Starting phenix.real_space_refine on Mon Sep 23 17:06:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1v_36805/09_2024/8k1v_36805.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1v_36805/09_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_36805/09_2024/8k1v_36805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1v_36805/09_2024/8k1v_36805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1v_36805/09_2024/8k1v_36805.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1v_36805/09_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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 2.96, per 1000 atoms: 0.73 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 455.8 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: 0.35 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: 1.13 Time building geometry restraints manager: 1.24 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: 0.00 - 0.98: 5577 0.98 - 1.96: 48 1.96 - 2.95: 7 2.95 - 3.93: 6 3.93 - 4.91: 6 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 3.040 nonbonded pdb=" OH TYR A 52 " pdb=" OD2 ASP B 58 " model vdw 2.304 3.040 nonbonded pdb=" OD2 ASP A 58 " pdb=" OH TYR B 52 " model vdw 2.316 3.040 nonbonded pdb=" OH TYR B 96 " pdb=" OG1 THR B 196 " model vdw 2.330 3.040 nonbonded pdb=" NZ LYS A 144 " pdb=" O ASP A 153 " model vdw 2.341 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.350 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.480 Find NCS groups from input model: 0.140 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.370 ------------------------------------------------------------------------------- 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 : 0.375 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: 0.2112 time to fit residues: 28.8927 Evaluate side-chains 95 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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: 0.8980 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7678 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4156 Z= 0.221 Angle : 0.502 5.798 5644 Z= 0.264 Chirality : 0.038 0.130 650 Planarity : 0.003 0.018 664 Dihedral : 5.310 31.075 952 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.45 % Allowed : 8.33 % Favored : 89.22 % 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: 5.39 (0.38), residues: 476 helix: 4.02 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 1.08 (0.87), 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 188 PHE 0.009 0.001 PHE B 223 TYR 0.021 0.002 TYR B 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 111 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 0.410 Fit side-chains REVERT: A 35 MET cc_start: 0.8270 (ttp) cc_final: 0.7833 (mmm) REVERT: A 36 ARG cc_start: 0.8246 (ttm-80) cc_final: 0.7392 (mtp180) REVERT: A 42 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7920 (tppt) REVERT: A 44 GLU cc_start: 0.8132 (tp30) cc_final: 0.7876 (tp30) REVERT: A 60 ARG cc_start: 0.8268 (tpp80) cc_final: 0.8000 (tpp80) REVERT: A 69 SER cc_start: 0.8900 (p) cc_final: 0.8279 (p) REVERT: A 73 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.6824 (mpp80) REVERT: A 180 GLN cc_start: 0.7670 (mm110) cc_final: 0.7098 (tt0) REVERT: A 243 VAL cc_start: 0.7764 (t) cc_final: 0.7558 (t) REVERT: B 35 MET cc_start: 0.8300 (ttp) cc_final: 0.8076 (mmm) REVERT: B 36 ARG cc_start: 0.8321 (tpp80) cc_final: 0.7574 (mtp180) REVERT: B 44 GLU cc_start: 0.8143 (tp30) cc_final: 0.7753 (tp30) REVERT: B 180 GLN cc_start: 0.7697 (mm110) cc_final: 0.7030 (tt0) outliers start: 10 outliers final: 4 residues processed: 107 average time/residue: 0.2239 time to fit residues: 28.0318 Evaluate side-chains 100 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 134 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 0.0040 chunk 32 optimal weight: 0.9980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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: 0.7714 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4156 Z= 0.166 Angle : 0.478 5.935 5644 Z= 0.248 Chirality : 0.035 0.103 650 Planarity : 0.002 0.015 664 Dihedral : 4.889 31.515 952 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.70 % Allowed : 10.78 % Favored : 86.52 % 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 (0.39), residues: 476 helix: 3.88 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 1.02 (0.85), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 78 HIS 0.001 0.000 HIS A 33 PHE 0.007 0.001 PHE A 16 TYR 0.016 0.001 TYR B 85 ARG 