Starting phenix.real_space_refine on Sun Mar 10 17:03:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9g_34566/03_2024/8h9g_34566.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9g_34566/03_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_34566/03_2024/8h9g_34566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9g_34566/03_2024/8h9g_34566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9g_34566/03_2024/8h9g_34566.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9g_34566/03_2024/8h9g_34566.pdb" } 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 Residue "K GLU 7": "OE1" <-> "OE2" Residue "K TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 83": "OD1" <-> "OD2" Residue "K TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 156": "OD1" <-> "OD2" Residue "K TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "M ASP 11": "OD1" <-> "OD2" Residue "M PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 17": "OE1" <-> "OE2" Residue "M ASP 52": "OD1" <-> "OD2" Residue "M ASP 67": "OD1" <-> "OD2" Residue "M PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 90": "OD1" <-> "OD2" Residue "M PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.34, per 1000 atoms: 0.69 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 611.9 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: 0.32 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: 0.81 Time building geometry restraints manager: 1.35 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: 98.98 - 105.98: 82 105.98 - 112.99: 1851 112.99 - 119.99: 1288 119.99 - 127.00: 1417 127.00 - 134.00: 36 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 2.440 nonbonded pdb=" NH1 ARG K 121 " pdb=" O ILE M 18 " model vdw 2.295 2.520 nonbonded pdb=" NH2 ARG K 143 " pdb=" O GLU L 96 " model vdw 2.298 2.520 nonbonded pdb=" NH1 ARG K 154 " pdb=" O THR L 89 " model vdw 2.324 2.520 nonbonded pdb=" O GLU M 35 " pdb=" OG1 THR M 38 " model vdw 2.326 2.440 ... (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 ========== 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: 5.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 26.900 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.880 Find NCS groups from input model: 0.080 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:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.270 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.448 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: 1.1584 time to fit residues: 78.8113 Evaluate side-chains 50 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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: 0.5980 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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: 0.7675 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3456 Z= 0.179 Angle : 0.573 8.174 4674 Z= 0.309 Chirality : 0.040 0.140 508 Planarity : 0.005 0.044 603 Dihedral : 5.335 54.534 452 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.82 % Allowed : 15.21 % 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: 0.39 (0.42), residues: 413 helix: 1.05 (0.29), residues: 287 sheet: None (None), residues: 0 loop : -1.56 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 53 HIS 0.004 0.001 HIS K 103 PHE 0.010 0.001 PHE M 15 TYR 0.009 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 64 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.402 Fit side-chains REVERT: K 150 GLU cc_start: 0.6763 (mm-30) cc_final: 0.6561 (mp0) REVERT: K 165 MET cc_start: 0.7726 (tpp) cc_final: 0.6873 (mmp) REVERT: L 40 GLN cc_start: 0.6006 (pt0) cc_final: 0.5786 (pt0) outliers start: 10 outliers final: 5 residues processed: 59 average time/residue: 0.9644 time to fit residues: 59.1338 Evaluate side-chains 52 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 0.0470 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 0.0670 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 overall best weight: 1.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1749 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= 0.270 Angle : 0.601 8.372 4674 Z= 0.322 Chirality : 0.042 0.138 508 Planarity : 0.005 0.044 603 Dihedral : 5.281 55.672 452 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.23 % Allowed : 17.46 % Favored : 78.31 % 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: 0.96 (0.42), residues: 413 helix: 1.55 (0.30), residues: 282 sheet: None (None), residues: 0 loop : -1.43 (0.58), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 33 HIS 0.003 0.001 HIS K 103 PHE 0.015 0.002 PHE K 125 TYR 0.009 0.001 TYR K 51 ARG 0.003 0.001 ARG K 166 *********************** 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 63 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 48 time to evaluate : 0.399 Fit side-chains REVERT: K 150 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6634 (mp0) REVERT: K 165 MET cc_start: 0.7722 (tpp) cc_final: 0.6817 (mmp) REVERT: M 141 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6581 (pm20) outliers start: 15 outliers final: 8 residues processed: 58 average time/residue: 1.0755 time to fit residues: 64.5997 Evaluate side-chains 54 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 164 MET 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 83 ASP 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=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: 1.