Starting phenix.real_space_refine on Mon Sep 23 17:03:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1j_36793/09_2024/8k1j_36793.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1j_36793/09_2024/8k1j_36793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1j_36793/09_2024/8k1j_36793.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1j_36793/09_2024/8k1j_36793.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1j_36793/09_2024/8k1j_36793.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1j_36793/09_2024/8k1j_36793.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 5 8.98 5 S 32 5.16 5 C 2706 2.51 5 N 616 2.21 5 O 710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4069 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1921 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain breaks: 1 Chain: "B" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1921 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain breaks: 1 Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 110 Unusual residues: {' K': 5, 'Y01': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 3.06, per 1000 atoms: 0.75 Number of scatterers: 4069 At special positions: 0 Unit cell: (69.3, 71.5, 90.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 5 19.00 S 32 16.00 O 710 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: 0.95 Conformation dependent library (CDL) restraints added in 452.8 milliseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 896 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 87.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 2 through 53 removed outlier: 5.638A pdb=" N ASP A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 removed outlier: 3.764A pdb=" N ARG A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 103 through 147 Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 155 through 183 Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 217 through 243 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'B' and resid 3 through 53 removed outlier: 5.634A pdb=" N ASP B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N HIS B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 70 removed outlier: 3.901A pdb=" N ARG B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 103 through 147 Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 155 through 183 Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 217 through 243 Processing helix chain 'B' and resid 244 through 247 333 hydrogen bonds defined for protein. 981 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 664 1.33 - 1.45: 1092 1.45 - 1.57: 2352 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 4156 Sorted by residual: bond pdb=" C ILE A 118 " pdb=" N PRO A 119 " ideal model delta sigma weight residual 1.335 1.343 -0.007 1.36e-02 5.41e+03 2.94e-01 bond pdb=" N LYS A 211 " pdb=" CA LYS A 211 " ideal model delta sigma weight residual 1.457 1.464 -0.007 1.29e-02 6.01e+03 2.64e-01 bond pdb=" C ILE B 118 " pdb=" N PRO B 119 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.36e-02 5.41e+03 2.43e-01 bond pdb=" C GLU A 70 " pdb=" N PRO A 71 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.36e-02 5.41e+03 2.42e-01 bond pdb=" CA LYS B 211 " pdb=" CB LYS B 211 " ideal model delta sigma weight residual 1.530 1.538 -0.008 1.69e-02 3.50e+03 2.33e-01 ... (remaining 4151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 5548 1.00 - 2.00: 75 2.00 - 3.00: 9 3.00 - 4.00: 6 4.00 - 5.00: 6 Bond angle restraints: 5644 Sorted by residual: angle pdb=" C THR A 210 " pdb=" N LYS A 211 " pdb=" CA LYS A 211 " ideal model delta sigma weight residual 121.54 125.68 -4.14 1.91e+00 2.74e-01 4.70e+00 angle pdb=" C THR B 210 " pdb=" N LYS B 211 " pdb=" CA LYS B 211 " ideal model delta sigma weight residual 121.54 125.66 -4.12 1.91e+00 2.74e-01 4.66e+00 angle pdb=" N GLY A 117 " pdb=" CA GLY A 117 " pdb=" C GLY A 117 " ideal model delta sigma weight residual 113.18 116.98 -3.80 2.37e+00 1.78e-01 2.57e+00 angle pdb=" N GLY B 117 " pdb=" CA GLY B 117 " pdb=" C GLY B 117 " ideal model delta sigma weight residual 113.18 116.93 -3.75 2.37e+00 1.78e-01 2.51e+00 angle pdb=" CA TYR A 18 " pdb=" CB TYR A 18 " pdb=" CG TYR A 18 " ideal model delta sigma weight residual 113.90 116.71 -2.81 1.80e+00 3.09e-01 2.44e+00 ... (remaining 5639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 2433 16.20 - 32.39: 211 32.39 - 48.59: 36 48.59 - 64.79: 20 64.79 - 80.99: 12 Dihedral angle restraints: 2712 sinusoidal: 1310 harmonic: 1402 Sorted by residual: dihedral pdb=" CG ARG B 3 " pdb=" CD ARG B 3 " pdb=" NE ARG B 3 " pdb=" CZ ARG B 3 " ideal model delta sinusoidal sigma weight residual 180.00 -139.84 -40.16 2 1.50e+01 4.44e-03 8.87e+00 dihedral pdb=" CG ARG A 3 " pdb=" CD ARG A 3 " pdb=" NE ARG A 3 " pdb=" CZ ARG A 3 " ideal model delta sinusoidal sigma weight residual -180.00 -139.85 -40.15 2 1.50e+01 4.44e-03 8.87e+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 80.30 -80.30 1 3.00e+01 1.11e-03 8.87e+00 ... (remaining 2709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 437 0.021 - 0.043: 96 0.043 - 0.064: 82 0.064 - 0.086: 20 0.086 - 0.107: 15 Chirality restraints: 650 Sorted by residual: 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 2.55 -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 2.55 -0.11 2.00e-01 2.50e+01 2.85e-01 chirality pdb=" CA VAL A 206 " pdb=" N VAL A 206 " pdb=" C VAL A 206 " pdb=" CB VAL A 206 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.10 2.00e-01 2.50e+01 2.73e-01 ... (remaining 647 not shown) Planarity restraints: 664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 18 " -0.009 2.00e-02 2.50e+03 6.07e-03 7.38e-01 pdb=" CG TYR B 18 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR B 18 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 18 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 18 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 18 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 18 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 18 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 18 " -0.009 2.00e-02 2.50e+03 5.99e-03 7.17e-01 pdb=" CG TYR A 18 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR A 18 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 18 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 18 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 18 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 18 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 18 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 113 " 0.006 2.00e-02 2.50e+03 4.21e-03 3.54e-01 pdb=" CG TYR A 113 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 113 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 113 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 113 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 113 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 113 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 113 " 0.002 2.00e-02 2.50e+03 ... (remaining 661 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.86: 1426 2.86 - 3.43: 4548 3.43 - 4.00: 7182 4.00 - 4.57: 10541 4.57 - 5.14: 14505 Nonbonded interactions: 38202 Sorted by model distance: nonbonded pdb=" OH TYR A 52 " pdb=" OD2 ASP B 58 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR A 96 " pdb=" OG1 THR A 196 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR B 96 " pdb=" OG1 THR B 196 " model vdw 2.301 3.040 nonbonded pdb=" O TYR A 113 " pdb=" OH TYR B 18 " model vdw 2.323 3.040 nonbonded pdb=" OH TYR A 18 " pdb=" O TYR B 113 " model vdw 2.324 3.040 ... (remaining 38197 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 248 or resid 301 through 303)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.380 Find NCS groups from input model: 0.130 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:10.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.012 4156 Z= 0.081 Angle : 0.341 4.999 5644 Z= 0.179 Chirality : 0.031 0.107 650 Planarity : 0.002 0.015 664 Dihedral : 13.842 80.987 1816 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.90 (0.38), residues: 476 helix: 4.48 (0.22), residues: 384 sheet: None (None), residues: 0 loop : 0.94 (0.85), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 184 HIS 0.002 0.000 HIS A 72 PHE 0.004 0.000 PHE A 135 TYR 0.014 0.001 TYR B 18 ARG 0.001 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.7254 (tt) cc_final: 0.6627 (tp) REVERT: B 244 LEU cc_start: 0.7241 (tt) cc_final: 0.6615 (tp) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 1.5599 time to fit residues: 91.2533 Evaluate side-chains 51 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4156 Z= 0.214 Angle : 0.486 6.261 5644 Z= 0.266 Chirality : 0.037 0.122 650 Planarity : 0.003 0.014 664 Dihedral : 6.564 46.794 952 