0.003 0.000 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 113 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 0.398 Fit side-chains REVERT: A 19 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7662 (mp) REVERT: A 35 MET cc_start: 0.8270 (ttp) cc_final: 0.7908 (mmt) REVERT: A 36 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.7430 (mtp180) REVERT: A 42 LYS cc_start: 0.8149 (ttmm) cc_final: 0.7425 (tppt) REVERT: A 44 GLU cc_start: 0.8159 (tp30) cc_final: 0.7856 (tp30) REVERT: A 45 GLU cc_start: 0.7350 (pt0) cc_final: 0.6920 (pp20) REVERT: A 60 ARG cc_start: 0.8356 (tpp80) cc_final: 0.8104 (tpp80) REVERT: A 180 GLN cc_start: 0.7739 (mm110) cc_final: 0.7079 (tt0) REVERT: B 19 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7629 (mp) REVERT: B 35 MET cc_start: 0.8266 (ttp) cc_final: 0.8064 (mmt) REVERT: B 36 ARG cc_start: 0.8370 (tpp80) cc_final: 0.7679 (mtp180) REVERT: B 44 GLU cc_start: 0.8175 (tp30) cc_final: 0.7765 (tp30) REVERT: B 58 ASP cc_start: 0.8231 (m-30) cc_final: 0.8014 (t0) REVERT: B 180 GLN cc_start: 0.7657 (mm110) cc_final: 0.6968 (tt0) outliers start: 11 outliers final: 6 residues processed: 111 average time/residue: 0.2144 time to fit residues: 27.9733 Evaluate side-chains 95 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 206 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.7842 moved from start: 0.4241 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= 0.276 Angle : 0.567 5.807 5644 Z= 0.299 Chirality : 0.039 0.115 650 Planarity : 0.003 0.014 664 Dihedral : 4.994 39.330 952 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.17 % Allowed : 14.71 % 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: 4.75 (0.38), residues: 476 helix: 3.63 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.55 (0.80), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 78 HIS 0.001 0.000 HIS A 33 PHE 0.013 0.002 PHE A 16 TYR 0.024 0.002 TYR B 85 ARG 0.004 0.001 ARG A 73 *********************** 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 121 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 0.354 Fit side-chains REVERT: A 19 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7650 (mp) REVERT: A 31 SER cc_start: 0.8294 (p) cc_final: 0.7892 (m) REVERT: A 35 MET cc_start: 0.8335 (ttp) cc_final: 0.7916 (mmt) REVERT: A 42 LYS cc_start: 0.8172 (ttmm) cc_final: 0.7949 (tppt) REVERT: A 44 GLU cc_start: 0.8212 (tp30) cc_final: 0.7874 (tp30) REVERT: A 60 ARG cc_start: 0.8398 (tpp80) cc_final: 0.8134 (tpp80) REVERT: A 180 GLN cc_start: 0.7752 (mm110) cc_final: 0.7242 (tt0) REVERT: B 19 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7621 (mp) REVERT: B 31 SER cc_start: 0.8340 (p) cc_final: 0.8070 (m) REVERT: B 35 MET cc_start: 0.8328 (ttp) cc_final: 0.7967 (mmt) REVERT: B 36 ARG cc_start: 0.8352 (tpp80) cc_final: 0.7631 (mtp180) REVERT: B 40 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8230 (ttmm) REVERT: B 44 GLU cc_start: 0.8213 (tp30) cc_final: 0.7787 (tp30) REVERT: B 58 ASP cc_start: 0.8218 (m-30) cc_final: 0.7920 (t0) REVERT: B 73 ARG cc_start: 0.8256 (tpp80) cc_final: 0.8048 (mmt90) REVERT: B 180 GLN cc_start: 0.7751 (mm110) cc_final: 0.7235 (tt0) outliers start: 17 outliers final: 12 residues processed: 113 average time/residue: 0.2325 time to fit residues: 30.4876 Evaluate side-chains 94 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 134 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 210 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 Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 210 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 0.2980 chunk 41 optimal weight: 0.0970 chunk 11 optimal weight: 0.0670 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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: 0.7786 moved from start: 0.4269 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= 0.160 Angle : 0.525 6.075 5644 Z= 0.270 Chirality : 0.035 0.113 650 Planarity : 0.002 0.015 664 Dihedral : 4.766 40.554 952 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.23 % Allowed : 20.83 % 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: 4.87 (0.38), residues: 476 helix: 3.70 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.67 (0.80), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 184 HIS 0.001 0.000 HIS B 72 PHE 0.011 0.001 PHE B 109 TYR 0.014 0.001 TYR A 138 ARG 0.003 0.001 ARG A 73 *********************** 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 92 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.495 