Starting phenix.real_space_refine on Wed Sep 25 23:15:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wz9_21971/09_2024/6wz9_21971.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wz9_21971/09_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_21971/09_2024/6wz9_21971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wz9_21971/09_2024/6wz9_21971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wz9_21971/09_2024/6wz9_21971.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wz9_21971/09_2024/6wz9_21971.cif" } 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. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 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: 9.66, per 1000 atoms: 0.81 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.0 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: 6.23 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: 4.44 Time building geometry restraints manager: 3.62 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: 0.00 - 2.23: 18186 2.23 - 4.47: 283 4.47 - 6.70: 11 6.70 - 8.93: 2 8.93 - 11.17: 2 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 3.040 nonbonded pdb=" NZ LYS F 59 " pdb=" OE2 GLU F 63 " model vdw 2.151 3.120 nonbonded pdb=" NH2 ARG C 20 " pdb=" OP1 DG I -42 " model vdw 2.186 3.120 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.253 3.040 nonbonded pdb=" OE1 GLU A 105 " pdb=" NH2 ARG E 129 " model vdw 2.298 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 15.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 36.170 Find NCS groups from input model: 0.320 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:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.720 ------------------------------------------------------------------------------- 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 : 0.779 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: 1.8034 time to fit residues: 306.6651 Evaluate side-chains 105 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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: 1.9990 chunk 25 optimal weight: 0.5980 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: 0.8980 chunk 57 optimal weight: 0.2980 chunk 88 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.1546 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= 0.212 Angle : 0.588 8.338 18484 Z= 0.352 Chirality : 0.035 0.133 2110 Planarity : 0.005 0.049 1312 Dihedral : 31.325 165.610 4063 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.90 % Allowed : 13.80 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.29), residues: 722 helix: 1.82 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.94 (0.38), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 82 PHE 0.019 0.002 PHE A 67 TYR 0.010 0.001 TYR H 118 ARG 0.007 0.000 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 144 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 125 GLN cc_start: 0.7303 (mt0) cc_final: 0.6898 (mp10) REVERT: B 92 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6053 (ptm160) REVERT: F 68 ASP cc_start: 0.7414 (m-30) cc_final: 0.6908 (m-30) REVERT: H 68 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: H 83 ARG cc_start: 0.7941 (mpt-90) cc_final: 0.7693 (mmt90) REVERT: H 90 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: H 113 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6850 (tmtt) outliers start: 24 outliers final: 6 residues processed: 130 average time/residue: 1.6466 time to fit residues: 227.1664 Evaluate side-chains 105 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 110 ASN 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: 3.9990 chunk 27 optimal weight: 0.0970 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 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: 1.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 25 ASN B 75 HIS C 24 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: 0.6912 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12741 Z= 0.354 Angle : 0.684 9.314 18484 Z= 0.400 Chirality : 0.040 0.164 2110 Planarity : 0.006 0.048 1312 Dihedral : 31.684 162.386 4060 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 6.17 % Allowed : 16.72 % Favored : 77.11 % 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: 1.40 (0.29), residues: 722 helix: 1.53 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.93 (0.41), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.003 HIS G 82 PHE 0.023 0.003 PHE A 67 TYR 0.013 0.002 TYR H 118 ARG 0.005 0.001 ARG H 96 *********************** 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 142 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 104 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.6848 (tm-30) REVERT: A 90 MET cc_start: 0.4960 (OUTLIER) cc_final: 0.4556 (ttm) REVERT: A 115 LYS cc_start: 0.7098 (mmtp) cc_final: 0.6849 (mtmm) REVERT: B 95 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7533 (mtp85) REVERT: F 68 ASP cc_start: 0.7509 (m-30) cc_final: 0.6975 (m-30) REVERT: H 68 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: H 90 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: H 113 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6916 (tmtt) outliers start: 38 outliers final: 17 residues processed: 125 average time/residue: 1.5373 time to fit residues: 205.0840 Evaluate side-chains 119 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 90 MET 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 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 E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 130 ILE 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 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: 0.7980 chunk 46 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 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: 0.0040 chunk 78 optimal weight: 1.