Starting phenix.real_space_refine on Thu Jul 18 21:59:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1q_36799/07_2024/8k1q_36799.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1q_36799/07_2024/8k1q_36799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1q_36799/07_2024/8k1q_36799.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1q_36799/07_2024/8k1q_36799.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1q_36799/07_2024/8k1q_36799.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1q_36799/07_2024/8k1q_36799.cif" } resolution = 3.68 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= 0.078 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 2 8.98 5 S 32 5.16 5 C 2706 2.51 5 N 616 2.21 5 O 702 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: 4058 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: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 107 Unusual residues: {' K': 2, 'Y01': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 3.04, per 1000 atoms: 0.75 Number of scatterers: 4058 At special positions: 0 Unit cell: (64.9, 73.7, 89.1, 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 2 19.00 S 32 16.00 O 702 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: 1.70 Conformation dependent library (CDL) restraints added in 720.1 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: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 2 through 53 removed outlier: 5.604A pdb=" N ASP A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N HIS A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 69 removed outlier: 3.952A pdb=" N ARG A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 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: 3.516A pdb=" N ILE B 12 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASP B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N HIS B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 69 removed outlier: 3.951A pdb=" N ARG B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLN B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 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 247 331 hydrogen bonds defined for protein. 969 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: 1.02 Time building geometry restraints manager: 1.82 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: 677 1.33 - 1.45: 1082 1.45 - 1.57: 2349 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 4156 Sorted by residual: bond pdb=" CA LYS B 42 " pdb=" C LYS B 42 " ideal model delta sigma weight residual 1.524 1.448 0.076 1.29e-02 6.01e+03 3.47e+01 bond pdb=" CA LYS A 42 " pdb=" C LYS A 42 " ideal model delta sigma weight residual 1.524 1.449 0.076 1.29e-02 6.01e+03 3.44e+01 bond pdb=" N MET A 156 " pdb=" CA MET A 156 " ideal model delta sigma weight residual 1.459 1.403 0.056 1.17e-02 7.31e+03 2.33e+01 bond pdb=" N MET B 156 " pdb=" CA MET B 156 " ideal model delta sigma weight residual 1.459 1.403 0.056 1.17e-02 7.31e+03 2.26e+01 bond pdb=" CA ARG A 73 " pdb=" C ARG A 73 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.37e-02 5.33e+03 1.11e+01 ... (remaining 4151 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.53: 90 106.53 - 113.39: 2274 113.39 - 120.25: 1499 120.25 - 127.11: 1757 127.11 - 133.96: 24 Bond angle restraints: 5644 Sorted by residual: angle pdb=" N LYS A 42 " pdb=" CA LYS A 42 " pdb=" C LYS A 42 " ideal model delta sigma weight residual 111.40 103.84 7.56 1.22e+00 6.72e-01 3.84e+01 angle pdb=" N LYS B 42 " pdb=" CA LYS B 42 " pdb=" C LYS B 42 " ideal model delta sigma weight residual 111.40 103.84 7.56 1.22e+00 6.72e-01 3.84e+01 angle pdb=" C SER B 155 " pdb=" N MET B 156 " pdb=" CA MET B 156 " ideal model delta sigma weight residual 120.65 114.81 5.84 1.32e+00 5.74e-01 1.96e+01 angle pdb=" C SER A 155 " pdb=" N MET A 156 " pdb=" CA MET A 156 " ideal model delta sigma weight residual 120.65 114.88 5.77 1.32e+00 5.74e-01 1.91e+01 angle pdb=" C LYS A 42 " pdb=" N ALA A 43 " pdb=" CA ALA A 43 " ideal model delta sigma weight residual 121.54 114.17 7.37 1.91e+00 2.74e-01 1.49e+01 ... (remaining 5639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 2402 16.57 - 33.13: 226 33.13 - 49.70: 58 49.70 - 66.27: 20 66.27 - 82.84: 6 Dihedral angle restraints: 2712 sinusoidal: 1310 harmonic: 