Starting phenix.real_space_refine on Wed Oct 9 18:13:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1q_36799/10_2024/8k1q_36799.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1q_36799/10_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_36799/10_2024/8k1q_36799.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1q_36799/10_2024/8k1q_36799.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1q_36799/10_2024/8k1q_36799.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1q_36799/10_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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 3.22, per 1000 atoms: 0.79 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 - 3.00 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: 1.13 Conformation dependent library (CDL) restraints added in 489.9 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: 0.43 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: 1.39 Time building geometry restraints manager: 1.27 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: 0.00 - 1.51: 5557 1.51 - 3.03: 55 3.03 - 4.54: 18 4.54 - 6.05: 10 6.05 - 7.56: 4 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 3.120 nonbonded pdb=" O MET A 156 " pdb=" N MET A 159 " model vdw 2.338 3.120 nonbonded pdb=" NZ LYS B 144 " pdb=" O ASP B 153 " model vdw 2.365 3.120 nonbonded pdb=" NZ LYS A 144 " pdb=" O ASP A 153 " model vdw 2.365 3.120 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 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 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.860 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.840 ------------------------------------------------------------------------------- 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 : 0.431 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: 0.2354 time to fit residues: 23.6961 Evaluate side-chains 76 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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: 0.5980 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4156 Z= 0.264 Angle : 0.570 4.981 5644 Z= 0.309 Chirality : 0.039 0.119 650 Planarity : 0.003 0.025 664 Dihedral : 8.328 52.766 956 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.96 % Allowed : 9.31 % Favored : 88.73 % 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: 3.86 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.57 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 78 HIS 0.004 0.001 HIS B 72 PHE 0.015 0.002 PHE B 223 TYR 0.020 0.002 TYR B 85 ARG 0.009 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 96 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 168 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.7101 (tpp) REVERT: A 229 LEU cc_start: 0.7146 (mt) cc_final: 0.6531 (tt) REVERT: A 241 LEU cc_start: 0.8582 (tp) cc_final: 0.8327 (tt) REVERT: B 42 LYS cc_start: 0.8275 (ttmt) cc_final: 0.8015 (ttpt) REVERT: B 168 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7129 (tpp) REVERT: B 183 GLU cc_start: 0.8231 (tp30) cc_final: 0.7996 (mt-10) REVERT: B 229 LEU cc_start: 0.7168 (mt) cc_final: 0.6523 (tt) REVERT: B 241 LEU cc_start: 0.8571 (tp) cc_final: 0.8291 (tt) outliers start: 8 outliers final: 6 residues processed: 90 average time/residue: 0.1855 time to fit residues: 20.6685 Evaluate side-chains 83 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 168 MET 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 168 MET 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: 1.9990 chunk 13 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7806 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 4156 Z= 0.188 Angle : 0.517 8.431 5644 Z= 0.262 Chirality : 0.036 0.130 650 Planarity : 0.003 0.025 664 Dihedral : 7.766 50.823 952 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.43 % Allowed : 13.48 % Favored : 83.09 % 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: 4.95 (0.39), residues: 476 helix: 3.96 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.43 (0.82), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 184 HIS 0.002 0.001 HIS B 98 PHE 0.027 0.001 PHE A 202 TYR 0.013 0.001 TYR B 85 ARG 0.006 0.001 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 100 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.511 Fit side-chains REVERT: A 47 ARG cc_start: 0.7849 (ttp80) cc_final: 0.7554 (tmm-80) REVERT: A 168 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7212 (tpp) REVERT: A 229 LEU cc_start: 0.7106 (mt) cc_final: 0.6512 (tt) REVERT: A 241 LEU cc_start: 0.8626 (tp) cc_final: 0.8366 (tt) REVERT: B 47 ARG cc_start: 0.8000 (tmm-80) cc_final: 0.7768 (ttp80) REVERT: B 64 LEU cc_start: 0.8594 (mt) cc_final: 0.8378 (tp) REVERT: B 168 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.7153 (tpp) REVERT: B 182 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8249 (mm-30) REVERT: B 183 GLU cc_start: 0.8145 (tp30) cc_final: 0.7818 (mt-10) REVERT: B 229 LEU cc_start: 0.7140 (mt) cc_final: 0.6530 (tt) REVERT: B 241 LEU cc_start: 0.8625 (tp) cc_final: 0.8376 (tt) outliers start: 14 outliers final: 6 residues processed: 87 average time/residue: 0.2340 time to fit residues: 24.3821 Evaluate side-chains 75 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 168 MET 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 168 MET 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: 1.