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN C 24 GLN C 38 ASN E 125 GLN H 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.2335 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= 0.224 Angle : 0.590 8.661 18484 Z= 0.352 Chirality : 0.035 0.139 2110 Planarity : 0.004 0.046 1312 Dihedral : 31.347 164.027 4060 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 5.36 % Allowed : 18.99 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.29), residues: 722 helix: 1.97 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.89 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 82 PHE 0.023 0.002 PHE A 67 TYR 0.009 0.001 TYR F 51 ARG 0.004 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 142 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 109 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 80 THR cc_start: 0.7562 (OUTLIER) cc_final: 0.7340 (t) REVERT: A 125 GLN cc_start: 0.7367 (mt0) cc_final: 0.6872 (mp10) REVERT: B 92 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6355 (ptm160) REVERT: E 120 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7316 (mtm) REVERT: E 131 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7184 (mtt180) REVERT: F 68 ASP cc_start: 0.7496 (m-30) cc_final: 0.7001 (m-30) REVERT: H 68 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: H 90 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: H 113 LYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6917 (tmtt) outliers start: 33 outliers final: 15 residues processed: 125 average time/residue: 1.7677 time to fit residues: 233.6633 Evaluate side-chains 122 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR 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 62 ILE Chi-restraints excluded: chain C residue 76 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 112 ILE Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 131 ARG 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN H 44 GLN H 46 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12741 Z= 0.323 Angle : 0.656 9.113 18484 Z= 0.385 Chirality : 0.038 0.150 2110 Planarity : 0.005 0.049 1312 Dihedral : 31.602 161.873 4060 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 6.66 % Allowed : 19.32 % Favored : 74.03 % 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: 1.53 (0.29), residues: 722 helix: 1.69 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.05 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS C 82 PHE 0.023 0.003 PHE A 67 TYR 0.017 0.002 TYR F 51 ARG 0.004 0.001 ARG H 96 *********************** 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 145 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 104 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 THR cc_start: 0.7696 (OUTLIER) cc_final: 0.7433 (t) REVERT: A 115 LYS cc_start: 0.7168 (mmtp) cc_final: 0.6906 (mtmm) REVERT: A 131 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7741 (mtt180) REVERT: B 95 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7519 (mtp85) REVERT: F 68 ASP cc_start: 0.7435 (m-30) cc_final: 0.6951 (m-30) REVERT: H 68 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: H 90 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: H 113 LYS cc_start: 0.7263 (OUTLIER) cc_final: 0.6955 (tmtt) outliers start: 41 outliers final: 19 residues processed: 123 average time/residue: 1.6943 time to fit residues: 220.7590 Evaluate side-chains 122 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR 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 B residue 95 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 D residue 98 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE 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 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=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: 0.6980 chunk 23 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN H 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 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 : 0.004 0.045 12741 Z= 0.220 Angle : 0.591 8.695 18484 Z= 0.352 Chirality : 0.035 0.140 2110 Planarity : 0.005 0.047 1312 Dihedral : 31.368 163.101 4060 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.84 % Allowed : 21.27 % Favored : 72.89 % 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: 1.95 (0.30), residues: 722 helix: 2.01 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.97 (0.41), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 82 PHE 0.025 0.002 PHE A 67 TYR 0.013 0.002 TYR G 50 ARG 0.007 0.000 ARG F 35 *********************** 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 145 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 109 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 80 THR cc_start: 0.7639 (OUTLIER) cc_final: 0.7437 (t) REVERT: A 115 LYS cc_start: 0.7165 (mmtp) cc_final: 0.6894 (mtmm) REVERT: A 120 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6662 (mtt) REVERT: A 125 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.6890 (mp10) REVERT: A 131 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7645 (mtt180) REVERT: C 99 ARG cc_start: 0.7220 (mpt180) cc_final: 0.7017 (mpp-170) REVERT: F 68 ASP cc_start: 0.7463 (m-30) cc_final: 0.6990 (m-30) REVERT: F 74 GLU cc_start: 0.6931 (tm-30) cc_final: 0.6729 (tp30) REVERT: H 68 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: H 90 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7028 (mp0) outliers start: 36 outliers final: 14 residues processed: 125 average time/residue: 1.5835 time to fit residues: 210.5744 Evaluate side-chains 122 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 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 62 ILE Chi-restraints excluded: chain C residue 76 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 E residue 112 ILE 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 32 GLU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 0.0050 chunk 43 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN E 125 GLN H 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.2854 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= 0.205 Angle : 0.578 8.368 18484 Z= 0.344 Chirality : 0.034 0.138 2110 Planarity : 0.004 0.048 1312 Dihedral : 31.162 162.533 4054 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.38 % Allowed : 23.38 % 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: 2.20 (0.30), residues: 722 helix: 2.21 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.92 (0.42), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 82 PHE 0.026 0.002 PHE A 67 TYR 0.015 0.001 TYR G 50 ARG 0.007 0.000 ARG F 35 *********************** 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 126 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7075 (mmtp) cc_final: 0.6819 (mtmm) REVERT: A 120 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6629 (mtt) REVERT: A 125 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.6881 (mp10) REVERT: A 131 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7386 (mtt180) REVERT: C 99 ARG cc_start: 0.7361 (mpt180) cc_final: 0.7158 (mpp-170) REVERT: D 31 LYS cc_start: 0.6868 (tppt) cc_final: 0.6607 (mptt) REVERT: F 68 ASP cc_start: 0.7497 (m-30) cc_final: 0.6988 (m-30) REVERT: H 43 LYS cc_start: 0.8205 (mmmm) cc_final: 0.7918 (mmtp) REVERT: H 68 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: H 90 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7005 (mp0) outliers start: 27 outliers final: 13 residues processed: 112 average time/residue: 1.6454 time to fit residues: 196.0014 Evaluate side-chains 113 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET 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 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 112 ILE 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 32 GLU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 68 GLU 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: 0.9980 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.2898 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= 0.251 Angle : 0.616 8.724 18484 Z= 0.363 Chirality : 0.035 0.142 2110 Planarity : 0.005 0.046 1312 Dihedral : 31.263 161.535 4054 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.36 % Allowed : 22.73 % 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: 2.07 (0.30), residues: 722 helix: 2.11 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.95 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 82 PHE 0.026 0.002 PHE A 67 TYR 0.017 0.002 TYR G 50 ARG 0.012 0.001 ARG B 35 *********************** 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 134 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 101 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7180 (mmtp) cc_final: 0.6900 (mtmm) REVERT: A 120 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6688 (mtt) REVERT: A 125 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.6905 (mp10) REVERT: A 131 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7351 (mtt180) REVERT: B 95 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7574 (mtp85) REVERT: C 99 ARG cc_start: 0.7295 (mpt180) cc_final: 0.7093 (mpp-170) REVERT: D 84 SER cc_start: 0.7425 (OUTLIER) cc_final: 0.7221 (t) REVERT: F 68 ASP cc_start: 0.7468 (m-30) cc_final: 0.7006 (m-30) REVERT: F 74 GLU cc_start: 0.6935 (tm-30) cc_final: 0.6731 (tp30) REVERT: H 68 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: H 90 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7057 (mp0) outliers start: 33 outliers final: 17 residues processed: 119 average time/residue: 1.6063 time to fit residues: 203.1238 Evaluate side-chains 119 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 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 B residue 95 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 56 MET Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 112 ILE 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 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 68 GLU 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: 0.9980 