1402 Sorted by residual: dihedral pdb=" CG ARG A 73 " pdb=" CD ARG A 73 " pdb=" NE ARG A 73 " pdb=" CZ ARG A 73 " ideal model delta sinusoidal sigma weight residual 90.00 132.20 -42.20 2 1.50e+01 4.44e-03 9.62e+00 dihedral pdb=" CB GLU A 130 " pdb=" CG GLU A 130 " pdb=" CD GLU A 130 " pdb=" OE1 GLU A 130 " ideal model delta sinusoidal sigma weight residual 0.00 82.84 -82.84 1 3.00e+01 1.11e-03 9.34e+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 82.78 -82.78 1 3.00e+01 1.11e-03 9.33e+00 ... (remaining 2709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 439 0.021 - 0.043: 91 0.043 - 0.064: 73 0.064 - 0.086: 31 0.086 - 0.107: 16 Chirality restraints: 650 Sorted by residual: chirality pdb=" CA ILE A 94 " pdb=" N ILE A 94 " pdb=" C ILE A 94 " pdb=" CB ILE A 94 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.86e-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 2.59e-01 chirality pdb=" CA VAL B 76 " pdb=" N VAL B 76 " pdb=" C VAL B 76 " pdb=" CB VAL B 76 " both_signs ideal model delta sigma weight residual False 2.44 2.54 -0.10 2.00e-01 2.50e+01 2.55e-01 ... (remaining 647 not shown) Planarity restraints: 664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 72 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.27e+00 pdb=" C HIS B 72 " 0.047 2.00e-02 2.50e+03 pdb=" O HIS B 72 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG B 73 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 72 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" C HIS A 72 " 0.044 2.00e-02 2.50e+03 pdb=" O HIS A 72 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG A 73 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 41 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.33e+00 pdb=" C LEU B 41 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU B 41 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS B 42 " 0.014 2.00e-02 2.50e+03 ... (remaining 661 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.90: 1533 2.90 - 3.46: 4686 3.46 - 4.02: 7120 4.02 - 4.58: 10281 4.58 - 5.14: 13857 Nonbonded interactions: 37477 Sorted by model distance: nonbonded pdb=" O MET B 156 " pdb=" N MET B 159 " model vdw 2.337 2.520 nonbonded pdb=" O MET A 156 " pdb=" N MET A 159 " model vdw 2.338 2.520 nonbonded pdb=" NZ LYS B 144 " pdb=" O ASP B 153 " model vdw 2.365 2.520 nonbonded pdb=" NZ LYS A 144 " pdb=" O ASP A 153 " model vdw 2.365 2.520 nonbonded pdb=" O LYS A 42 " pdb=" C ALA A 43 " model vdw 2.403 3.270 ... (remaining 37472 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 group one per residue 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: 0.340 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 16.220 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 4156 Z= 0.215 Angle : 0.502 7.563 5644 Z= 0.327 Chirality : 0.032 0.107 650 Planarity : 0.003 0.027 664 Dihedral : 14.128 82.835 1816 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.25 % Allowed : 0.25 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.91 (0.38), residues: 476 helix: 4.13 (0.24), residues: 380 sheet: None (None), residues: 0 loop : -0.92 (0.62), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 184 HIS 0.002 0.001 HIS A 98 PHE 0.005 0.000 PHE A 109 TYR 0.004 0.000 TYR A 96 ARG 0.001 0.000 ARG B 3 *********************** 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 84 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.400 Fit side-chains REVERT: A 47 ARG cc_start: 0.7817 (ttp80) cc_final: 0.7343 (ttp80) REVERT: A 73 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7077 (ttp-170) REVERT: A 229 LEU cc_start: 0.6785 (mt) cc_final: 0.6348 (tt) REVERT: B 229 LEU cc_start: 0.6635 (mt) cc_final: 0.6383 (tt) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.2142 time to fit residues: 21.3116 Evaluate side-chains 76 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 4156 Z= 0.305 Angle : 0.604 5.423 5644 Z= 0.329 Chirality : 0.039 0.124 650 Planarity : 0.004 0.035 664 Dihedral : 8.422 53.920 956 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.21 % Allowed : 9.80 % Favored : 87.99 % 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: 3.75 (0.23), residues: 390 sheet: None (None), residues: 0 loop : -0.62 (0.76), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 