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 ASN B 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4156 Z= 0.227 Angle : 0.534 5.812 5644 Z= 0.275 Chirality : 0.037 0.116 650 Planarity : 0.003 0.016 664 Dihedral : 7.461 49.678 952 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.94 % Allowed : 15.69 % 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: 4.78 (0.39), residues: 476 helix: 3.87 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.68 (0.79), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 184 HIS 0.002 0.000 HIS B 98 PHE 0.021 0.001 PHE A 202 TYR 0.014 0.001 TYR B 85 ARG 0.004 0.001 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 97 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 168 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7281 (tpp) REVERT: A 229 LEU cc_start: 0.7030 (mt) cc_final: 0.6471 (tt) REVERT: A 241 LEU cc_start: 0.8727 (tp) cc_final: 0.8461 (tt) REVERT: B 42 LYS cc_start: 0.8348 (tttt) cc_final: 0.7561 (tppt) REVERT: B 47 ARG cc_start: 0.8227 (tmm-80) cc_final: 0.7785 (ttp80) REVERT: B 64 LEU cc_start: 0.8654 (mt) cc_final: 0.8408 (tp) REVERT: B 168 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7189 (tpp) REVERT: B 241 LEU cc_start: 0.8704 (tp) cc_final: 0.8430 (tt) outliers start: 12 outliers final: 7 residues processed: 86 average time/residue: 0.2083 time to fit residues: 21.3872 Evaluate side-chains 86 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 168 MET Chi-restraints excluded: chain A residue 215 GLN 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 168 MET 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: 1.9990 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 158 ASN A 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4314 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= 0.184 Angle : 0.500 5.228 5644 Z= 0.260 Chirality : 0.036 0.119 650 Planarity : 0.002 0.017 664 Dihedral : 6.931 49.438 952 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.94 % Allowed : 16.91 % Favored : 80.15 % 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: 4.78 (0.39), residues: 476 helix: 3.88 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.73 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 184 HIS 0.001 0.000 HIS B 98 PHE 0.018 0.001 PHE A 202 TYR 0.011 0.001 TYR B 85 ARG 0.005 0.001 ARG B 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 81 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.531 Fit side-chains REVERT: A 168 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7130 (tpp) REVERT: A 182 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8105 (mm-30) REVERT: A 241 LEU cc_start: 0.8723 (tp) cc_final: 0.8414 (tt) REVERT: B 44 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7486 (tm-30) REVERT: B 47 ARG cc_start: 0.8210 (tmm-80) cc_final: 0.7830 (ttp80) REVERT: B 168 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7132 (tpp) REVERT: B 241 LEU cc_start: 0.8708 (tp) cc_final: 0.8391 (tt) outliers start: 12 outliers final: 7 residues processed: 70 average time/residue: 0.2503 time to fit residues: 21.3028 Evaluate side-chains 75 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 168 MET Chi-restraints excluded: chain A residue 215 GLN 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 168 MET 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: 0.0030 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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: 0.7877 moved from start: 0.4462 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= 0.167 Angle : 0.485 4.792 5644 Z= 0.253 Chirality : 0.035 0.110 650 Planarity : 0.002 0.017 664 Dihedral : 6.576 48.787 952 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.17 % Allowed : 15.93 % Favored : 79.90 % 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 (0.39), residues: 476 helix: 3.95 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.78 (0.79), residues: 86 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 0.017 0.001 PHE A 202 TYR 0.010 0.001 TYR B 85 ARG 0.005 0.001 ARG B 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 86 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 69 time to evaluate : 0.422 Fit side-chains REVERT: A 182 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7999 (mm-30) REVERT: A 241 LEU cc_start: 0.8813 (tp) cc_final: 0.8490 (tt) REVERT: B 45 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7390 (tm-30) REVERT: B 47 ARG cc_start: 0.8196 (tmm-80) cc_final: 0.7748 (ttp80) REVERT: B 241 LEU cc_start: 0.8799 (tp) cc_final: 0.8479 (tt) outliers start: 17 outliers final: 8 residues processed: 73 average time/residue: 0.2053 time to fit residues: 18.2253 Evaluate side-chains 69 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 215 GLN 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 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: 0.9980 chunk 25 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7904 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4156 Z= 0.189 Angle : 0.510 4.803 5644 Z= 0.269 Chirality : 0.035 0.119 650 Planarity : 0.003 0.021 664 Dihedral : 6.493 46.746 952 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.70 % Allowed : 19.12 % 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: 4.78 (0.39), residues: 476 helix: 3.91 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.90 (0.77), residues: 86 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 0.028 0.001 PHE A 