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.23 % Allowed : 10.78 % 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: 5.29 (0.37), residues: 476 helix: 4.09 (0.23), residues: 390 sheet: None (None), residues: 0 loop : 0.28 (0.78), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 184 HIS 0.002 0.001 HIS A 98 PHE 0.012 0.002 PHE B 223 TYR 0.024 0.002 TYR A 85 ARG 0.005 0.000 ARG B 137 *********************** 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 57 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 180 GLN cc_start: 0.7849 (tp40) cc_final: 0.7463 (mp10) REVERT: A 244 LEU cc_start: 0.7245 (tt) cc_final: 0.6835 (tp) REVERT: B 180 GLN cc_start: 0.7850 (tp40) cc_final: 0.7462 (mp10) REVERT: B 244 LEU cc_start: 0.7233 (tt) cc_final: 0.6820 (tp) outliers start: 5 outliers final: 5 residues processed: 53 average time/residue: 1.6888 time to fit residues: 91.8980 Evaluate side-chains 54 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 245 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 29 optimal weight: 0.0060 chunk 12 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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: 0.7766 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4156 Z= 0.158 Angle : 0.426 5.420 5644 Z= 0.233 Chirality : 0.035 0.139 650 Planarity : 0.003 0.023 664 Dihedral : 5.952 41.433 952 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.72 % Allowed : 11.03 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.30 (0.37), residues: 476 helix: 4.11 (0.23), residues: 390 sheet: None (None), residues: 0 loop : 0.21 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 184 HIS 0.001 0.000 HIS A 98 PHE 0.011 0.001 PHE A 135 TYR 0.018 0.001 TYR B 85 ARG 0.005 0.000 ARG B 137 *********************** 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 60 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.381 Fit side-chains REVERT: A 140 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7134 (mm) REVERT: A 180 GLN cc_start: 0.7980 (tp40) cc_final: 0.7578 (mp10) REVERT: A 190 TYR cc_start: 0.8781 (t80) cc_final: 0.8429 (t80) REVERT: A 244 LEU cc_start: 0.7323 (tt) cc_final: 0.6939 (tp) REVERT: B 140 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7161 (mm) REVERT: B 180 GLN cc_start: 0.7993 (tp40) cc_final: 0.7594 (mp10) REVERT: B 190 TYR cc_start: 0.8779 (t80) cc_final: 0.8416 (t80) outliers start: 7 outliers final: 3 residues processed: 54 average time/residue: 1.8635 time to fit residues: 103.3718 Evaluate side-chains 58 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 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: 0.7872 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4156 Z= 0.209 Angle : 0.472 5.173 5644 Z= 0.258 Chirality : 0.037 0.153 650 Planarity : 0.003 0.023 664 Dihedral : 5.482 35.328 952 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.45 % Allowed : 12.01 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.04 (0.38), residues: 476 helix: 3.95 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.05 (0.74), 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 0.008 0.001 PHE A 16 TYR 0.028 0.002 TYR B 85 ARG 0.008 0.001 ARG A 245 *********************** 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 73 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.383 Fit side-chains REVERT: A 39 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7175 (pt0) REVERT: A 180 GLN cc_start: 0.7940 (tp40) cc_final: 0.7534 (mp10) REVERT: A 190 TYR cc_start: 0.8862 (t80) cc_final: 0.8498 (t80) REVERT: B 140 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7180 (mm) REVERT: B 180 GLN cc_start: 0.7948 (tp40) cc_final: 0.7543 (mp10) REVERT: B 190 TYR cc_start: 0.8850 (t80) cc_final: 0.8474 (t80) outliers start: 10 outliers final: 3 residues processed: 68 average time/residue: 1.6919 time to fit residues: 117.9888 Evaluate side-chains 67 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4156 Z= 0.195 Angle : 0.468 6.684 5644 Z= 0.258 Chirality : 0.036 0.154 650 Planarity : 0.003 0.027 664 Dihedral : 5.209 32.437 952 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.45 % Allowed : 13.73 % Favored : 83.82 % 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: 4.85 (0.38), residues: 476 helix: 3.83 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.18 (0.73), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 184 HIS 0.002 0.000 HIS B 98 PHE 