184 HIS 0.005 0.001 HIS B 72 PHE 0.017 0.002 PHE B 80 TYR 0.022 0.002 TYR A 85 ARG 0.006 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 101 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7175 (mt) cc_final: 0.6506 (tt) REVERT: A 241 LEU cc_start: 0.8607 (tp) cc_final: 0.8332 (tt) REVERT: B 42 LYS cc_start: 0.8303 (ttmt) cc_final: 0.8029 (ttpt) REVERT: B 47 ARG cc_start: 0.8048 (tmm-80) cc_final: 0.7805 (ttp80) REVERT: B 116 LEU cc_start: 0.8300 (tp) cc_final: 0.8029 (tt) REVERT: B 183 GLU cc_start: 0.8246 (tp30) cc_final: 0.8037 (mt-10) REVERT: B 229 LEU cc_start: 0.7204 (mt) cc_final: 0.6510 (tt) REVERT: B 241 LEU cc_start: 0.8651 (tp) cc_final: 0.8351 (tt) outliers start: 9 outliers final: 6 residues processed: 93 average time/residue: 0.1712 time to fit residues: 19.5767 Evaluate side-chains 86 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 242 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: 0.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 43 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 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: 0.7832 moved from start: 0.3638 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= 0.185 Angle : 0.517 7.864 5644 Z= 0.261 Chirality : 0.036 0.132 650 Planarity : 0.002 0.023 664 Dihedral : 7.875 50.152 952 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.70 % Allowed : 13.24 % Favored : 84.07 % 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: 4.82 (0.39), residues: 476 helix: 3.87 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.50 (0.80), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 184 HIS 0.002 0.001 HIS B 98 PHE 0.028 0.001 PHE A 202 TYR 0.013 0.001 TYR B 85 ARG 0.006 0.000 ARG A 47 *********************** 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 98 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.440 Fit side-chains REVERT: A 47 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7681 (tmm-80) REVERT: A 57 GLU cc_start: 0.7641 (pm20) cc_final: 0.7164 (pm20) REVERT: A 229 LEU cc_start: 0.7160 (mt) cc_final: 0.6559 (tt) REVERT: A 241 LEU cc_start: 0.8645 (tp) cc_final: 0.8368 (tt) REVERT: B 47 ARG cc_start: 0.8005 (tmm-80) cc_final: 0.7411 (ttp80) REVERT: B 183 GLU cc_start: 0.8201 (tp30) cc_final: 0.7893 (mt-10) REVERT: B 241 LEU cc_start: 0.8644 (tp) cc_final: 0.8375 (tt) outliers start: 11 outliers final: 6 residues processed: 88 average time/residue: 0.2032 time to fit residues: 21.5221 Evaluate side-chains 70 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 242 VAL 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: 0.7980 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 0.0870 chunk 12 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 158 ASN A 209 GLN B 158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4084 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= 0.210 Angle : 0.511 5.374 5644 Z= 0.263 Chirality : 0.036 0.119 650 Planarity : 0.003 0.019 664 Dihedral : 7.469 49.806 952 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.96 % Allowed : 16.18 % Favored : 81.86 % 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 (0.39), residues: 476 helix: 3.84 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.71 (0.78), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 184 HIS 0.002 0.000 HIS B 98 PHE 0.019 0.001 PHE A 202 TYR 0.013 0.001 TYR B 85 ARG 0.004 0.000 ARG A 47 *********************** 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 90 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.427 Fit side-chains REVERT: A 229 LEU cc_start: 0.7043 (mt) cc_final: 0.6469 (tt) REVERT: A 241 LEU cc_start: 0.8733 (tp) cc_final: 0.8451 (tt) REVERT: B 241 LEU cc_start: 0.8735 (tp) cc_final: 0.8454 (tt) outliers start: 8 outliers final: 6 residues processed: 83 average time/residue: 0.2116 time to fit residues: 20.8584 Evaluate side-chains 73 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 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: 0.7896 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4156 Z= 0.194 Angle : 0.505 5.398 5644 Z= 0.263 Chirality : 0.035 0.118 650 Planarity : 0.003 0.020 664 Dihedral : 7.047 49.245 952 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.21 % Allowed : 16.42 % Favored : 