Fit side-chains REVERT: A 19 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7623 (mp) REVERT: A 31 SER cc_start: 0.8332 (p) cc_final: 0.7813 (m) REVERT: A 35 MET cc_start: 0.8381 (ttp) cc_final: 0.7834 (mmm) REVERT: A 42 LYS cc_start: 0.8282 (ttmm) cc_final: 0.7570 (tppt) REVERT: A 44 GLU cc_start: 0.8134 (tp30) cc_final: 0.7799 (tp30) REVERT: A 45 GLU cc_start: 0.7659 (pt0) cc_final: 0.7046 (pp20) REVERT: A 60 ARG cc_start: 0.8380 (tpp80) cc_final: 0.8118 (tpp80) REVERT: A 180 GLN cc_start: 0.7635 (mm110) cc_final: 0.7180 (tt0) REVERT: B 19 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7608 (mp) REVERT: B 31 SER cc_start: 0.8325 (p) cc_final: 0.7916 (m) REVERT: B 35 MET cc_start: 0.8313 (ttp) cc_final: 0.7969 (mmm) REVERT: B 36 ARG cc_start: 0.8317 (tpp80) cc_final: 0.7637 (mtp180) REVERT: B 44 GLU cc_start: 0.8164 (tp30) cc_final: 0.7790 (tp30) REVERT: B 180 GLN cc_start: 0.7645 (mm110) cc_final: 0.7189 (tt0) REVERT: B 226 MET cc_start: 0.8839 (mmp) cc_final: 0.8572 (mmm) outliers start: 5 outliers final: 3 residues processed: 91 average time/residue: 0.2312 time to fit residues: 24.8011 Evaluate side-chains 84 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 19 LEU 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: 0.7980 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.7833 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4156 Z= 0.223 Angle : 0.541 5.952 5644 Z= 0.282 Chirality : 0.037 0.118 650 Planarity : 0.002 0.017 664 Dihedral : 4.840 41.401 952 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.96 % Allowed : 19.85 % Favored : 78.19 % 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: 4.75 (0.38), residues: 476 helix: 3.63 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.51 (0.78), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 78 HIS 0.001 0.000 HIS B 98 PHE 0.009 0.001 PHE B 16 TYR 0.013 0.002 TYR B 85 ARG 0.004 0.001 ARG A 73 *********************** 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 91 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.454 Fit side-chains REVERT: A 19 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7661 (mp) REVERT: A 31 SER cc_start: 0.8407 (p) cc_final: 0.8008 (m) REVERT: A 35 MET cc_start: 0.8399 (ttp) cc_final: 0.7924 (mmt) REVERT: A 42 LYS cc_start: 0.8296 (ttmm) cc_final: 0.7577 (tppt) REVERT: A 44 GLU cc_start: 0.8145 (tp30) cc_final: 0.7840 (tp30) REVERT: A 45 GLU cc_start: 0.7697 (pt0) cc_final: 0.6962 (pp20) REVERT: A 180 GLN cc_start: 0.7693 (mm110) cc_final: 0.7234 (tt0) REVERT: B 19 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7595 (mp) REVERT: B 31 SER cc_start: 0.8397 (p) cc_final: 0.8009 (m) REVERT: B 35 MET cc_start: 0.8314 (ttp) cc_final: 0.7941 (mmt) REVERT: B 36 ARG cc_start: 0.8254 (tpp80) cc_final: 0.7588 (mtp180) REVERT: B 44 GLU cc_start: 0.8180 (tp30) cc_final: 0.7784 (tp30) REVERT: B 180 GLN cc_start: 0.7692 (mm110) cc_final: 0.7226 (tt0) REVERT: B 226 MET cc_start: 0.8897 (mmp) cc_final: 0.8666 (mmm) outliers start: 8 outliers final: 6 residues processed: 89 average time/residue: 0.2349 time to fit residues: 24.7270 Evaluate side-chains 88 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 ASP 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: 0.9990 chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7828 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4156 Z= 0.199 Angle : 0.535 7.144 5644 Z= 0.275 Chirality : 0.036 0.115 650 Planarity : 0.002 0.019 664 Dihedral : 4.838 43.088 952 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.94 % Allowed : 18.38 % Favored : 78.68 % 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: 3.62 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.50 (0.78), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 184 HIS 0.001 0.000 HIS A 33 PHE 0.010 0.001 PHE B 109 TYR 0.011 0.001 TYR A 138 ARG 0.004 0.001 ARG A 73 *********************** 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 97 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.399 Fit side-chains REVERT: A 19 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7663 (mp) REVERT: A 31 SER cc_start: 0.8365 (p) cc_final: 0.7984 (m) REVERT: A 35 MET cc_start: 0.8423 (ttp) cc_final: 0.7858 (mmt) REVERT: A 42 LYS cc_start: 0.8293 (ttmm) cc_final: 0.8043 (tppt) REVERT: A 44 GLU cc_start: 0.8128 (tp30) cc_final: 0.7820 (tp30) REVERT: A 45 GLU cc_start: 0.7829 (pt0) cc_final: 0.7608 (pt0) REVERT: A 128 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7512 (mp) REVERT: A 180 GLN