443 (mtp85) REVERT: C 29 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6697 (ttm110) REVERT: F 68 ASP cc_start: 0.7406 (m-30) cc_final: 0.6877 (m-30) REVERT: H 90 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: H 113 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6949 (tmtt) outliers start: 41 outliers final: 19 residues processed: 124 average time/residue: 1.8718 time to fit residues: 245.6578 Evaluate side-chains 123 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 43 optimal weight: 0.3980 chunk 58 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 93 GLN C 94 ASN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN G 38 ASN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12741 Z= 0.198 Angle : 0.573 7.860 18484 Z= 0.343 Chirality : 0.033 0.131 2110 Planarity : 0.004 0.044 1312 Dihedral : 31.008 163.016 4057 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 5.19 % Allowed : 21.43 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.30), residues: 722 helix: 2.27 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.92 (0.41), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 82 PHE 0.027 0.002 PHE A 67 TYR 0.014 0.001 TYR G 50 ARG 0.004 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 105 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 80 THR cc_start: 0.7875 (p) cc_final: 0.7658 (t) REVERT: A 90 MET cc_start: 0.5457 (mmt) cc_final: 0.4995 (ttm) REVERT: A 125 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7213 (mt0) REVERT: A 131 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7647 (mtt180) REVERT: C 29 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6874 (ttm110) REVERT: D 31 LYS cc_start: 0.6500 (OUTLIER) cc_final: 0.6276 (mmmt) REVERT: D 59 MET cc_start: 0.7670 (mmm) cc_final: 0.7305 (tpt) REVERT: E 120 MET cc_start: 0.7421 (mtm) cc_final: 0.7160 (mtm) REVERT: E 124 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8038 (mm) REVERT: F 68 ASP cc_start: 0.7406 (m-30) cc_final: 0.6926 (m-30) REVERT: H 43 LYS cc_start: 0.8335 (mmmm) cc_final: 0.8005 (mmtp) REVERT: H 90 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6999 (mp0) outliers start: 32 outliers final: 13 residues processed: 121 average time/residue: 1.7588 time to fit residues: 225.8978 Evaluate side-chains 118 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 93 GLN C 94 ASN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12741 Z= 0.222 Angle : 0.592 8.211 18484 Z= 0.351 Chirality : 0.035 0.174 2110 Planarity : 0.004 0.045 1312 Dihedral : 31.041 161.778 4053 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.68 % Allowed : 21.59 % Favored : 72.73 % 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: 2.22 (0.30), residues: 722 helix: 2.23 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.93 (0.41), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 82 PHE 0.027 0.002 PHE A 67 TYR 0.020 0.002 TYR G 50 ARG 0.014 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 103 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.5530 (mmt) cc_final: 0.5050 (ttm) REVERT: A 120 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6691 (mtt) REVERT: A 131 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7659 (mtt180) REVERT: B 95 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7615 (mtp85) REVERT: C 29 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6666 (ttm110) REVERT: C 41 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: D 31 LYS cc_start: 0.6536 (OUTLIER) cc_final: 0.6315 (mmmt) REVERT: E 124 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8023 (mm) REVERT: F 68 ASP cc_start: 0.7403 (m-30) cc_final: 0.6849 (m-30) REVERT: H 90 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6992 (mp0) outliers start: 35 outliers final: 19 residues processed: 122 average time/residue: 1.7801 time to fit residues: 230.7746 Evaluate side-chains 128 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 93 GLN C 94 ASN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN F 27 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 12741 Z= 0.332 Angle : 0.670 9.196 18484 Z= 0.392 Chirality : 0.039 0.244 2110 Planarity : 0.005 0.043 1312 Dihedral : 31.427 161.098 4053 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.52 % Allowed : 22.24 % Favored : 72.24 % 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: 722 helix: 1.75 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.17 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS C 82 PHE 0.028 0.003 PHE A 67 TYR 0.026 0.002 TYR G 50 ARG 0.018 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 101 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.5616 (mmt) cc_final: 0.5119 (ttm) REVERT: A 120 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6710 (mtt) REVERT: A 131 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7735 (mtt180) REVERT: B 95 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7464 (mtp85) REVERT: C 29 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6771 (ttm110) REVERT: C 41 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: D 30 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6833 (ttt180) REVERT: D 31 LYS cc_start: 0.6414 (OUTLIER) cc_final: 0.6165 (mmmt) REVERT: F 68 ASP cc_start: 0.7453 (m-30) cc_final: 0.6941 (m-30) REVERT: H 90 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7139 (mp0) outliers start: 34 outliers final: 20 residues processed: 123 average time/residue: 1.8015 time to fit residues: 234.9591 Evaluate side-chains 127 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 93 GLN C 94 ASN D 44 GLN E 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12741 Z= 0.249 Angle : 0.625 8.654 18484 Z= 0.369 Chirality : 0.036 0.167 2110 Planarity : 0.005 0.046 1312 Dihedral : 31.250 161.742 4053 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.71 % Allowed : 23.38 % Favored : 71.92 % 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: 1.80 (0.30), residues: 722 helix: 1.94 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -1.15 (0.42), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 82 PHE 0.031 0.002 PHE A 67 TYR 0.031 0.002 TYR G 50 ARG 0.017 0.001 ARG D 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 103 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.5490 (mmt) cc_final: 0.5013 (ttm) REVERT: A 120 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6682 (mtt) REVERT: A 131 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7670 (mtt180) REVERT: B 95 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7486 (mtp85) REVERT: C 29 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6812 (ttm110) REVERT: C 41 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: D 30 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6765 (ttt180) REVERT: D 31 LYS cc_start: 0.6574 (OUTLIER) cc_final: 0.6329 (mmmt) REVERT: E 124 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8025 (mm) REVERT: F 68 ASP cc_start: 0.7405 (m-30) cc_final: 0.6879 (m-30) REVERT: H 90 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7081 (mp0) outliers start: 29 outliers final: 17 residues processed: 116 average time/residue: 1.8053 time to fit residues: 221.6744 Evaluate side-chains 129 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 103 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 68 optimal weight: 0.0000 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 93 GLN C 94 ASN E 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.127686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.112055 restraints weight = 23842.838| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 0.98 r_work: 0.3811 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3718 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12741 Z= 0.220 Angle : 0.627 10.797 18484 Z= 0.367 Chirality : 0.035 0.218 2110 Planarity : 0.005 0.044 1312 Dihedral : 31.249 161.873 4053 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 5.19 % Allowed : 22.73 % Favored : 72.08 % 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: 1.93 (0.30), residues: 722 helix: 2.03 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -1.10 (0.42), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 82 PHE 0.030 0.002 PHE A 67 TYR 0.032 0.002 TYR G 50 ARG 0.018 0.000 ARG D 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4653.24 seconds wall clock time: 84 minutes 50.81 seconds (5090.81 seconds total)