Starting phenix.real_space_refine on Thu Nov 14 02:13:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9g_34566/11_2024/8h9g_34566.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9g_34566/11_2024/8h9g_34566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9g_34566/11_2024/8h9g_34566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9g_34566/11_2024/8h9g_34566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9g_34566/11_2024/8h9g_34566.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9g_34566/11_2024/8h9g_34566.cif" } resolution = 2.95 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= 0.019 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: 4 Type Number sf(0) Gaussians S 11 5.16 5 C 2176 2.51 5 N 560 2.21 5 O 634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 3 Chain: "K" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1573 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 62} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1259 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 144} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 4.91, per 1000 atoms: 1.45 Number of scatterers: 3381 At special positions: 0 Unit cell: (79.57, 101.47, 205.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 11 16.00 O 634 8.00 N 560 7.00 C 2176 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: 0.92 Conformation dependent library (CDL) restraints added in 419.1 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 814 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 1 sheets defined 72.7% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'K' and resid 19 through 30 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 32 through 48 Processing helix chain 'K' and resid 54 through 121 removed outlier: 3.970A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix Processing helix chain 'K' and resid 122 through 182 Processing helix chain 'K' and resid 194 through 206 removed outlier: 4.074A pdb=" N LEU K 201 " --> pdb=" O CYS K 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 55 Processing helix chain 'L' and resid 67 through 83 removed outlier: 4.409A pdb=" N ARG L 73 " --> pdb=" O GLN L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 18 removed outlier: 3.761A pdb=" N ILE M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 43 Processing helix chain 'M' and resid 53 through 58 Processing helix chain 'M' and resid 64 through 75 Processing helix chain 'M' and resid 85 through 123 removed outlier: 3.810A pdb=" N VAL M 89 " --> pdb=" O TYR M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 130 removed outlier: 3.735A pdb=" N MET M 130 " --> pdb=" O PHE M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 139 removed outlier: 3.538A pdb=" N LEU M 135 " --> pdb=" O THR M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 143 removed outlier: 3.517A pdb=" N LYS M 143 " --> pdb=" O PRO M 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 140 through 143' Processing sheet with id=AA1, first strand: chain 'K' and resid 12 through 13 236 hydrogen bonds defined for protein. 702 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: 0.95 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1086 1.34 - 1.46: 576 1.46 - 1.57: 1773 1.57 - 1.69: 0 1.69 - 1.81: 21 Bond restraints: 3456 Sorted by residual: bond pdb=" CB PRO M 153 " pdb=" CG PRO M 153 " ideal model delta sigma weight residual 1.506 1.437 0.069 3.90e-02 6.57e+02 3.09e+00 bond pdb=" CG1 ILE M 10 " pdb=" CD1 ILE M 10 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.44e+00 bond pdb=" N SER K 184 " pdb=" CA SER K 184 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.26e+00 bond pdb=" CB VAL K 118 " pdb=" CG2 VAL K 118 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.88e+00 bond pdb=" N HIS K 122 " pdb=" CA HIS K 122 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.35e-02 5.49e+03 1.43e+00 ... (remaining 3451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 4325 1.34 - 2.68: 284 2.68 - 4.02: 54 4.02 - 5.36: 8 5.36 - 6.70: 3 Bond angle restraints: 4674 Sorted by residual: angle pdb=" N ILE L 103 " pdb=" CA ILE L 103 " pdb=" C ILE L 103 " ideal model delta sigma weight residual 113.42 107.77 5.65 1.17e+00 7.31e-01 2.34e+01 angle pdb=" CA ILE L 103 " pdb=" C ILE L 103 " pdb=" N GLU L 104 " ideal model delta sigma weight residual 118.90 115.40 3.50 9.40e-01 1.13e+00 1.38e+01 angle pdb=" C PHE K 125 " pdb=" N ASP K 126 " pdb=" CA ASP K 126 " ideal model delta sigma weight residual 120.72 115.25 5.47 1.67e+00 3.59e-01 1.07e+01 angle pdb=" N ARG K 121 " pdb=" CA ARG K 121 " pdb=" C ARG K 121 " ideal model delta sigma weight residual 111.75 115.83 -4.08 1.28e+00 6.10e-01 