0.009 0.001 PHE B 135 TYR 0.020 0.001 TYR B 85 ARG 0.007 0.001 ARG B 245 *********************** 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 74 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.408 Fit side-chains REVERT: A 39 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7299 (pt0) REVERT: A 180 GLN cc_start: 0.7859 (tp40) cc_final: 0.7432 (mp10) REVERT: A 190 TYR cc_start: 0.8866 (t80) cc_final: 0.8473 (t80) REVERT: B 140 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7194 (mm) REVERT: B 180 GLN cc_start: 0.7871 (tp40) cc_final: 0.7443 (mp10) REVERT: B 190 TYR cc_start: 0.8851 (t80) cc_final: 0.8444 (t80) outliers start: 10 outliers final: 3 residues processed: 68 average time/residue: 1.6322 time to fit residues: 113.9023 Evaluate side-chains 69 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.0170 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.7418 ------------------------------------------------------------------------------- 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: 0.7898 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4156 Z= 0.200 Angle : 0.479 7.750 5644 Z= 0.262 Chirality : 0.036 0.166 650 Planarity : 0.003 0.025 664 Dihedral : 5.007 34.541 952 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.98 % Allowed : 15.20 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.73 (0.38), residues: 476 helix: 3.79 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.41 (0.70), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 184 HIS 0.002 0.000 HIS A 98 PHE 0.007 0.001 PHE A 16 TYR 0.019 0.001 TYR B 85 ARG 0.005 0.000 ARG B 137 *********************** 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 69 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.435 Fit side-chains REVERT: A 39 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7329 (pt0) REVERT: A 156 MET cc_start: 0.5996 (tpp) cc_final: 0.5770 (tpt) REVERT: A 180 GLN cc_start: 0.7838 (tp40) cc_final: 0.7428 (mp10) REVERT: A 190 TYR cc_start: 0.8877 (t80) cc_final: 0.8468 (t80) REVERT: B 180 GLN cc_start: 0.7845 (tp40) cc_final: 0.7438 (mp10) REVERT: B 190 TYR cc_start: 0.8873 (t80) cc_final: 0.8453 (t80) outliers start: 4 outliers final: 3 residues processed: 65 average time/residue: 1.7150 time to fit residues: 114.1888 Evaluate side-chains 65 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 159 MET 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: 3.9990 chunk 25 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4156 Z= 0.217 Angle : 0.498 8.169 5644 Z= 0.274 Chirality : 0.037 0.179 650 Planarity : 0.003 0.027 664 Dihedral : 4.926 37.261 952 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.72 % Allowed : 13.97 % Favored : 84.31 % 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: 4.61 (0.38), residues: 476 helix: 3.71 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.49 (0.69), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 78 HIS 0.002 0.000 HIS A 98 PHE 0.010 0.001 PHE A 135 TYR 0.020 0.002 TYR B 85 ARG 0.006 0.000 ARG B 137 *********************** 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 69 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.422 Fit side-chains REVERT: A 39 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7338 (pt0) REVERT: A 47 ARG cc_start: 0.7113 (ttp80) cc_final: 0.6852 (ttt-90) REVERT: A 140 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7221 (mm) REVERT: A 180 GLN cc_start: 0.7789 (tp40) cc_final: 0.7267 (mp10) REVERT: A 190 TYR cc_start: 0.8884 (t80) cc_final: 0.8457 (t80) REVERT: B 180 GLN cc_start: 0.7788 (tp40) cc_final: 0.7264 (mp10) REVERT: B 190 TYR cc_start: 0.8879 (t80) cc_final: 0.8509 (t80) outliers start: 7 outliers final: 3 residues processed: 64 average time/residue: 1.7627 time to fit residues: 115.4827 Evaluate side-chains 66 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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: 0.7926 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4156 Z= 0.218 Angle : 0.502 8.257 5644 Z= 0.273 Chirality : 0.037 0.174 650 Planarity : 0.003 0.026 664 Dihedral : 4.910 38.113 952 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.47 % Allowed : 14.71 % Favored : 83.82 % 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: 4.60 (0.38), residues: 476 helix: 3.69 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.44 (0.69), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 