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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: 0.7753 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3456 Z= 0.364 Angle : 0.630 7.894 4674 Z= 0.340 Chirality : 0.044 0.145 508 Planarity : 0.005 0.041 603 Dihedral : 5.464 58.229 452 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.79 % Allowed : 18.31 % Favored : 76.90 % 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: 1.10 (0.42), residues: 413 helix: 1.62 (0.30), residues: 282 sheet: None (None), residues: 0 loop : -1.28 (0.59), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP K 176 HIS 0.002 0.001 HIS K 172 PHE 0.018 0.002 PHE K 125 TYR 0.011 0.002 TYR K 51 ARG 0.003 0.001 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 64 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 47 time to evaluate : 0.419 Fit side-chains REVERT: K 104 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7780 (mp) REVERT: K 150 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6721 (mp0) REVERT: K 165 MET cc_start: 0.7763 (tpp) cc_final: 0.7048 (mmp) REVERT: M 141 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6626 (pm20) outliers start: 17 outliers final: 8 residues processed: 59 average time/residue: 0.9954 time to fit residues: 60.9345 Evaluate side-chains 53 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 164 MET 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 83 ASP 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: 0.9990 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3456 Z= 0.173 Angle : 0.549 8.480 4674 Z= 0.294 Chirality : 0.039 0.134 508 Planarity : 0.005 0.039 603 Dihedral : 5.021 53.517 452 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.07 % Allowed : 20.28 % 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: 1.71 (0.43), residues: 413 helix: 2.19 (0.30), residues: 284 sheet: None (None), residues: 0 loop : -1.37 (0.59), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 12 HIS 0.003 0.001 HIS K 103 PHE 0.010 0.001 PHE M 15 TYR 0.006 0.001 TYR K 157 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 67 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 49 time to evaluate : 0.396 Fit side-chains REVERT: K 104 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7748 (mp) REVERT: K 150 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6688 (mp0) REVERT: K 165 MET cc_start: 0.7826 (tpp) cc_final: 0.6996 (mmp) REVERT: K 174 ILE cc_start: 0.5016 (tt) cc_final: 0.4293 (pp) REVERT: M 141 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6418 (pm20) outliers start: 18 outliers final: 7 residues processed: 63 average time/residue: 0.9298 time to fit residues: 60.8531 Evaluate side-chains 54 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 164 MET Chi-restraints excluded: chain L residue 71 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.0470 chunk 20 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3456 Z= 0.152 Angle : 0.539 9.307 4674 Z= 0.290 Chirality : 0.038 0.134 508 Planarity : 0.005 0.040 603 Dihedral : 4.753 50.468 452 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.23 % Allowed : 21.97 % 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: 2.05 (0.43), residues: 413 helix: 2.42 (0.30), residues: 287 sheet: None (None), residues: 0 loop : -1.28 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 12 HIS 0.003 0.001 HIS K 103 PHE 0.009 0.001 PHE M 15 TYR 0.015 0.001 TYR M 56 ARG 0.004 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 63 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 48 time to evaluate : 0.376 Fit side-chains REVERT: K 104 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7710 (mp) REVERT: K 150 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6756 (mp0) REVERT: K 165 MET cc_start: 0.7814 (tpp) cc_final: 0.7103 (mmp) REVERT: K 174 ILE cc_start: 0.5113 (tt) cc_final: 0.4458 (pp) REVERT: L 82 PHE cc_start: 0.6966 (m-10) cc_final: 0.6725 (m-10) REVERT: M 141 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6396 (pm20) outliers start: 15 outliers final: 6 residues processed: 59 average time/residue: 1.0833 time to fit residues: 66.0141 Evaluate side-chains 51 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 175 ASN Chi-restraints excluded: chain L residue 71 LEU 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: 9.9990 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3456 Z= 0.209 Angle : 0.568 9.064 4674 Z= 0.299 Chirality : 0.040 0.138 508 Planarity : 0.005 0.039 603 Dihedral : 4.837 53.283 452 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.95 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: 2.11 (0.43), residues: 413 helix: 2.46 (0.30), residues: 287 sheet: None (None), residues: 0 loop : -1.22 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 176 HIS 0.002 0.001 HIS K 103 PHE 0.012 0.001 PHE K 125 TYR 0.012 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 68 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 50 time to evaluate : 0.419 Fit side-chains REVERT: K 104 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7749 (mp) REVERT: K 150 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6754 (mp0) REVERT: K 165 MET cc_start: 0.7853 (tpp) cc_final: 0.7149 (mmp) REVERT: K 174 ILE cc_start: 0.5180 (tt) cc_final: 0.4477 (pp) REVERT: M 141 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6430 (pm20) outliers start: 18 outliers final: 9 residues processed: 65 average time/residue: 1.1746 time to fit residues: 78.6854 Evaluate side-chains 58 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 175 ASN Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 71 LEU 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: 0.6980 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 23 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7663 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3456 Z= 0.169 Angle : 0.545 9.584 4674 Z= 0.290 Chirality : 0.039 0.137 508 Planarity : 0.005 0.038 603 Dihedral : 4.750 52.450 452 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.79 % Allowed : 22.54 % Favored : 72.68 % 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: 