202 TYR 0.010 0.001 TYR A 85 ARG 0.005 0.001 ARG B 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 73 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.473 Fit side-chains REVERT: A 182 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8033 (mm-30) REVERT: A 241 LEU cc_start: 0.8844 (tp) cc_final: 0.8404 (tt) REVERT: B 64 LEU cc_start: 0.8686 (tp) cc_final: 0.8172 (tp) REVERT: B 241 LEU cc_start: 0.8834 (tp) cc_final: 0.8396 (tt) outliers start: 11 outliers final: 9 residues processed: 65 average time/residue: 0.2070 time to fit residues: 16.2996 Evaluate side-chains 66 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 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 215 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4156 Z= 0.201 Angle : 0.523 4.825 5644 Z= 0.276 Chirality : 0.036 0.131 650 Planarity : 0.003 0.019 664 Dihedral : 6.385 44.723 952 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.94 % Allowed : 19.85 % 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: 4.72 (0.39), residues: 476 helix: 3.84 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -0.85 (0.76), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 184 HIS 0.001 0.000 HIS A 98 PHE 0.024 0.001 PHE A 202 TYR 0.011 0.001 TYR B 85 ARG 0.005 0.000 ARG B 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: 12 poor density : 57 time to evaluate : 0.441 Fit side-chains REVERT: A 182 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7999 (mm-30) REVERT: B 45 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7349 (tm-30) outliers start: 12 outliers final: 11 residues processed: 61 average time/residue: 0.2143 time to fit residues: 15.6748 Evaluate side-chains 66 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 215 GLN 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 39 GLU 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: 0.9980 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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: 0.7941 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4156 Z= 0.221 Angle : 0.535 4.820 5644 Z= 0.283 Chirality : 0.037 0.134 650 Planarity : 0.003 0.019 664 Dihedral : 6.377 42.895 952 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.94 % Allowed : 19.36 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.68 (0.39), residues: 476 helix: 3.81 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -0.92 (0.76), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 184 HIS 0.001 0.000 HIS A 98 PHE 0.025 0.001 PHE A 202 TYR 0.011 0.001 TYR B 85 ARG 0.005 0.000 ARG B 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 72 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.422 Fit side-chains REVERT: B 36 ARG cc_start: 0.7960 (mtm-85) cc_final: 0.7618 (mtm-85) outliers start: 12 outliers final: 10 residues processed: 64 average time/residue: 0.2143 time to fit residues: 16.6161 Evaluate side-chains 64 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 215 GLN 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 39 GLU 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: 3.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 0.0970 chunk 30 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 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: 0.7906 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4156 Z= 0.174 Angle : 0.506 4.770 5644 Z= 0.268 Chirality : 0.035 0.131 650 Planarity : 0.003 0.022 664 Dihedral : 6.161 43.421 952 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.70 % Allowed : 19.85 % 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: 4.75 (0.39), residues: 476 helix: 3.85 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -0.84 (0.77), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 184 HIS 0.001 0.000 HIS A 98 PHE 0.032 0.001 PHE B 202 TYR 0.008 0.001 TYR B 85 ARG 0.005 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: 11 poor density : 62 time to evaluate : 0.713 Fit side-chains REVERT: A 36 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7674 (mtp180) REVERT: A 182 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7875 (mm-30) outliers start: 11 outliers final: 9 residues processed: 65 average time/residue: 0.2231 time to fit residues: 17.7291 Evaluate side-chains 67 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 215 GLN 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 38 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.153364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.110173 restraints weight = 4172.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.110813 restraints weight = 3849.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.110813 restraints weight = 3655.383| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4156 Z= 0.216 Angle : 0.544 5.812 5644 Z= 0.288 Chirality : 0.037 0.135 650 Planarity : 0.003 0.023 664 Dihedral : 6.266 41.958 952 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.70 % Allowed : 20.59 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.68 (0.38), residues: 476 helix: 3.83 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -1.02 (0.72), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 184 HIS 0.001 0.000 HIS A 98 PHE 0.030 0.002 PHE B 202 TYR 0.011 0.001 TYR B 113 ARG 0.005 0.000 ARG B 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1104.87 seconds wall clock time: 27 minutes 38.88 seconds (1658.88 seconds total)