Starting phenix.real_space_refine on Sat Mar 16 05:06:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ea5_31039/03_2024/7ea5_31039_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ea5_31039/03_2024/7ea5_31039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ea5_31039/03_2024/7ea5_31039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ea5_31039/03_2024/7ea5_31039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ea5_31039/03_2024/7ea5_31039_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ea5_31039/03_2024/7ea5_31039_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 290 5.49 5 S 33 5.16 5 C 7743 2.51 5 N 2547 2.21 5 O 3154 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 71": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13770 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 830 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} 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: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} 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: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1896 Unusual residues: {' ZN': 3} Classifications: {'peptide': 229, 'undetermined': 3} Link IDs: {'PTRANS': 4, 'TRANS': 223, None: 4} Not linked: pdbres="GLY K 260 " pdbres=" ZN K 301 " Not linked: pdbres=" ZN K 301 " pdbres=" ZN K 302 " Not linked: pdbres=" ZN K 302 " pdbres=" ZN K 303 " Not linked: pdbres=" ZN K 303 " pdbres="SAM K 304 " List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12277 SG CYS K 82 65.116 67.711 47.853 1.00 53.52 S ATOM 12395 SG CYS K 97 60.815 66.338 50.205 1.00 41.97 S ATOM 12450 SG CYS K 105 64.400 68.875 51.580 1.00 57.96 S ATOM 12168 SG CYS K 68 65.754 65.298 51.958 1.00 49.16 S ATOM 12182 SG CYS K 70 68.099 67.624 50.381 1.00 61.08 S ATOM 12277 SG CYS K 82 65.116 67.711 47.853 1.00 53.52 S ATOM 13648 SG CYS K 248 53.165 52.723 14.294 1.00 68.97 S ATOM 13705 SG CYS K 255 56.658 49.593 12.841 1.00 58.18 S Time building chain proxies: 7.37, per 1000 atoms: 0.54 Number of scatterers: 13770 At special positions: 0 Unit cell: (154.78, 91.56, 130.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 33 16.00 P 290 15.00 O 3154 8.00 N 2547 7.00 C 7743 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.84 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 82 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 105 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 97 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 68 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 82 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 70 " pdb=" ZN K 303 " pdb="ZN ZN K 303 " - pdb=" SG CYS K 255 " pdb="ZN ZN K 303 " - pdb=" SG CYS K 248 " 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1832 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 2 sheets defined 52.0% alpha, 1.2% beta 143 base pairs and 240 stacking pairs defined. Time for finding SS restraints: 5.75 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 87 through 113 removed outlier: 3.638A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 41 removed outlier: 3.534A pdb=" N ARG B 36 " --> pdb=" O PRO B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.894A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 47 through 72 removed outlier: 3.755A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 102 through 119 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 86 through 113 removed outlier: 3.792A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 removed outlier: 3.529A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 28 through 36 Processing helix chain 'G' and resid 47 through 73 removed outlier: 4.004A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 35 through 45 removed outlier: 3.868A pdb=" N TYR H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 119 removed outlier: 3.761A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 43 removed outlier: 3.706A pdb=" N LEU K 41 " --> pdb=" O GLU K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 92 No H-bonds generated for 'chain 'K' and resid 89 through 92' Processing helix chain 'K' and resid 156 through 168 removed outlier: 4.152A pdb=" N ASP K 161 " --> pdb=" O MET K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 193 through 195 No H-bonds generated for 'chain 'K' and resid 193 through 195' Processing sheet with id= A, first strand: chain 'K' and resid 122 through 124 removed outlier: 4.030A pdb=" N ALA K 123 " --> pdb=" O ARG K 135 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 152 through 155 352 hydrogen bonds defined for protein. 