Starting phenix.real_space_refine on Thu Jul 18 22:02:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1v_36805/07_2024/8k1v_36805.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1v_36805/07_2024/8k1v_36805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1v_36805/07_2024/8k1v_36805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1v_36805/07_2024/8k1v_36805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1v_36805/07_2024/8k1v_36805.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1v_36805/07_2024/8k1v_36805.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.070 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 K 5 8.98 5 S 32 5.16 5 C 2706 2.51 5 N 616 2.21 5 O 700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4059 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1921 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain breaks: 1 Chain: "B" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1921 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain breaks: 1 Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 110 Unusual residues: {' K': 5, 'Y01': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.04, per 1000 atoms: 0.75 Number of scatterers: 4059 At special positions: 0 Unit cell: (67.1, 71.5, 90.2, 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) K 5 19.00 S 32 16.00 O 700 8.00 N 616 7.00 C 2706 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 707.4 milliseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 896 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 87.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 2 through 53 removed outlier: 5.615A pdb=" N ASP A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N HIS A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 removed outlier: 3.718A pdb=" N ARG A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 103 through 147 Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 155 through 183 Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 217 through 243 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'B' and resid 3 through 53 removed outlier: 5.613A pdb=" N ASP B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N HIS B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 70 removed outlier: 3.706A pdb=" N ARG B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 103 through 147 Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 155 through 183 Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 217 through 243 Processing helix chain 'B' and resid 244 through 247 333 hydrogen bonds defined for protein. 981 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 1.75 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: 664 1.33 - 1.45: 1092 1.45 - 1.57: 2352 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 4156 Sorted by residual: bond pdb=" C ILE B 118 " pdb=" N PRO B 119 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.36e-02 5.41e+03 3.25e-01 bond pdb=" C ILE A 118 " pdb=" N PRO A 119 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.36e-02 5.41e+03 3.13e-01 bond pdb=" C GLU B 70 " pdb=" N PRO B 71 " ideal model delta sigma weight residual 1.335 1.341 -0.006 1.28e-02 6.10e+03 2.24e-01 bond pdb=" N LYS A 211 " pdb=" CA LYS A 211 " ideal model delta sigma weight residual 1.457 1.463 -0.006 1.29e-02 6.01e+03 2.08e-01 bond pdb=" CA LYS B 211 " pdb=" CB LYS B 211 " ideal model delta sigma weight residual 1.530 1.538 -0.008 1.69e-02 3.50e+03 2.07e-01 ... (remaining 4151 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.84: 90 106.84 - 