81.37 % 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 (0.39), residues: 476 helix: 3.86 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.73 (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 B 98 PHE 0.020 0.001 PHE B 246 TYR 0.011 0.001 TYR B 85 ARG 0.004 0.001 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 69 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.425 Fit side-chains REVERT: A 44 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7327 (tm-30) REVERT: A 241 LEU cc_start: 0.8732 (tp) cc_final: 0.8409 (tt) REVERT: B 44 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7376 (tm-30) REVERT: B 241 LEU cc_start: 0.8724 (tp) cc_final: 0.8399 (tt) outliers start: 9 outliers final: 6 residues processed: 63 average time/residue: 0.2081 time to fit residues: 16.0114 Evaluate side-chains 68 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.0070 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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: 0.7900 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4156 Z= 0.181 Angle : 0.492 4.809 5644 Z= 0.257 Chirality : 0.035 0.114 650 Planarity : 0.003 0.018 664 Dihedral : 6.620 48.416 952 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.70 % Allowed : 18.14 % 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: 4.76 (0.39), residues: 476 helix: 3.85 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -0.75 (0.76), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 184 HIS 0.001 0.000 HIS B 98 PHE 0.017 0.001 PHE A 246 TYR 0.010 0.001 TYR B 85 ARG 0.003 0.001 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 74 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.430 Fit side-chains REVERT: A 36 ARG cc_start: 0.7815 (mtm-85) cc_final: 0.7569 (mtp180) REVERT: A 47 ARG cc_start: 0.7820 (ttp-170) cc_final: 0.7544 (ttp80) REVERT: A 182 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7975 (mm-30) REVERT: A 241 LEU cc_start: 0.8869 (tp) cc_final: 0.8554 (tt) REVERT: B 44 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7478 (tm-30) REVERT: B 182 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7980 (mm-30) REVERT: B 241 LEU cc_start: 0.8845 (tp) cc_final: 0.8527 (tt) outliers start: 11 outliers final: 7 residues processed: 65 average time/residue: 0.2031 time to fit residues: 15.9632 Evaluate side-chains 66 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7895 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4156 Z= 0.168 Angle : 0.478 4.947 5644 Z= 0.251 Chirality : 0.035 0.114 650 Planarity : 0.002 0.017 664 Dihedral : 6.421 47.128 952 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.45 % Allowed : 19.36 % 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: 3.86 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -0.89 (0.72), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 184 HIS 0.001 0.000 HIS A 98 PHE 0.029 0.001 PHE A 202 TYR 0.009 0.001 TYR B 85 ARG 0.003 0.000 ARG A 36 *********************** 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 71 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.416 Fit side-chains REVERT: A 36 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.7575 (mtp180) REVERT: A 182 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7888 (mm-30) REVERT: A 241 LEU cc_start: 0.8840 (tp) cc_final: 0.8384 (tt) REVERT: B 182 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8087 (mm-30) REVERT: B 241 LEU cc_start: 0.8826 (tp) cc_final: 0.8369 (tt) outliers start: 10 outliers final: 6 residues processed: 63 average time/residue: 0.1998 time to fit residues: 15.2179 Evaluate side-chains 62 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.0570 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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: 0.7871 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4156 Z= 0.150 Angle : 0.473 5.047 5644 Z= 0.248 Chirality : 0.034 0.113 650 Planarity : 0.002 0.017 664 Dihedral : 6.154 46.652 952 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.21 % Allowed : 20.34 % 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: 4.83 (0.38), residues: 476 helix: 3.91 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -0.82 (0.74), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 184 