1032 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 734 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 240 stacking parallelities Total time for adding SS restraints: 4.83 Time building geometry restraints manager: 7.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3042 1.34 - 1.46: 4521 1.46 - 1.58: 6418 1.58 - 1.70: 578 1.70 - 1.82: 51 Bond restraints: 14610 Sorted by residual: bond pdb=" C2 SAM K 304 " pdb=" N3 SAM K 304 " ideal model delta sigma weight residual 1.322 1.382 -0.060 2.00e-02 2.50e+03 8.89e+00 bond pdb=" C8 SAM K 304 " pdb=" N7 SAM K 304 " ideal model delta sigma weight residual 1.298 1.351 -0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" C2 SAM K 304 " pdb=" N1 SAM K 304 " ideal model delta sigma weight residual 1.329 1.381 -0.052 2.00e-02 2.50e+03 6.67e+00 bond pdb=" C6 SAM K 304 " pdb=" N1 SAM K 304 " ideal model delta sigma weight residual 1.337 1.379 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C3' DA J 19 " pdb=" O3' DA J 19 " ideal model delta sigma weight residual 1.422 1.479 -0.057 3.00e-02 1.11e+03 3.60e+00 ... (remaining 14605 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.53: 1439 105.53 - 112.63: 7889 112.63 - 119.74: 4824 119.74 - 126.84: 6020 126.84 - 133.94: 795 Bond angle restraints: 20967 Sorted by residual: angle pdb=" C3' DA J 19 " pdb=" O3' DA J 19 " pdb=" P DC J 20 " ideal model delta sigma weight residual 120.20 124.75 -4.55 1.50e+00 4.44e-01 9.20e+00 angle pdb=" N SER D 84 " pdb=" CA SER D 84 " pdb=" C SER D 84 " ideal model delta sigma weight residual 114.56 110.74 3.82 1.27e+00 6.20e-01 9.07e+00 angle pdb=" C GLY C 46 " pdb=" N ALA C 47 " pdb=" CA ALA C 47 " ideal model delta sigma weight residual 119.78 123.45 -3.67 1.24e+00 6.50e-01 8.74e+00 angle pdb=" CA LYS B 31 " pdb=" C LYS B 31 " pdb=" N PRO B 32 " ideal model delta sigma weight residual 118.44 123.01 -4.57 1.59e+00 3.96e-01 8.28e+00 angle pdb=" O SAM K 304 " pdb=" C SAM K 304 " pdb=" OXT SAM K 304 " ideal model delta sigma weight residual 126.77 118.14 8.63 3.00e+00 1.11e-01 8.28e+00 ... (remaining 20962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 6773 35.35 - 70.70: 1261 70.70 - 106.05: 16 106.05 - 141.41: 3 141.41 - 176.76: 1 Dihedral angle restraints: 8054 sinusoidal: 5214 harmonic: 2840 Sorted by residual: dihedral pdb=" C4' DA J 19 " pdb=" C3' DA J 19 " pdb=" O3' DA J 19 " pdb=" P DC J 20 " ideal model delta sinusoidal sigma weight residual -140.00 36.76 -176.76 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 81.82 138.18 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 82.01 137.99 1 3.50e+01 8.16e-04 1.37e+01 ... (remaining 8051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1846 0.044 - 0.089: 398 0.089 - 0.133: 97 0.133 - 0.177: 14 0.177 - 0.222: 3 Chirality restraints: 2358 Sorted by residual: chirality pdb=" SD SAM K 304 " pdb=" CG SAM K 304 " pdb=" CE SAM K 304 " pdb=" C5' SAM K 304 " both_signs ideal model delta sigma weight residual False 5.50 5.28 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C1' SAM K 304 " pdb=" C2' SAM K 304 " pdb=" N9 SAM K 304 " pdb=" O4' SAM K 304 " both_signs ideal model delta sigma weight residual False 2.30 2.48 -0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" C2' SAM K 304 " pdb=" C1' SAM K 304 " pdb=" C3' SAM K 304 " pdb=" O2' SAM K 304 " both_signs ideal model delta sigma weight residual False -2.76 -2.57 -0.18 2.00e-01 2.50e+01 8.25e-01 ... (remaining 2355 not shown) Planarity restraints: 1663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU K 252 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.52e+00 pdb=" N PRO K 253 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO K 253 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO K 253 