113.62: 2288 113.62 - 120.40: 1589 120.40 - 127.18: 1653 127.18 - 133.96: 24 Bond angle restraints: 5644 Sorted by residual: angle pdb=" C THR A 210 " pdb=" N LYS A 211 " pdb=" CA LYS A 211 " ideal model delta sigma weight residual 121.54 125.66 -4.12 1.91e+00 2.74e-01 4.66e+00 angle pdb=" C THR B 210 " pdb=" N LYS B 211 " pdb=" CA LYS B 211 " ideal model delta sigma weight residual 121.54 125.63 -4.09 1.91e+00 2.74e-01 4.58e+00 angle pdb=" N GLY B 117 " pdb=" CA GLY B 117 " pdb=" C GLY B 117 " ideal model delta sigma weight residual 113.18 116.68 -3.50 2.37e+00 1.78e-01 2.18e+00 angle pdb=" N GLY A 117 " pdb=" CA GLY A 117 " pdb=" C GLY A 117 " ideal model delta sigma weight residual 113.18 116.61 -3.43 2.37e+00 1.78e-01 2.09e+00 angle pdb=" CA LYS A 211 " pdb=" CB LYS A 211 " pdb=" CG LYS A 211 " ideal model delta sigma weight residual 114.10 116.55 -2.45 2.00e+00 2.50e-01 1.50e+00 ... (remaining 5639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 2406 16.01 - 32.03: 233 32.03 - 48.04: 49 48.04 - 64.06: 12 64.06 - 80.07: 12 Dihedral angle restraints: 2712 sinusoidal: 1310 harmonic: 1402 Sorted by residual: dihedral pdb=" CG ARG A 3 " pdb=" CD ARG A 3 " pdb=" NE ARG A 3 " pdb=" CZ ARG A 3 " ideal model delta sinusoidal sigma weight residual -180.00 -139.67 -40.33 2 1.50e+01 4.44e-03 8.94e+00 dihedral pdb=" CG ARG B 3 " pdb=" CD ARG B 3 " pdb=" NE ARG B 3 " pdb=" CZ ARG B 3 " ideal model delta sinusoidal sigma weight residual -180.00 -139.74 -40.26 2 1.50e+01 4.44e-03 8.91e+00 dihedral pdb=" CB GLU B 130 " pdb=" CG GLU B 130 " pdb=" CD GLU B 130 " pdb=" OE1 GLU B 130 " ideal model delta sinusoidal sigma weight residual 0.00 79.78 -79.78 1 3.00e+01 1.11e-03 8.77e+00 ... (remaining 2709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 451 0.021 - 0.042: 82 0.042 - 0.063: 79 0.063 - 0.085: 20 0.085 - 0.106: 18 Chirality restraints: 650 Sorted by residual: chirality pdb=" CA VAL B 206 " pdb=" N VAL B 206 " pdb=" C VAL B 206 " pdb=" CB VAL B 206 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.80e-01 chirality pdb=" CA VAL A 206 " pdb=" N VAL A 206 " pdb=" C VAL A 206 " pdb=" CB VAL A 206 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.10 2.00e-01 2.50e+01 2.73e-01 chirality pdb=" CA VAL A 76 " pdb=" N VAL A 76 " pdb=" C VAL A 76 " pdb=" CB VAL A 76 " both_signs ideal model delta sigma weight residual False 2.44 2.54 -0.10 2.00e-01 2.50e+01 2.64e-01 ... (remaining 647 not shown) Planarity restraints: 664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 100 " 0.011 5.00e-02 4.00e+02 1.69e-02 4.58e-01 pdb=" N PRO A 101 " -0.029 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " 0.009 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 100 " -0.010 5.00e-02 4.00e+02 1.52e-02 3.68e-01 pdb=" N PRO B 101 " 0.026 5.00e-02 4.00e+02 pdb=" CA PRO B 101 " -0.008 5.00e-02 4.00e+02 pdb=" CD PRO B 101 " -0.008 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 154 " 0.003 2.00e-02 2.50e+03 5.95e-03 3.54e-01 pdb=" C VAL A 154 " -0.010 2.00e-02 2.50e+03 pdb=" O VAL A 154 " 0.004 2.00e-02 2.50e+03 pdb=" N SER A 155 " 0.003 2.00e-02 2.50e+03 ... (remaining 661 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 1400 2.85 - 3.43: 4457 3.43 - 4.00: 7154 4.00 - 4.57: 10305 4.57 - 5.14: 14285 Nonbonded interactions: 37601 Sorted by model distance: nonbonded pdb=" OH TYR A 96 " pdb=" OG1 THR A 196 " model vdw 2.283 2.440 nonbonded pdb=" OH TYR A 52 " pdb=" OD2 ASP B 58 " model vdw 2.304 2.440 nonbonded pdb=" OD2 ASP A 58 " pdb=" OH TYR B 52 " model vdw 2.316 2.440 nonbonded pdb=" OH TYR B 96 " pdb=" OG1 THR B 196 " model vdw 2.330 2.440 nonbonded pdb=" NZ LYS A 144 " pdb=" O ASP A 153 " model vdw 2.341 2.520 ... (remaining 37596 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 2 through 248 or resid 301 through 303)) selection = chain 'B' } 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: 0.440 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.950 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 : 0.001 0.011 4156 Z= 0.075 Angle : 0.315 4.911 5644 Z= 0.164 Chirality : 0.031 0.106 650 Planarity : 0.001 0.017 664 Dihedral : 13.710 80.074 1816 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 5.96 (0.37), residues: 476 helix: 4.59 (0.23), residues: 384 sheet: None (None), residues: 0 loop : 0.62 (0.73), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 184 HIS 0.001 0.000 HIS A 72 PHE 0.004 0.000 PHE B 109 TYR 0.010 0.001 TYR B 18 ARG 0.001 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.440 Fit side-chains REVERT: A 35 MET cc_start: 0.8058 (ttp) cc_final: 0.7822 (mmm) REVERT: A 42 LYS cc_start: 0.8140 (ttmm) cc_final: 0.7922 (tppt) REVERT: A 44 GLU cc_start: 0.8050 (tp30) cc_final: 0.7708 (tp30) REVERT: A 173 ILE cc_start: 0.7809 (mt) cc_final: 0.7532 (mt) REVERT: A 180 GLN cc_start: 0.7621 (mm110) cc_final: 0.6825 (tt0) REVERT: A 182 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7076 (mm-30) REVERT: B 35 MET cc_start: 0.8050 (ttp) cc_final: 0.7837 (mmm) REVERT: B 44 GLU cc_start: 0.8068 (tp30) cc_final: 0.7600 (tp30) REVERT: B 173 ILE cc_start: 0.7803 (mt) cc_final: 0.7525 (mt) REVERT: B 180 GLN cc_start: 0.7533 (mm110) cc_final: 0.6732 (tt0) REVERT: B 182 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7119 (mm-30) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2241 time to fit residues: 30.5782 Evaluate side-chains 95 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4156 Z= 0.168 Angle : 0.450 5.480 5644 Z= 0.234 Chirality : 0.035 0.116 650 Planarity : 0.002 0.016 664 Dihedral : 5.406 32.737 952 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.94 % Allowed : 7.60 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.67 (0.39), residues: 476 helix: 4.20 (0.23), residues: 390 sheet: None (None), residues: 0 loop : 1.24 (0.90), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 184 HIS 0.000 0.000 HIS B 188 PHE 0.008 0.001 PHE B 223 TYR 0.015 0.001 TYR A 85 ARG 0.003 0.001 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 0.392 Fit side-chains REVERT: A 35 MET cc_start: 0.8251 (ttp) cc_final: 0.7902 (mmm) REVERT: A 36 ARG cc_start: 0.8237 (ttm-80) cc_final: 0.7389 (mtp180) REVERT: A 44 GLU cc_start: 0.8100 (tp30) cc_final: 0.7776 (tp30) REVERT: A 180 GLN cc_start: 0.7672 (mm110) cc_final: 0.6977 (tt0) REVERT: B 35 MET cc_start: 0.8309 (ttp) cc_final: 0.8008 (mmm) REVERT: B 36 ARG cc_start: 0.8324 (tpp80) cc_final: 0.7623 (mtp180) REVERT: B 44 GLU cc_start: 0.8098 (tp30) cc_final: 0.7629 (tp30) REVERT: B 180 GLN cc_start: 0.7686 (mm110) cc_final: 0.6978 (tt0) outliers start: 12 outliers final: 5 residues processed: 108 average time/residue: 0.2226 time to fit residues: 28.0758 Evaluate side-chains 93 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 136 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS B 33 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4156 Z= 0.263 Angle : 0.548 6.340 5644 Z= 0.287 Chirality : 0.038 0.111 650 Planarity : 0.003 0.017 664 Dihedral : 5.042 38.049 952 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.68 % Allowed : 9.56 % Favored : 86.76 % 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: 