cc_start: 0.7675 (mm110) cc_final: 0.7222 (tt0) REVERT: B 19 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7665 (mp) REVERT: B 31 SER cc_start: 0.8404 (p) cc_final: 0.8052 (m) REVERT: B 35 MET cc_start: 0.8327 (ttp) cc_final: 0.7966 (mmt) REVERT: B 36 ARG cc_start: 0.8281 (tpp80) cc_final: 0.7629 (mtp180) REVERT: B 44 GLU cc_start: 0.8206 (tp30) cc_final: 0.7857 (tp30) REVERT: B 58 ASP cc_start: 0.8329 (m-30) cc_final: 0.8026 (m-30) REVERT: B 128 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7512 (mp) REVERT: B 180 GLN cc_start: 0.7648 (mm110) cc_final: 0.7155 (tt0) REVERT: B 226 MET cc_start: 0.8894 (mmp) cc_final: 0.8682 (mmm) outliers start: 12 outliers final: 8 residues processed: 95 average time/residue: 0.2228 time to fit residues: 24.8335 Evaluate side-chains 94 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 ASP 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 19 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 128 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 43 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7824 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4156 Z= 0.194 Angle : 0.527 6.757 5644 Z= 0.276 Chirality : 0.036 0.114 650 Planarity : 0.002 0.019 664 Dihedral : 4.854 44.207 952 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.94 % Allowed : 18.14 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.77 (0.38), residues: 476 helix: 3.65 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.52 (0.78), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 184 HIS 0.001 0.000 HIS A 33 PHE 0.010 0.001 PHE B 109 TYR 0.015 0.001 TYR B 138 ARG 0.004 0.001 ARG B 73 *********************** 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 96 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.498 Fit side-chains REVERT: A 19 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7670 (mp) REVERT: A 31 SER cc_start: 0.8351 (p) cc_final: 0.7958 (m) REVERT: A 35 MET cc_start: 0.8437 (ttp) cc_final: 0.7869 (mmt) REVERT: A 42 LYS cc_start: 0.8299 (ttmm) cc_final: 0.8023 (tppt) REVERT: A 44 GLU cc_start: 0.8174 (tp30) cc_final: 0.7848 (tp30) REVERT: A 45 GLU cc_start: 0.7835 (pt0) cc_final: 0.7549 (pt0) REVERT: A 128 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7553 (mp) REVERT: A 180 GLN cc_start: 0.7633 (mm110) cc_final: 0.7153 (tt0) REVERT: B 19 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7676 (mp) REVERT: B 31 SER cc_start: 0.8398 (p) cc_final: 0.8059 (m) REVERT: B 35 MET cc_start: 0.8381 (ttp) cc_final: 0.7913 (mmt) REVERT: B 36 ARG cc_start: 0.8275 (tpp80) cc_final: 0.7631 (mtp180) REVERT: B 44 GLU cc_start: 0.8213 (tp30) cc_final: 0.7864 (tp30) REVERT: B 128 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7571 (mp) REVERT: B 180 GLN cc_start: 0.7640 (mm110) cc_final: 0.7147 (tt0) REVERT: B 226 MET cc_start: 0.8899 (mmp) cc_final: 0.8694 (mmm) outliers start: 12 outliers final: 8 residues processed: 94 average time/residue: 0.2392 time to fit residues: 26.3003 Evaluate side-chains 94 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 ASP 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 19 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 128 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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: 0.7831 moved from start: 0.4739 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= 0.207 Angle : 0.544 6.316 5644 Z= 0.281 Chirality : 0.036 0.115 650 Planarity : 0.002 0.018 664 Dihedral : 4.893 44.642 952 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.19 % Allowed : 18.38 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.74 (0.38), residues: 476 helix: 3.63 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.49 (0.78), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 184 HIS 0.001 0.000 HIS A 33 PHE 0.010 0.001 PHE B 109 TYR 0.013 0.001 TYR A 138 ARG 0.004 0.001 ARG B 73 *********************** 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 97 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.447 Fit side-chains REVERT: A 19 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7671 (mp) REVERT: A 31 SER cc_start: 0.8364 (p) cc_final: 0.7963 (m) REVERT: A 35 MET cc_start: 0.8430 (ttp) cc_final: 0.7948 (mmt) REVERT: A 42 LYS cc_start: 0.8302 (ttmm) cc_final: 0.8019 (tppt) REVERT: A 44 GLU cc_start: 0.8123 (tp30) cc_final: 0.7807 (tp30) REVERT: A 128 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7558 (mp) REVERT: A 180 GLN cc_start: 0.7642 (mm110) cc_final: 