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.034 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO C 80 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO G 80 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.027 5.00e-02 4.00e+02 ... (remaining 1660 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3573 2.84 - 3.35: 10841 3.35 - 3.87: 25442 3.87 - 4.38: 29073 4.38 - 4.90: 42196 Nonbonded interactions: 111125 Sorted by model distance: nonbonded pdb=" O ILE K 89 " pdb=" OG1 THR K 93 " model vdw 2.319 2.440 nonbonded pdb=" O CYS K 197 " pdb=" OH TYR K 236 " model vdw 2.320 2.440 nonbonded pdb=" OG1 THR D 29 " pdb=" OP1 DT I 104 " model vdw 2.339 2.440 nonbonded pdb=" NH1 ARG C 42 " pdb=" OG1 THR D 85 " model vdw 2.377 2.520 nonbonded pdb=" OG1 THR A 118 " pdb=" NH1 ARG B 45 " model vdw 2.402 2.520 ... (remaining 111120 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 30 through 120) 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: 0.580 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: 3.730 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 42.580 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 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 : 0.004 0.060 14610 Z= 0.205 Angle : 0.682 8.630 20967 Z= 0.410 Chirality : 0.041 0.222 2358 Planarity : 0.005 0.059 1663 Dihedral : 24.985 176.756 6222 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: -3.00 (0.21), residues: 957 helix: -1.43 (0.17), residues: 568 sheet: -2.01 (1.11), residues: 28 loop : -2.78 (0.27), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.005 TRP K 210 HIS 0.005 0.001 HIS F 75 PHE 0.019 0.002 PHE G 25 TYR 0.013 0.001 TYR F 98 ARG 0.004 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8625 (mttt) cc_final: 0.8311 (mtpp) REVERT: C 101 THR cc_start: 0.8310 (m) cc_final: 0.8042 (m) REVERT: F 31 LYS cc_start: 0.8787 (tttt) cc_final: 0.8463 (tttm) REVERT: K 85 ASP cc_start: 0.6343 (m-30) cc_final: 0.6074 (t0) REVERT: K 233 THR cc_start: 0.6394 (p) cc_final: 0.6042 (p) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.4000 time to fit residues: 141.5806 Evaluate side-chains 159 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN A 125 GLN C 68 ASN D 106 HIS E 39 HIS E 68 GLN F 25 ASN G 38 ASN G 84 GLN H 46 HIS ** K 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14610 Z= 0.175 Angle : 0.515 6.523 20967 Z= 0.306 Chirality : 0.033 0.152 2358 Planarity : 0.004 0.041 1663 Dihedral : 29.168 179.650 4280 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.45 % Allowed : 7.38 % Favored : 91.16 % 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: -0.66 (0.26), residues: 957 helix: 0.83 (0.22), residues: 568 sheet: -1.52 (1.16), residues: 28 loop : -2.50 (0.27), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 210 HIS 0.004 0.001 HIS E 39 PHE 0.012 0.002 PHE K 174 TYR 0.012 0.001 TYR K 132 ARG 0.007 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 171 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8625 (mttt) cc_final: 0.8324 (mtpp) REVERT: D 76 ARG cc_start: 0.7796 (mtm-85) cc_final: 0.7563 (mtm-85) REVERT: D 82 LYS cc_start: 0.8832 (mmtm) cc_final: 0.8623 (mmtp) REVERT: E 39 HIS cc_start: 0.7668 (OUTLIER) cc_final: 0.7158 (t-170) REVERT: E 115 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8204 (mtmm) REVERT: F 59 LYS cc_start: 0.8420 (tttt) cc_final: 0.7946 (tttp) REVERT: F 63 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7162 (mt-10) REVERT: G 36 LYS cc_start: 0.8123 (ttpt) cc_final: 0.7811 (tttp) REVERT: K 85 ASP cc_start: 0.6524 (m-30) cc_final: 0.6253 (t0) REVERT: K 178 MET cc_start: 0.7279 (tpp) cc_final: 0.6548 (tpp) REVERT: K 233 THR cc_start: 0.6398 (p) cc_final: 0.6159 (p) outliers start: 12 outliers final: 5 residues processed: 178 average time/residue: 0.3441 time to fit residues: 82.0608 Evaluate side-chains 157 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 150 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN F 25 ASN G 31 HIS G 73 ASN K 79 ASN K 144 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14610 Z= 0.295 Angle : 0.588 6.756 20967 Z= 0.343 Chirality : 0.037 0.145 2358 Planarity : 0.005 0.042 1663 Dihedral : 29.556 