5.20 (0.38), residues: 476 helix: 3.87 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 1.08 (0.85), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 184 HIS 0.001 0.000 HIS B 33 PHE 0.011 0.002 PHE A 80 TYR 0.027 0.002 TYR B 85 ARG 0.008 0.001 ARG B 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 0.418 Fit side-chains REVERT: A 19 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7656 (mp) REVERT: A 31 SER cc_start: 0.8260 (p) cc_final: 0.8003 (m) REVERT: A 35 MET cc_start: 0.8313 (ttp) cc_final: 0.7937 (mmt) REVERT: A 36 ARG cc_start: 0.8303 (ttm-80) cc_final: 0.7443 (mtp180) REVERT: A 180 GLN cc_start: 0.7812 (mm110) cc_final: 0.7184 (tt0) REVERT: B 19 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7783 (mp) REVERT: B 31 SER cc_start: 0.8264 (p) cc_final: 0.8029 (m) REVERT: B 35 MET cc_start: 0.8286 (ttp) cc_final: 0.8080 (mmt) REVERT: B 36 ARG cc_start: 0.8360 (tpp80) cc_final: 0.7609 (mtp180) REVERT: B 44 GLU cc_start: 0.8168 (tp30) cc_final: 0.7635 (tp30) REVERT: B 180 GLN cc_start: 0.7818 (mm110) cc_final: 0.7186 (tt0) REVERT: B 243 VAL cc_start: 0.7899 (t) cc_final: 0.7691 (t) outliers start: 15 outliers final: 8 residues processed: 114 average time/residue: 0.2204 time to fit residues: 29.5030 Evaluate side-chains 87 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 134 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4156 Z= 0.266 Angle : 0.547 7.130 5644 Z= 0.286 Chirality : 0.038 0.116 650 Planarity : 0.003 0.016 664 Dihedral : 5.010 39.660 952 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.41 % Allowed : 14.46 % Favored : 81.13 % 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: 4.80 (0.38), residues: 476 helix: 3.63 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.78 (0.81), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 78 HIS 0.000 0.000 HIS B 98 PHE 0.010 0.001 PHE A 16 TYR 0.020 0.002 TYR B 85 ARG 0.003 0.000 ARG B 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.354 Fit side-chains REVERT: A 19 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7676 (mp) REVERT: A 31 SER cc_start: 0.8346 (p) cc_final: 0.7950 (m) REVERT: A 35 MET cc_start: 0.8360 (ttp) cc_final: 0.7964 (mmt) REVERT: A 180 GLN cc_start: 0.7748 (mm110) cc_final: 0.7249 (tt0) REVERT: B 19 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7719 (mp) REVERT: B 31 SER cc_start: 0.8349 (p) cc_final: 0.7898 (m) REVERT: B 35 MET cc_start: 0.8350 (ttp) cc_final: 0.8006 (mmm) REVERT: B 36 ARG cc_start: 0.8364 (tpp80) cc_final: 0.7596 (mtp180) REVERT: B 44 GLU cc_start: 0.8182 (tp30) cc_final: 0.7592 (tp30) REVERT: B 130 GLU cc_start: 0.7772 (tp30) cc_final: 0.7492 (tp30) REVERT: B 180 GLN cc_start: 0.7802 (mm110) cc_final: 0.7176 (tt0) outliers start: 18 outliers final: 14 residues processed: 92 average time/residue: 0.2174 time to fit residues: 23.8856 Evaluate side-chains 90 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 179 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7839 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4156 Z= 0.199 Angle : 0.496 6.338 5644 Z= 0.260 Chirality : 0.035 0.111 650 Planarity : 0.002 0.017 664 Dihedral : 4.925 41.491 952 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.19 % Allowed : 17.16 % Favored : 79.66 % 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: 4.84 (0.38), residues: 476 helix: 3.68 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.66 (0.81), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 184 HIS 0.001 0.000 HIS B 98 PHE 0.010 0.001 PHE B 109 TYR 0.014 0.001 TYR A 138 