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 79 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 0.0010 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.2990 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= 0.238 Angle : 0.617 8.573 18484 Z= 0.363 Chirality : 0.035 0.186 2110 Planarity : 0.005 0.048 1312 Dihedral : 31.216 161.686 4054 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.71 % Allowed : 23.70 % Favored : 71.59 % 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: 2.07 (0.30), residues: 722 helix: 2.13 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -1.02 (0.42), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 82 PHE 0.029 0.002 PHE A 67 TYR 0.020 0.002 TYR G 50 ARG 0.014 0.001 ARG B 35 *********************** 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 126 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 97 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7055 (mmtp) cc_final: 0.6801 (mtmm) REVERT: A 120 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6672 (mtt) REVERT: A 125 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.6886 (mp10) REVERT: A 131 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7276 (mtt180) REVERT: B 95 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7507 (mtp85) REVERT: C 99 ARG cc_start: 0.7297 (mpt180) cc_final: 0.7096 (mpp-170) REVERT: D 31 LYS cc_start: 0.6656 (mmmt) cc_final: 0.6212 (mptt) REVERT: F 68 ASP cc_start: 0.7471 (m-30) cc_final: 0.6994 (m-30) REVERT: F 74 GLU cc_start: 0.6950 (tm-30) cc_final: 0.6730 (tp30) REVERT: H 68 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: H 90 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6994 (mp0) outliers start: 29 outliers final: 16 residues processed: 112 average time/residue: 1.6982 time to fit residues: 201.7193 Evaluate side-chains 117 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 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 B residue 67 ARG Chi-restraints excluded: chain B residue 95 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 56 MET Chi-restraints excluded: chain E residue 112 ILE 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 32 GLU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 68 GLU 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: 4.9990 chunk 44 optimal weight: 0.6980 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: 0.0770 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12741 Z= 0.269 Angle : 0.638 10.959 18484 Z= 0.374 Chirality : 0.036 0.251 2110 Planarity : 0.005 0.055 1312 Dihedral : 31.319 161.183 4054 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.55 % Allowed : 24.19 % Favored : 71.27 % 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: 1.91 (0.30), residues: 722 helix: 1.97 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -1.04 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 82 PHE 0.030 0.002 PHE A 67 TYR 0.023 0.002 TYR G 50 ARG 0.012 0.001 ARG B 35 ********************** 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 123 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6719 (mtt) REVERT: A 125 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6916 (mp10) REVERT: A 131 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7378 (mtt180) REVERT: B 95 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7585 (mtp85) REVERT: D 31 LYS cc_start: 0.6858 (mmmt) cc_final: 0.6243 (mptt) REVERT: F 68 ASP cc_start: 0.7444 (m-30) cc_final: 0.6986 (m-30) REVERT: F 79 LYS cc_start: 0.8132 (mtmp) cc_final: 0.7884 (mtmt) REVERT: H 68 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: H 90 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7034 (mp0) outliers start: 28 outliers final: 16 residues processed: 112 average time/residue: 1.6287 time to fit residues: 194.0919 Evaluate side-chains 114 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET 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 B residue 67 ARG Chi-restraints excluded: chain B residue 95 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 56 MET Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 112 ILE 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 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 68 GLU 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: 0.9990 chunk 71 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.127472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.111822 restraints weight = 23763.769| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 0.98 r_work: 0.3806 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 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 0.049 12741 Z= 0.243 Angle : 0.633 9.776 18484 Z= 0.372 Chirality : 0.036 0.176 2110 Planarity : 0.006 0.078 1312 Dihedral : 31.315 161.404 4054 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.38 % Allowed : 24.51 % Favored : 71.10 % 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: 1.92 (0.30), residues: 722 helix: 1.99 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -1.07 (0.43), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 82 PHE 0.030 0.002 PHE A 67 TYR 0.025 0.002 TYR G 50 ARG 0.009 0.001 ARG B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4350.56 seconds wall clock time: 77 minutes 13.71 seconds (4633.71 seconds total)