179.995 4280 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.18 % Allowed : 10.17 % Favored : 87.65 % 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: -0.31 (0.27), residues: 957 helix: 1.20 (0.23), residues: 564 sheet: -1.29 (1.18), residues: 28 loop : -2.50 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP K 210 HIS 0.023 0.002 HIS E 39 PHE 0.028 0.003 PHE G 25 TYR 0.015 0.002 TYR D 37 ARG 0.009 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 1.024 Fit side-chains REVERT: A 80 THR cc_start: 0.9022 (p) cc_final: 0.8811 (t) REVERT: B 79 LYS cc_start: 0.8664 (mttt) cc_final: 0.8357 (mtpp) REVERT: D 48 ASP cc_start: 0.7417 (p0) cc_final: 0.7160 (p0) REVERT: G 77 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7839 (mtm180) REVERT: H 90 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7952 (mp0) REVERT: K 85 ASP cc_start: 0.6575 (m-30) cc_final: 0.6209 (t0) outliers start: 18 outliers final: 11 residues processed: 181 average time/residue: 0.3616 time to fit residues: 85.3198 Evaluate side-chains 164 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 152 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 117 optimal weight: 0.0070 chunk 58 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 overall best weight: 2.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14610 Z= 0.265 Angle : 0.554 6.782 20967 Z= 0.326 Chirality : 0.035 0.140 2358 Planarity : 0.004 0.044 1663 Dihedral : 29.486 178.663 4280 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.66 % Allowed : 11.38 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.27), residues: 957 helix: 1.41 (0.23), residues: 562 sheet: -1.08 (1.20), residues: 28 loop : -2.25 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 210 HIS 0.004 0.001 HIS A 113 PHE 0.028 0.002 PHE K 159 TYR 0.012 0.001 TYR D 37 ARG 0.009 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8686 (mttt) cc_final: 0.8416 (mtpp) REVERT: D 48 ASP cc_start: 0.7403 (p0) cc_final: 0.7134 (p0) REVERT: D 56 MET cc_start: 0.8666 (tpt) cc_final: 0.7918 (tpt) REVERT: E 59 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7683 (pm20) REVERT: H 56 MET cc_start: 0.8102 (tpp) cc_final: 0.7709 (tpt) outliers start: 22 outliers final: 18 residues processed: 163 average time/residue: 0.3385 time to fit residues: 73.6326 Evaluate side-chains 161 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 197 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14610 Z= 0.199 Angle : 0.524 6.475 20967 Z= 0.312 Chirality : 0.034 0.137 2358 Planarity : 0.004 0.042 1663 Dihedral : 29.423 178.491 4280 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.66 % Allowed : 12.95 % Favored : 84.38 % 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: 0.34 (0.28), residues: 957 helix: 1.69 (0.23), residues: 562 sheet: -1.13 (0.95), residues: 38 loop : -2.13 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 210 HIS 0.003 0.001 HIS K 199 PHE 0.030 0.002 PHE K 159 TYR 0.009 0.001 TYR D 37 ARG 0.009 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8661 (mttt) cc_final: 0.8395 (mtpp) REVERT: B 92 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7590 (ttp-170) REVERT: D 48 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.7101 (p0) REVERT: D 56 MET cc_start: 0.8619 (tpt) cc_final: 0.7870 (tpt) REVERT: E 59 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7668 (pm20) REVERT: H 56 MET cc_start: 0.8043 (tpp) cc_final: 0.7312 (tpt) outliers start: 22 outliers final: 16 residues processed: 156 average time/residue: 0.3551 time to fit residues: 73.1752 Evaluate side-chains 160 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.0570 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 0.0670 chunk 29 optimal weight: 4.9990 chunk 118 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14610 Z= 0.172 Angle : 0.507 6.124 20967 Z= 0.304 Chirality : 0.033 0.143 2358 Planarity : 0.004 0.042 1663 Dihedral : 29.300 178.075 4280 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.66 % Allowed : 13.20 % Favored : 84.14 % 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: 0.69 (0.28), residues: 957 helix: 1.96 (0.23), residues: 561 sheet: -0.97 (0.98), residues: 