0.7160 (tt0) REVERT: B 19 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7676 (mp) REVERT: B 31 SER cc_start: 0.8432 (p) cc_final: 0.8081 (m) REVERT: B 35 MET cc_start: 0.8393 (ttp) cc_final: 0.7926 (mmt) REVERT: B 36 ARG cc_start: 0.8275 (tpp80) cc_final: 0.7627 (mtp180) REVERT: B 44 GLU cc_start: 0.8214 (tp30) cc_final: 0.7873 (tp30) REVERT: B 128 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7524 (mp) REVERT: B 180 GLN cc_start: 0.7655 (mm110) cc_final: 0.7151 (tt0) REVERT: B 226 MET cc_start: 0.8904 (mmp) cc_final: 0.8703 (mmm) outliers start: 13 outliers final: 8 residues processed: 95 average time/residue: 0.2217 time to fit residues: 24.7370 Evaluate side-chains 94 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 ASP 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 19 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 128 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 29 optimal weight: 0.5980 chunk 23 optimal weight: 0.0040 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.0030 chunk 35 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.4202 ------------------------------------------------------------------------------- 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: 0.7795 moved from start: 0.4708 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= 0.165 Angle : 0.526 6.348 5644 Z= 0.270 Chirality : 0.035 0.109 650 Planarity : 0.002 0.020 664 Dihedral : 4.831 46.115 952 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.94 % Allowed : 18.14 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.81 (0.38), residues: 476 helix: 3.68 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.48 (0.78), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 184 HIS 0.001 0.000 HIS A 33 PHE 0.011 0.001 PHE A 109 TYR 0.014 0.001 TYR B 138 ARG 0.004 0.001 ARG B 73 ********************** 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 96 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.420 Fit side-chains REVERT: A 19 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7761 (mp) REVERT: A 31 SER cc_start: 0.8351 (p) cc_final: 0.7958 (m) REVERT: A 35 MET cc_start: 0.8441 (ttp) cc_final: 0.7871 (mmt) REVERT: A 42 LYS cc_start: 0.8394 (ttmm) cc_final: 0.8138 (tppt) REVERT: A 44 GLU cc_start: 0.8075 (tp30) cc_final: 0.7829 (tp30) REVERT: A 58 ASP cc_start: 0.8436 (m-30) cc_final: 0.8212 (m-30) REVERT: A 128 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7576 (mp) REVERT: A 180 GLN cc_start: 0.7606 (mm110) cc_final: 0.7153 (tt0) REVERT: B 19 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7653 (mp) REVERT: B 31 SER cc_start: 0.8439 (p) cc_final: 0.8083 (m) REVERT: B 35 MET cc_start: 0.8392 (ttp) cc_final: 0.7920 (mmt) REVERT: B 36 ARG cc_start: 0.8273 (tpp80) cc_final: 0.7631 (mtp180) REVERT: B 44 GLU cc_start: 0.8261 (tp30) cc_final: 0.7917 (tp30) REVERT: B 58 ASP cc_start: 0.8223 (m-30) cc_final: 0.8018 (t0) REVERT: B 60 ARG cc_start: 0.8370 (mmm160) cc_final: 0.7933 (tpp80) REVERT: B 128 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7577 (mp) REVERT: B 180 GLN cc_start: 0.7611 (mm110) cc_final: 0.7130 (tt0) outliers start: 12 outliers final: 8 residues processed: 94 average time/residue: 0.2264 time to fit residues: 24.9570 Evaluate side-chains 102 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 ASP 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 19 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 128 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 0.0670 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.7522 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.157914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.111199 restraints weight = 4551.083| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.26 r_work: 0.2976 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4156 Z= 0.199 Angle : 0.538 5.984 5644 Z= 0.276 Chirality : 0.036 0.117 650 Planarity : 0.003 0.024 664 Dihedral : 4.898 45.518 952 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.94 % Allowed : 18.38 % Favored : 78.68 % 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: 4.79 (0.38), residues: 476 helix: 3.70 (0.24), residues: 390 sheet: None (None), residues: 0 loop : 0.33 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 184 HIS 0.000 0.000 HIS A 33 PHE 0.010 0.001 PHE A 109 TYR 0.014 0.001 TYR A 138 ARG 0.005 0.001 ARG B 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1230.96 seconds wall clock time: 22 minutes 52.17 seconds (1372.17 seconds total)