1.02e+01 angle pdb=" C ILE K 174 " pdb=" N ASN K 175 " pdb=" CA ASN K 175 " ideal model delta sigma weight residual 120.68 116.19 4.49 1.70e+00 3.46e-01 6.96e+00 ... (remaining 4669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 1855 16.69 - 33.37: 206 33.37 - 50.06: 40 50.06 - 66.75: 9 66.75 - 83.43: 3 Dihedral angle restraints: 2113 sinusoidal: 862 harmonic: 1251 Sorted by residual: dihedral pdb=" CA PHE L 100 " pdb=" C PHE L 100 " pdb=" N GLU L 101 " pdb=" CA GLU L 101 " ideal model delta harmonic sigma weight residual 180.00 -159.81 -20.19 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ARG K 121 " pdb=" C ARG K 121 " pdb=" N HIS K 122 " pdb=" CA HIS K 122 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ILE M 10 " pdb=" C ILE M 10 " pdb=" N ASP M 11 " pdb=" CA ASP M 11 " ideal model delta harmonic sigma weight residual 180.00 162.25 17.75 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 2110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 262 0.034 - 0.067: 169 0.067 - 0.101: 58 0.101 - 0.135: 15 0.135 - 0.169: 4 Chirality restraints: 508 Sorted by residual: chirality pdb=" CA ILE M 125 " pdb=" N ILE M 125 " pdb=" C ILE M 125 " pdb=" CB ILE M 125 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CA ILE L 103 " pdb=" N ILE L 103 " pdb=" C ILE L 103 " pdb=" CB ILE L 103 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CB VAL K 177 " pdb=" CA VAL K 177 " pdb=" CG1 VAL K 177 " pdb=" CG2 VAL K 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 505 not shown) Planarity restraints: 603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE K 71 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C ILE K 71 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE K 71 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS K 72 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU M 44 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO M 45 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO M 45 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO M 45 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE M 69 " 0.012 2.00e-02 2.50e+03 1.22e-02 2.60e+00 pdb=" CG PHE M 69 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE M 69 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE M 69 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE M 69 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE M 69 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE M 69 " 0.003 2.00e-02 2.50e+03 ... (remaining 600 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 925 2.80 - 3.33: 3321 3.33 - 3.85: 5378 3.85 - 4.38: 5777 4.38 - 4.90: 9940 Nonbonded interactions: 25341 Sorted by model distance: nonbonded pdb=" OG1 THR L 56 " pdb=" O GLY L 59 " model vdw 2.278 3.040 nonbonded pdb=" NH1 ARG K 121 " pdb=" O ILE M 18 " model vdw 2.295 3.120 nonbonded pdb=" NH2 ARG K 143 " pdb=" O GLU L 96 " model vdw 2.298 3.120 nonbonded pdb=" NH1 ARG K 154 " pdb=" O THR L 89 " model vdw 2.324 3.120 nonbonded pdb=" O GLU M 35 " pdb=" OG1 THR M 38 " model vdw 2.326 3.040 ... (remaining 25336 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.120 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:13.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 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 : 0.008 0.069 3456 Z= 0.483 Angle : 0.770 6.703 4674 Z= 0.449 Chirality : 0.048 0.169 508 Planarity : 0.005 0.042 603 Dihedral : 14.927 83.433 1299 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.39 (0.34), residues: 413 helix: -1.14 (0.25), residues: 283 sheet: None (None), residues: 0 loop : -2.34 (0.50), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP M 103 HIS 0.003 0.001 HIS K 103 PHE 0.028 0.003 PHE M 69 TYR 0.014 0.002 TYR K 51 ARG 0.004 0.001 ARG M 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.396 Fit side-chains REVERT: K 98 GLN cc_start: 0.7378 (mm110) cc_final: 0.7164 (mt0) REVERT: K 150 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6701 (mm-30) REVERT: K 165 MET cc_start: 0.7818 (tpp) cc_final: 0.7109 (mmp) REVERT: K 173 MET cc_start: 0.6700 (tpp) cc_final: 0.6448 (tpt) REVERT: L 40 GLN cc_start: 0.6025 (pt0) cc_final: 0.5796 (pt0) REVERT: L 96 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7909 (mt-10) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 1.1549 time to fit residues: 78.6535 Evaluate side-chains 50 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 88 GLN K 98 GLN K 115 GLN K 130 ASN K 175 ASN K 183 GLN M 136 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3456 Z= 0.226 Angle : 0.614 9.805 4674 Z= 0.331 Chirality : 0.042 0.155 508 Planarity : 0.005 0.044 603 Dihedral : 5.479 55.764 452 