2.22 (0.43), residues: 413 helix: 2.55 (0.30), residues: 287 sheet: None (None), residues: 0 loop : -1.21 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 12 HIS 0.003 0.001 HIS K 103 PHE 0.009 0.001 PHE K 125 TYR 0.012 0.001 TYR M 56 ARG 0.004 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 65 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 48 time to evaluate : 0.424 Fit side-chains REVERT: K 104 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7766 (mp) REVERT: K 150 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6742 (mp0) REVERT: K 152 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6601 (ttmt) REVERT: K 165 MET cc_start: 0.7838 (tpp) cc_final: 0.7166 (mmp) REVERT: K 174 ILE cc_start: 0.5276 (tt) cc_final: 0.4648 (pp) REVERT: L 48 ARG cc_start: 0.7417 (ppt170) cc_final: 0.7137 (ppt170) REVERT: M 141 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6421 (pm20) outliers start: 17 outliers final: 9 residues processed: 62 average time/residue: 1.1197 time to fit residues: 71.7099 Evaluate side-chains 57 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 152 LYS 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 71 LEU 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: 0.7980 chunk 23 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 0.0030 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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: 0.7646 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3456 Z= 0.154 Angle : 0.553 9.845 4674 Z= 0.293 Chirality : 0.039 0.136 508 Planarity : 0.005 0.039 603 Dihedral : 4.673 51.064 452 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.94 % Allowed : 22.54 % Favored : 73.52 % 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: 2.35 (0.43), residues: 413 helix: 2.65 (0.30), residues: 287 sheet: None (None), residues: 0 loop : -1.16 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 12 HIS 0.003 0.001 HIS K 103 PHE 0.008 0.001 PHE M 15 TYR 0.011 0.001 TYR M 56 ARG 0.004 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 60 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 46 time to evaluate : 0.336 Fit side-chains REVERT: K 104 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7715 (mp) REVERT: K 150 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6429 (mp0) REVERT: K 165 MET cc_start: 0.7845 (tpp) cc_final: 0.7174 (mmp) REVERT: K 174 ILE cc_start: 0.5240 (tt) cc_final: 0.4603 (pp) REVERT: L 48 ARG cc_start: 0.7400 (ppt170) cc_final: 0.7080 (ppt170) REVERT: M 118 MET cc_start: 0.7108 (tpp) cc_final: 0.6905 (tpp) REVERT: M 141 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6951 (pm20) outliers start: 14 outliers final: 7 residues processed: 58 average time/residue: 1.2312 time to fit residues: 73.4665 Evaluate side-chains 54 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 175 ASN Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain L residue 71 LEU 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: 0.0980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 0.0670 chunk 1 optimal weight: 0.8980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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: 0.7638 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3456 Z= 0.153 Angle : 0.558 9.978 4674 Z= 0.294 Chirality : 0.038 0.136 508 Planarity : 0.004 0.039 603 Dihedral : 4.610 50.119 452 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.10 % Allowed : 23.38 % Favored : 73.52 % 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: 2.41 (0.43), residues: 413 helix: 2.69 (0.30), residues: 287 sheet: None (None), residues: 0 loop : -1.13 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 12 HIS 0.003 0.001 HIS K 103 PHE 0.008 0.001 PHE M 15 TYR 0.011 0.001 TYR M 56 ARG 0.004 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 58 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 0.450 Fit side-chains REVERT: K 150 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6404 (mp0) REVERT: K 165 MET cc_start: 0.7836 (tpp) cc_final: 0.7095 (mmp) REVERT: K 173 MET cc_start: 0.6468 (tpt) cc_final: 0.6265 (tpp) REVERT: K 174 ILE cc_start: 0.5214 (tt) cc_final: 0.4611 (pp) REVERT: L 48 ARG cc_start: 0.7422 (ppt170) cc_final: 0.7125 (ppt170) REVERT: L 68 GLN cc_start: 0.7831 (tp-100) cc_final: 0.7615 (pm20) REVERT: M 141 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6926 (pm20) outliers start: 11 outliers final: 8 residues processed: 56 average time/residue: 1.2111 time to fit residues: 70.0258 Evaluate side-chains 53 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 147 VAL 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 71 LEU 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: 5.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4182 r_free = 0.4182 target = 0.178352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.143703 restraints weight = 4953.798| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.19 r_work: 0.3606 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: 0.7777 moved from start: 0.2959 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= 0.165 Angle : 0.552 9.850 4674 Z= 0.290 Chirality : 0.038 0.136 508 Planarity : 0.005 0.040 603 Dihedral : 4.600 50.437 452 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.66 % Allowed : 22.54 % 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: 2.45 (0.43), residues: 413 helix: 2.72 (0.30), residues: 287 sheet: None (None), residues: 0 loop : -1.09 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 176 HIS 0.003 0.001 HIS K 103 PHE 0.009 0.001 PHE K 125 TYR 0.010 0.001 TYR M 56 ARG 0.004 0.000 ARG K 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2389.42 seconds wall clock time: 43 minutes 3.39 seconds (2583.39 seconds total)