ARG 0.003 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.392 Fit side-chains REVERT: A 19 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7669 (mp) REVERT: A 31 SER cc_start: 0.8350 (p) cc_final: 0.7953 (m) REVERT: A 35 MET cc_start: 0.8427 (ttp) cc_final: 0.7890 (mmt) REVERT: A 180 GLN cc_start: 0.7695 (mm110) cc_final: 0.7116 (tt0) REVERT: B 19 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7690 (mp) REVERT: B 31 SER cc_start: 0.8358 (p) cc_final: 0.8008 (m) REVERT: B 35 MET cc_start: 0.8362 (ttp) cc_final: 0.8031 (mmt) REVERT: B 36 ARG cc_start: 0.8298 (tpp80) cc_final: 0.7608 (mtp180) REVERT: B 44 GLU cc_start: 0.8197 (tp30) cc_final: 0.7682 (tp30) REVERT: B 130 GLU cc_start: 0.7633 (tp30) cc_final: 0.7343 (tp30) REVERT: B 180 GLN cc_start: 0.7701 (mm110) cc_final: 0.7126 (tt0) outliers start: 13 outliers final: 11 residues processed: 84 average time/residue: 0.2225 time to fit residues: 22.1384 Evaluate side-chains 85 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7845 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4156 Z= 0.202 Angle : 0.491 5.555 5644 Z= 0.259 Chirality : 0.035 0.110 650 Planarity : 0.002 0.018 664 Dihedral : 4.910 43.224 952 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.43 % Allowed : 17.16 % Favored : 79.41 % 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: 4.76 (0.38), residues: 476 helix: 3.63 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.57 (0.80), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 184 HIS 0.000 0.000 HIS A 72 PHE 0.011 0.001 PHE B 109 TYR 0.014 0.001 TYR B 138 ARG 0.003 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.424 Fit side-chains REVERT: A 19 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7693 (mp) REVERT: A 31 SER cc_start: 0.8374 (p) cc_final: 0.8023 (m) REVERT: A 35 MET cc_start: 0.8448 (ttp) cc_final: 0.7928 (mmt) REVERT: A 180 GLN cc_start: 0.7700 (mm110) cc_final: 0.7132 (tt0) REVERT: B 19 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7731 (mp) REVERT: B 31 SER cc_start: 0.8386 (p) cc_final: 0.8027 (m) REVERT: B 35 MET cc_start: 0.8408 (ttp) cc_final: 0.8009 (mmt) REVERT: B 36 ARG cc_start: 0.8263 (tpp80) cc_final: 0.7601 (mtp180) REVERT: B 37 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7982 (tt0) REVERT: B 44 GLU cc_start: 0.8221 (tp30) cc_final: 0.7720 (tp30) REVERT: B 60 ARG cc_start: 0.8308 (tpp80) cc_final: 0.8049 (tpp80) REVERT: B 180 GLN cc_start: 0.7704 (mm110) cc_final: 0.7140 (tt0) outliers start: 14 outliers final: 12 residues processed: 86 average time/residue: 0.2195 time to fit residues: 22.2685 Evaluate side-chains 86 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.7864 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4156 Z= 0.234 Angle : 0.524 7.482 5644 Z= 0.273 Chirality : 0.036 0.115 650 Planarity : 0.002 0.019 664 Dihedral : 5.028 43.420 952 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.90 % Allowed : 15.93 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.68 (0.38), residues: 476 helix: 3.59 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.45 (0.78), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 184 HIS 0.000 0.000 HIS A 72 PHE 0.010 0.001 PHE A 109 TYR 0.015 0.002 TYR A 138 ARG 0.003 0.001 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 0.429 Fit side-chains REVERT: A 19 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7720 (mp) REVERT: A 31 SER cc_start: 0.8407 (p) cc_final: 0.8043 (m) REVERT: A 35 MET cc_start: 0.8461 (ttp) cc_final: 0.7932 (mmt) REVERT: A 128 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7544 (mp) REVERT: A 180 GLN cc_start: 0.7739 (mm110) cc_final: 0.7167 (tt0) REVERT: B 19 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7749 (mp) REVERT: B 31 SER cc_start: 0.8414 (p) cc_final: 0.8046 (m) REVERT: B 35 MET cc_start: 0.8429 (ttp) cc_final: 0.8026 (mmt) REVERT: B 36 ARG cc_start: 0.8269 (tpp80) cc_final: 0.7615 (mtp180) REVERT: B 37 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7878 (tt0) REVERT: B 44 GLU cc_start: 0.8235 (tp30) cc_final: 0.7727 (tp30) REVERT: B 128 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7565 (mp) REVERT: B 180 GLN cc_start: 0.7745 (mm110) cc_final: 0.7172 (tt0) outliers start: 20 outliers final: 15 residues processed: 93 average time/residue: 0.2164 time to fit residues: 23.7328 Evaluate side-chains 93 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 74 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7846 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4156 Z= 0.192 Angle : 0.507 6.672 5644 Z= 0.265 Chirality : 0.035 0.111 650 Planarity : 0.002 0.020 664 Dihedral : 4.984 45.399 952 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.68 % Allowed : 18.38 % Favored : 77.94 % 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: 4.73 (0.38), residues: 476 helix: 3.63 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.44 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 184 HIS 0.000 0.000 HIS A 33 PHE 0.011 0.001 PHE A 109 TYR 0.014 0.001 TYR A 138 ARG 0.003 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.424 Fit side-chains REVERT: A 19 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7749 (mp) REVERT: A 31 SER cc_start: 0.8422 (p) cc_final: 0.8056 (m) REVERT: A 35 MET cc_start: 0.8460 (ttp) cc_final: 0.7927 (mmt) REVERT: A 180 GLN cc_start: 0.7700 (mm110) cc_final: 0.7142 (tt0) REVERT: B 19 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7747 (mp) REVERT: B 31 SER cc_start: 0.8428 (p) cc_final: 0.8075 (m) REVERT: B 35 MET cc_start: 0.8440 (ttp) cc_final: 0.7982 (mmt) REVERT: B 36 ARG cc_start: 0.8264 (tpp80) cc_final: 0.7613 (mtp180) REVERT: B 37 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7908 (tt0) REVERT: B 44 GLU cc_start: 0.8248 (tp30) cc_final: 0.7774 (tp30) REVERT: B 180 GLN cc_start: 0.7727 (mm110) cc_final: 0.7162 (tt0) outliers start: 15 outliers final: 13 residues processed: 84 average time/residue: 0.2220 time to fit residues: 21.9410 Evaluate side-chains 87 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.7876 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4156 Z= 0.236 Angle : 0.531 6.386 5644 Z= 0.280 Chirality : 0.037 0.116 650 Planarity : 0.002 0.021 664 Dihedral : 5.149 44.645 952 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 5.15 % Allowed : 17.16 % Favored : 77.70 % 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: 4.62 (0.38), residues: 476 helix: 3.56 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.37 (0.76), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 78 HIS 0.000 0.000 HIS A 33 PHE 0.010 0.001 PHE B 109 TYR 0.014 0.001 TYR A 138 ARG 0.002 0.000 ARG B 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 0.429 Fit side-chains REVERT: A 18 TYR cc_start: 0.8829 (t80) cc_final: 0.8394 (t80) REVERT: A 19 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7748 (mp) REVERT: A 31 SER cc_start: 0.8452 (p) cc_final: 0.8074 (m) REVERT: A 35 MET cc_start: 0.8482 (ttp) cc_final: 0.7949 (mmt) REVERT: A 128 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7559 (mp) REVERT: A 180 GLN cc_start: 0.7766 (mm110) cc_final: 0.7196 (tt0) REVERT: B 18 TYR cc_start: 0.8850 (t80) cc_final: 0.8419 (t80) REVERT: B 19 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7801 (mp) REVERT: B 31 SER cc_start: 0.8458 (p) cc_final: 0.8095 (m) REVERT: B 35 MET cc_start: 0.8481 (ttp) cc_final: 0.7996 (mmt) REVERT: B 36 ARG cc_start: 0.8268 (tpp80) cc_final: 0.7608 (mtp180) REVERT: B 37 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7873 (tt0) REVERT: B 44 GLU cc_start: 0.8263 (tp30) cc_final: 0.7773 (tp30) REVERT: B 128 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7560 (mp) REVERT: B 180 GLN cc_start: 0.7776 (mm110) cc_final: 0.7199 (tt0) outliers start: 21 outliers final: 15 residues processed: 94 average time/residue: 0.2145 time to fit residues: 23.8563 Evaluate side-chains 94 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.0270 chunk 38 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4156 Z= 0.175 Angle : 0.504 6.333 5644 Z= 0.260 Chirality : 0.035 0.110 650 Planarity : 0.002 0.021 664 Dihedral : 5.049 46.524 952 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.41 % Allowed : 18.14 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.73 (0.38), residues: 476 helix: 3.63 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.48 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 184 HIS 0.000 0.000 HIS A 72 PHE 0.012 0.001 PHE B 109 TYR 0.013 0.001 TYR A 138 ARG 0.004 0.000 ARG A 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 0.423 Fit side-chains REVERT: A 18 TYR cc_start: 0.8806 (t80) cc_final: 0.8348 (t80) REVERT: A 19 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7759 (mp) REVERT: A 31 SER cc_start: 0.8456 (p) cc_final: 0.8079 (m) REVERT: A 35 MET cc_start: 0.8473 (ttp) cc_final: 0.7940 (mmt) REVERT: A 60 ARG cc_start: 0.8459 (mmm160) cc_final: 0.7989 (tpp80) REVERT: A 180 GLN cc_start: 0.7706 (mm110) cc_final: 0.7153 (tt0) REVERT: B 18 TYR cc_start: 0.8799 (t80) cc_final: 0.8339 (t80) REVERT: B 19 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7679 (mp) REVERT: B 31 SER cc_start: 0.8466 (p) cc_final: 0.8113 (m) REVERT: B 35 MET cc_start: 0.8472 (ttp) cc_final: 0.7990 (mmt) REVERT: B 36 ARG cc_start: 0.8260 (tpp80) cc_final: 0.7601 (mtp180) REVERT: B 37 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7940 (tt0) REVERT: B 44 GLU cc_start: 0.8245 (tp30) cc_final: 0.7800 (tp30) REVERT: B 60 ARG cc_start: 0.8532 (mmm160) cc_final: 0.8054 (tpp80) REVERT: B 180 GLN cc_start: 0.7721 (mm110) cc_final: 0.7156 (tt0) outliers start: 18 outliers final: 15 residues processed: 89 average time/residue: 0.2349 time to fit residues: 24.6474 Evaluate side-chains 92 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.156035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.111492 restraints weight = 4583.470| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.19 r_work: 0.3015 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4156 Z= 0.228 Angle : 0.526 7.333 5644 Z= 0.273 Chirality : 0.036 0.112 650 Planarity : 0.002 0.022 664 Dihedral : 5.191 45.728 952 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.66 % Allowed : 18.63 % Favored : 76.72 % 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: 4.64 (0.38), residues: 476 helix: 3.57 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.41 (0.76), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 184 HIS 0.000 0.000 HIS B 98 PHE 0.010 0.001 PHE A 109 TYR 0.015 0.001 TYR A 138 ARG 0.005 0.001 ARG B 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1136.48 seconds wall clock time: 20 minutes 55.47 seconds (1255.47 seconds total)