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.38 % Allowed : 14.65 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.22 (0.41), residues: 413 helix: 0.88 (0.29), residues: 287 sheet: None (None), residues: 0 loop : -1.52 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 53 HIS 0.004 0.001 HIS K 103 PHE 0.011 0.002 PHE K 58 TYR 0.010 0.001 TYR K 157 ARG 0.003 0.001 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.380 Fit side-chains REVERT: K 98 GLN cc_start: 0.7272 (mm-40) cc_final: 0.7071 (mt0) REVERT: K 150 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6511 (mm-30) REVERT: K 165 MET cc_start: 0.7752 (tpp) cc_final: 0.7123 (mmp) REVERT: L 40 GLN cc_start: 0.6054 (pt0) cc_final: 0.5800 (pt0) REVERT: L 96 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7917 (mt-10) REVERT: M 141 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6910 (pt0) outliers start: 12 outliers final: 5 residues processed: 63 average time/residue: 1.0247 time to fit residues: 66.8374 Evaluate side-chains 55 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 141 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 7.9990 chunk 24 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 0.0050 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 0.0010 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 23 GLN M 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3456 Z= 0.188 Angle : 0.567 8.660 4674 Z= 0.307 Chirality : 0.040 0.150 508 Planarity : 0.005 0.043 603 Dihedral : 5.063 53.360 452 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.23 % Allowed : 17.75 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.19 (0.43), residues: 413 helix: 1.74 (0.30), residues: 282 sheet: None (None), residues: 0 loop : -1.37 (0.59), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 33 HIS 0.004 0.001 HIS K 103 PHE 0.009 0.001 PHE L 82 TYR 0.008 0.001 TYR K 157 ARG 0.004 0.001 ARG L 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.410 Fit side-chains REVERT: K 150 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6572 (mp0) REVERT: K 154 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6704 (mmm-85) REVERT: K 165 MET cc_start: 0.7734 (tpp) cc_final: 0.7108 (mmp) REVERT: L 96 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7961 (mt-10) outliers start: 15 outliers final: 6 residues processed: 60 average time/residue: 1.0735 time to fit residues: 66.8269 Evaluate side-chains 51 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 0.0970 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3456 Z= 0.228 Angle : 0.565 9.188 4674 Z= 0.306 Chirality : 0.041 0.153 508 Planarity : 0.005 0.040 603 Dihedral : 5.104 54.577 452 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.51 % Allowed : 18.03 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.48 (0.43), residues: 413 helix: 1.95 (0.30), residues: 282 sheet: None (None), residues: 0 loop : -1.23 (0.59), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 33 HIS 0.003 0.001 HIS K 103 PHE 0.012 0.001 PHE K 125 TYR 0.012 0.001 TYR M 56 ARG 0.003 0.000 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.357 Fit side-chains REVERT: K 98 GLN cc_start: 0.7248 (mm-40) cc_final: 0.6969 (mt0) REVERT: K 104 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7747 (mp) REVERT: K 150 GLU cc_start: 0.6851 (mm-30) cc_final: 0.6600 (mp0) REVERT: K 165 MET cc_start: 0.7724 (tpp) cc_final: 0.6873 (mmp) REVERT: L 48 ARG cc_start: 0.7414 (ppt170) cc_final: 0.7148 (ppt170) REVERT: L 96 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7996 (mt-10) REVERT: M 141 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6424 (pm20) outliers start: 16 outliers final: 6 residues processed: 61 average time/residue: 1.0461 time to fit residues: 66.2062 Evaluate side-chains 53 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 141 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN M 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3456 Z= 0.181 Angle : 0.556 8.284 4674 Z= 0.297 Chirality : 0.039 0.149 508 Planarity : 0.005 0.041 603 Dihedral : 4.920 53.539 452 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.51 % Allowed : 20.56 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.72 (0.43), residues: 413 helix: 2.18 (0.30), residues: 284 sheet: None (None), residues: 0 loop : -1.33 (0.59), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 33 HIS 0.003 0.001 HIS K 103 PHE 0.009 0.001 PHE K 125 TYR 0.009 0.001 TYR M 56 ARG 0.004 0.000 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.457 Fit side-chains REVERT: K 104 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7728 (mp) REVERT: K 150 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6637 (mp0) REVERT: K 154 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6719 (mmm-85) REVERT: K 165 MET cc_start: 0.7699 (tpp) cc_final: 0.6929 (mmp) REVERT: K 174 ILE cc_start: 0.5138 (tt) cc_final: 0.4393 (pp) REVERT: L 48 ARG cc_start: 0.7463 (ppt170) cc_final: 0.7208 (ppt170) REVERT: L 96 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7965 (mt-10) REVERT: M 141 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6353 (pm20) outliers start: 16 outliers final: 5 residues processed: 58 average time/residue: 1.1181 time to fit residues: 67.2311 Evaluate side-chains 50 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 141 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 0.0980 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN M 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3456 Z= 0.166 Angle : 0.557 9.941 4674 Z= 0.299 Chirality : 0.039 0.147 508 Planarity : 0.005 0.041 603 Dihedral : 4.819 52.135 452 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.51 % Allowed : 20.85 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.97 (0.43), residues: 413 helix: 2.35 (0.30), residues: 284 sheet: None (None), residues: 0 loop : -1.17 (0.60), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 33 HIS 0.003 0.001 HIS K 103 PHE 0.008 0.001 PHE M 15 TYR 0.008 0.001 TYR M 56 ARG 0.003 0.000 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.406 Fit side-chains REVERT: K 150 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6655 (mp0) REVERT: K 154 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6755 (mmm-85) REVERT: K 165 MET cc_start: 0.7737 (tpp) cc_final: 0.7044 (mmp) REVERT: K 174 ILE cc_start: 0.5014 (tt) cc_final: 0.4322 (pp) REVERT: L 96 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7923 (mt-10) REVERT: M 141 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6341 (pm20) outliers start: 16 outliers final: 8 residues processed: 66 average time/residue: 1.1527 time to fit residues: 78.4405 Evaluate side-chains 57 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 141 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 175 ASN L 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3456 Z= 0.168 Angle : 0.561 9.125 4674 Z= 0.294 Chirality : 0.039 0.147 508 Planarity : 0.005 0.040 603 Dihedral : 4.721 52.432 452 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 5.35 % Allowed : 20.85 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.08 (0.43), residues: 413 helix: 2.41 (0.30), residues: 287 sheet: None (None), residues: 0 loop : -1.18 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 12 HIS 0.002 0.001 HIS K 103 PHE 0.010 0.001 PHE L 82 TYR 0.007 0.001 TYR M 56 ARG 0.004 0.000 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.427 Fit side-chains REVERT: K 104 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7689 (mp) REVERT: K 150 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6655 (mp0) REVERT: K 154 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6764 (mmm-85) REVERT: K 165 MET cc_start: 0.7840 (tpp) cc_final: 0.7108 (mmp) REVERT: K 174 ILE cc_start: 0.5232 (tt) cc_final: 0.4492 (pp) REVERT: L 48 ARG cc_start: 0.7339 (ppt170) cc_final: 0.7101 (ppt170) REVERT: L 96 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7889 (mt-10) REVERT: M 141 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6372 (pm20) outliers start: 19 outliers final: 10 residues processed: 60 average time/residue: 1.0667 time to fit residues: 66.2461 Evaluate side-chains 57 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 175 ASN Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 141 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.0010 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 175 ASN L 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3456 Z= 0.209 Angle : 0.570 10.048 4674 Z= 0.303 Chirality : 0.040 0.149 508 Planarity : 0.005 0.039 603 Dihedral : 4.767 53.313 452 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.07 % Allowed : 21.69 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.16 (0.43), residues: 413 helix: 2.48 (0.30), residues: 284 sheet: None (None), residues: 0 loop : -1.04 (0.61), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 12 HIS 0.002 0.001 HIS K 103 PHE 0.011 0.001 PHE K 125 TYR 0.007 0.001 TYR M 56 ARG 0.003 0.000 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.455 Fit side-chains REVERT: K 150 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6622 (mp0) REVERT: K 154 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.6770 (mmm-85) REVERT: K 165 MET cc_start: 0.7845 (tpp) cc_final: 0.7131 (mmp) REVERT: K 174 ILE cc_start: 0.5037 (tt) cc_final: 0.4387 (pp) REVERT: L 