38 loop : -1.94 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 210 HIS 0.002 0.001 HIS C 82 PHE 0.025 0.001 PHE K 159 TYR 0.008 0.001 TYR D 37 ARG 0.008 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 1.135 Fit side-chains REVERT: B 79 LYS cc_start: 0.8662 (mttt) cc_final: 0.8396 (mtpp) REVERT: B 92 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7593 (ttp-170) REVERT: D 48 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.7051 (p0) REVERT: E 59 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7645 (pm20) REVERT: H 56 MET cc_start: 0.7946 (tpp) cc_final: 0.7192 (tpt) REVERT: H 90 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7563 (mm-30) REVERT: K 217 ARG cc_start: 0.7820 (mmt90) cc_final: 0.7603 (mtt180) outliers start: 22 outliers final: 14 residues processed: 162 average time/residue: 0.3377 time to fit residues: 72.9750 Evaluate side-chains 162 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 212 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 86 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14610 Z= 0.246 Angle : 0.547 6.480 20967 Z= 0.323 Chirality : 0.035 0.137 2358 Planarity : 0.004 0.077 1663 Dihedral : 29.381 179.396 4280 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.91 % Allowed : 13.68 % Favored : 83.41 % 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: 0.58 (0.28), residues: 957 helix: 1.82 (0.23), residues: 562 sheet: -1.01 (0.98), residues: 38 loop : -1.90 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 210 HIS 0.004 0.001 HIS K 170 PHE 0.041 0.002 PHE K 159 TYR 0.011 0.001 TYR F 51 ARG 0.009 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 1.129 Fit side-chains REVERT: B 79 LYS cc_start: 0.8685 (mttt) cc_final: 0.8403 (mtpp) REVERT: D 48 ASP cc_start: 0.7403 (p0) cc_final: 0.7141 (p0) REVERT: E 59 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: F 74 GLU cc_start: 0.7768 (tt0) cc_final: 0.7489 (tt0) REVERT: H 90 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7589 (mm-30) REVERT: K 241 TYR cc_start: 0.5941 (OUTLIER) cc_final: 0.5186 (p90) outliers start: 24 outliers final: 21 residues processed: 156 average time/residue: 0.3354 time to fit residues: 70.3965 Evaluate side-chains 164 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 218 MET Chi-restraints excluded: chain K residue 241 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 0.0270 chunk 22 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 58 optimal weight: 0.0570 chunk 10 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14610 Z= 0.152 Angle : 0.521 9.469 20967 Z= 0.311 Chirality : 0.033 0.146 2358 Planarity : 0.004 0.043 1663 Dihedral : 29.272 177.748 4280 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.94 % Allowed : 14.53 % Favored : 83.54 % 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: 0.99 (0.28), residues: 957 helix: 2.20 (0.23), residues: 559 sheet: -0.93 (1.00), residues: 38 loop : -1.78 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 210 HIS 0.002 0.001 HIS C 82 PHE 0.052 0.001 PHE K 159 TYR 0.008 0.001 TYR F 51 ARG 0.010 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 1.197 Fit side-chains REVERT: B 79 LYS cc_start: 0.8655 (mttt) cc_final: 0.8380 (mtpp) REVERT: B 92 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7555 (ttp-170) REVERT: D 48 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.7061 (p0) REVERT: H 56 MET cc_start: 0.7994 (tpp) cc_final: 0.7634 (tpt) REVERT: H 90 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7576 (mm-30) REVERT: K 217 ARG cc_start: 0.7844 (mmt90) cc_final: 0.7623 (mtt180) REVERT: K 241 TYR cc_start: 0.5938 (OUTLIER) cc_final: 0.5046 (p90) outliers start: 16 outliers final: 8 residues processed: 151 average time/residue: 0.3494 time to fit residues: 70.3081 Evaluate side-chains 154 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 218 MET Chi-restraints excluded: chain K residue 241 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 chunk 103 optimal weight: 0.0040 chunk 71 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14610 Z= 0.235 Angle : 0.554 10.528 20967 Z= 0.324 Chirality : 0.035 0.133 2358 Planarity : 0.004 0.043 1663 Dihedral : 29.314 179.213 4280 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.94 % Allowed : 14.65 % Favored : 83.41 % 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: 0.81 (0.28), residues: 957 helix: 2.01 (0.23), residues: 562 sheet: -0.88 (1.00), residues: 38 loop : -1.82 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 210 HIS 0.007 0.001 HIS K 170 PHE 0.040 0.002 PHE K 159 TYR 0.011 0.001 TYR F 51 ARG 0.009 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8674 (mttt) cc_final: 0.8384 (mtpp) REVERT: B 92 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7607 (ttp-170) REVERT: D 48 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7141 (p0) REVERT: E 59 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7501 (pm20) REVERT: G 77 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7624 (mtm180) REVERT: H 43 LYS cc_start: 0.8326 (mmmt) cc_final: 0.8100 (mmtm) REVERT: H 56 MET cc_start: 0.8175 (tpp) cc_final: 0.7745 (tpt) REVERT: H 90 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7585 (mm-30) REVERT: K 241 TYR cc_start: 0.5883 (OUTLIER) cc_final: 0.5126 (p90) outliers start: 16 outliers final: 10 residues processed: 152 average time/residue: 0.3565 time to fit residues: 71.7800 Evaluate side-chains 156 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 140 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 218 MET Chi-restraints excluded: chain K residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 121 optimal weight: 0.4980 chunk 111 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 10 optimal weight: 0.0270 chunk 74 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.1044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14610 Z= 0.268 Angle : 0.572 13.546 20967 Z= 0.332 Chirality : 0.036 0.136 2358 Planarity : 0.004 0.043 1663 Dihedral : 29.377 179.133 4280 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.42 % Allowed : 14.65 % Favored : 82.93 % 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: 0.65 (0.28), residues: 957 helix: 1.86 (0.23), residues: 560 sheet: -1.05 (0.89), residues: 43 loop : -1.80 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 210 HIS 0.004 0.001 HIS A 113 PHE 0.034 0.002 PHE K 159 TYR 0.011 0.001 TYR F 51 ARG 0.009 0.001 ARG H 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 1.261 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7435 (mtp85) REVERT: B 79 LYS cc_start: 0.8706 (mttt) cc_final: 0.8413 (mtpp) REVERT: D 48 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7148 (p0) REVERT: E 59 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7540 (pm20) REVERT: H 43 LYS cc_start: 0.8345 (mmmt) cc_final: 0.8131 (mmtm) REVERT: H 56 MET cc_start: 0.8247 (tpp) cc_final: 0.7802 (tpt) REVERT: K 241 TYR cc_start: 0.5925 (OUTLIER) cc_final: 0.5243 (p90) outliers start: 20 outliers final: 13 residues processed: 151 average time/residue: 0.3561 time to fit residues: 71.6327 Evaluate side-chains 156 residues out of total 826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 212 VAL Chi-restraints excluded: chain K residue 218 MET Chi-restraints excluded: chain K residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 85 optimal weight: 30.0000 chunk 5 optimal weight: 0.7980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.173030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.120997 restraints weight = 17233.956| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.38 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14610 Z= 0.307 Angle : 0.596 12.950 20967 Z= 0.344 Chirality : 0.037 0.179 2358 Planarity : 0.004 0.043 1663 Dihedral : 29.447 179.759 4280 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.30 % Allowed : 14.65 % Favored : 83.05 % 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: 0.48 (0.28), residues: 957 helix: 1.70 (0.22), residues: 558 sheet: -1.06 (0.88), residues: 43 loop : -1.84 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP K 210 HIS 0.005 0.001 HIS A 113 PHE 0.029 0.003 PHE K 159 TYR 0.012 0.001 TYR F 51 ARG 0.009 0.001 ARG H 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2437.01 seconds wall clock time: 44 minutes 32.13 seconds (2672.13 seconds total)