HIS 0.001 0.000 HIS A 98 PHE 0.024 0.001 PHE A 202 TYR 0.007 0.001 TYR B 85 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 69 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.387 Fit side-chains REVERT: A 36 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.7559 (mtp180) REVERT: A 47 ARG cc_start: 0.7839 (ttp-170) cc_final: 0.7589 (ttp-170) REVERT: A 182 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7801 (mm-30) REVERT: A 241 LEU cc_start: 0.8905 (tp) cc_final: 0.8422 (tt) REVERT: B 182 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8038 (mm-30) REVERT: B 241 LEU cc_start: 0.8892 (tp) cc_final: 0.8406 (tt) outliers start: 9 outliers final: 7 residues processed: 63 average time/residue: 0.2157 time to fit residues: 16.3692 Evaluate side-chains 63 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7919 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4156 Z= 0.204 Angle : 0.513 6.110 5644 Z= 0.268 Chirality : 0.036 0.115 650 Planarity : 0.002 0.020 664 Dihedral : 6.238 44.060 952 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.45 % Allowed : 20.34 % Favored : 77.21 % 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 (0.39), residues: 476 helix: 3.89 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -0.96 (0.74), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 184 HIS 0.001 0.000 HIS A 98 PHE 0.024 0.001 PHE A 202 TYR 0.010 0.001 TYR B 85 ARG 0.003 0.000 ARG A 36 *********************** 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 66 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.447 Fit side-chains REVERT: A 36 ARG cc_start: 0.7920 (mtm-85) cc_final: 0.7669 (mtp180) REVERT: A 182 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7822 (mm-30) REVERT: B 45 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7411 (tm-30) REVERT: B 182 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7982 (mm-30) outliers start: 10 outliers final: 8 residues processed: 59 average time/residue: 0.2101 time to fit residues: 15.0286 Evaluate side-chains 62 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7895 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4156 Z= 0.164 Angle : 0.483 5.567 5644 Z= 0.253 Chirality : 0.035 0.113 650 Planarity : 0.002 0.017 664 Dihedral : 6.047 44.282 952 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.45 % Allowed : 20.34 % Favored : 77.21 % 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: 4.83 (0.39), residues: 476 helix: 3.93 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -0.92 (0.75), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 184 HIS 0.001 0.000 HIS A 98 PHE 0.023 0.001 PHE A 202 TYR 0.007 0.001 TYR B 85 ARG 0.002 0.000 ARG A 36 ********************** 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 73 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.425 Fit side-chains REVERT: A 36 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7657 (mtp180) REVERT: A 47 ARG cc_start: 0.7813 (ttp-170) cc_final: 0.7544 (ttp-170) REVERT: B 182 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7925 (mm-30) outliers start: 10 outliers final: 10 residues processed: 64 average time/residue: 0.2081 time to fit residues: 16.1229 Evaluate side-chains 70 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.154261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.110982 restraints weight = 4170.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.111606 restraints weight = 3763.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.111666 restraints weight = 3551.822| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4156 Z= 0.199 Angle : 0.521 6.094 5644 Z= 0.272 Chirality : 0.035 0.114 650 Planarity : 0.003 0.029 664 Dihedral : 6.107 42.798 952 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.70 % Allowed : 21.08 % Favored : 76.23 % 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 (0.39), residues: 476 helix: 3.90 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -1.07 (0.73), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 184 HIS 0.001 0.000 HIS A 98 PHE 0.024 0.001 PHE A 202 TYR 0.010 0.001 TYR B 85 ARG 0.002 0.000 ARG A 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1084.43 seconds wall clock time: 19 minutes 55.93 seconds (1195.93 seconds total)