96 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7900 (mt-10) REVERT: M 82 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.4062 (pm20) REVERT: M 141 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6399 (pm20) outliers start: 18 outliers final: 10 residues processed: 61 average time/residue: 1.1230 time to fit residues: 70.8836 Evaluate side-chains 59 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 175 ASN Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 141 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.3980 chunk 23 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 0.0000 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 175 ASN L 40 GLN M 22 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3456 Z= 0.166 Angle : 0.573 9.827 4674 Z= 0.302 Chirality : 0.039 0.146 508 Planarity : 0.005 0.039 603 Dihedral : 4.716 52.399 452 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 5.07 % Allowed : 21.97 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.24 (0.43), residues: 413 helix: 2.54 (0.30), residues: 284 sheet: None (None), residues: 0 loop : -1.03 (0.60), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 12 HIS 0.002 0.001 HIS K 172 PHE 0.008 0.001 PHE K 125 TYR 0.008 0.001 TYR M 56 ARG 0.003 0.000 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.370 Fit side-chains REVERT: K 150 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6621 (mp0) REVERT: K 154 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.6767 (mmm-85) REVERT: K 165 MET cc_start: 0.7832 (tpp) cc_final: 0.7140 (mmp) REVERT: K 174 ILE cc_start: 0.5167 (tt) cc_final: 0.4486 (pp) REVERT: L 96 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7911 (mt-10) REVERT: M 82 GLU cc_start: 0.6039 (OUTLIER) cc_final: 0.4007 (pm20) REVERT: M 141 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6354 (pm20) outliers start: 18 outliers final: 11 residues processed: 65 average time/residue: 1.1762 time to fit residues: 79.0626 Evaluate side-chains 60 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 175 ASN Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 141 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 175 ASN L 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3456 Z= 0.195 Angle : 0.601 10.409 4674 Z= 0.316 Chirality : 0.039 0.147 508 Planarity : 0.005 0.041 603 Dihedral : 4.729 52.658 452 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.23 % Allowed : 23.38 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.23 (0.43), residues: 413 helix: 2.55 (0.30), residues: 284 sheet: None (None), residues: 0 loop : -1.07 (0.60), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 176 HIS 0.002 0.001 HIS K 103 PHE 0.009 0.001 PHE K 125 TYR 0.010 0.001 TYR K 148 ARG 0.003 0.000 ARG K 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.395 Fit side-chains REVERT: K 150 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6643 (mp0) REVERT: K 154 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.6770 (mmm-85) REVERT: K 165 MET cc_start: 0.7839 (tpp) cc_final: 0.7147 (mmp) REVERT: K 174 ILE cc_start: 0.5207 (tt) cc_final: 0.4572 (pp) REVERT: L 96 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7913 (mt-10) REVERT: M 82 GLU cc_start: 0.6044 (OUTLIER) cc_final: 0.4033 (pm20) REVERT: M 128 ASP cc_start: 0.8624 (p0) cc_final: 0.8412 (p0) REVERT: M 141 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6392 (pm20) outliers start: 15 outliers final: 11 residues processed: 60 average time/residue: 1.0859 time to fit residues: 67.4430 Evaluate side-chains 61 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 175 ASN Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 141 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 175 ASN L 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.177859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.143008 restraints weight = 4935.507| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.18 r_work: 0.3605 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3456 Z= 0.186 Angle : 0.593 10.235 4674 Z= 0.309 Chirality : 0.039 0.146 508 Planarity : 0.005 0.040 603 Dihedral : 4.692 52.403 452 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.51 % Allowed : 22.54 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.18 (0.43), residues: 413 helix: 2.52 (0.30), residues: 286 sheet: None (None), residues: 0 loop : -1.19 (0.59), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 176 HIS 0.004 0.001 HIS K 172 PHE 0.009 0.001 PHE K 125 TYR 0.007 0.001 TYR M 56 ARG 0.003 0.000 ARG K 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2348.34 seconds wall clock time: 42 minutes 44.91 seconds (2564.91 seconds total)