78 HIS 0.002 0.000 HIS A 98 PHE 0.008 0.001 PHE B 109 TYR 0.018 0.002 TYR B 85 ARG 0.006 0.000 ARG B 137 *********************** 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 66 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.449 Fit side-chains REVERT: A 39 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7342 (pt0) REVERT: A 140 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7220 (mm) REVERT: A 180 GLN cc_start: 0.7778 (tp40) cc_final: 0.7250 (mp10) REVERT: A 190 TYR cc_start: 0.8881 (t80) cc_final: 0.8512 (t80) REVERT: B 180 GLN cc_start: 0.7787 (tp40) cc_final: 0.7259 (mp10) REVERT: B 190 TYR cc_start: 0.8876 (t80) cc_final: 0.8497 (t80) outliers start: 6 outliers final: 5 residues processed: 62 average time/residue: 1.7737 time to fit residues: 112.6341 Evaluate side-chains 66 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 MET 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: 0.6980 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4156 Z= 0.197 Angle : 0.492 8.596 5644 Z= 0.269 Chirality : 0.036 0.176 650 Planarity : 0.003 0.025 664 Dihedral : 4.846 38.815 952 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.72 % Allowed : 15.44 % Favored : 82.84 % 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: 3.72 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.42 (0.69), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 184 HIS 0.002 0.000 HIS B 98 PHE 0.008 0.001 PHE B 109 TYR 0.016 0.001 TYR B 85 ARG 0.005 0.000 ARG B 137 *********************** 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 63 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.404 Fit side-chains REVERT: A 39 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7342 (pt0) REVERT: A 140 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7213 (mm) REVERT: A 180 GLN cc_start: 0.7753 (tp40) cc_final: 0.7220 (mp10) REVERT: B 180 GLN cc_start: 0.7763 (tp40) cc_final: 0.7231 (mp10) REVERT: B 190 TYR cc_start: 0.8870 (t80) cc_final: 0.8460 (t80) outliers start: 7 outliers final: 5 residues processed: 59 average time/residue: 1.7403 time to fit residues: 105.2013 Evaluate side-chains 61 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7910 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4156 Z= 0.190 Angle : 0.487 8.398 5644 Z= 0.267 Chirality : 0.036 0.174 650 Planarity : 0.003 0.029 664 Dihedral : 4.816 39.635 952 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.72 % Allowed : 15.44 % Favored : 82.84 % 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: 4.66 (0.38), residues: 476 helix: 3.73 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.39 (0.69), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 184 HIS 0.002 0.000 HIS A 98 PHE 0.008 0.001 PHE B 109 TYR 0.015 0.001 TYR B 85 ARG 0.006 0.000 ARG B 137 ********************** 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 66 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.419 Fit side-chains REVERT: A 140 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7210 (mm) REVERT: A 180 GLN cc_start: 0.7735 (tp40) cc_final: 0.7199 (mp10) REVERT: A 190 TYR cc_start: 0.8893 (t80) cc_final: 0.8536 (t80) REVERT: B 180 GLN cc_start: 0.7749 (tp40) cc_final: 0.7214 (mp10) REVERT: B 190 TYR cc_start: 0.8886 (t80) cc_final: 0.8520 (t80) outliers start: 7 outliers final: 5 residues processed: 61 average time/residue: 1.7831 time to fit residues: 111.4515 Evaluate side-chains 65 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.180714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.131108 restraints weight = 4148.328| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.91 r_work: 0.3287 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4156 Z= 0.215 Angle : 0.504 8.224 5644 Z= 0.277 Chirality : 0.037 0.175 650 Planarity : 0.003 0.030 664 Dihedral : 4.855 40.817 952 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.96 % Allowed : 15.69 % Favored : 82.35 % 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 (0.37), residues: 476 helix: 3.79 (0.24), residues: 386 sheet: None (None), residues: 0 loop : -0.26 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 184 HIS 0.002 0.001 HIS A 98 PHE 0.026 0.001 PHE B 135 TYR 0.015 0.001 TYR B 85 ARG 0.007 0.001 ARG B 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2094.26 seconds wall clock time: 37 minutes 24.49 seconds (2244.49 seconds total)