Starting phenix.real_space_refine on Thu Dec 7 17:27:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqt_28545/12_2023/8eqt_28545_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqt_28545/12_2023/8eqt_28545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqt_28545/12_2023/8eqt_28545.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqt_28545/12_2023/8eqt_28545.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqt_28545/12_2023/8eqt_28545_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eqt_28545/12_2023/8eqt_28545_neut_updated.pdb" } resolution = 3.4 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 16 5.16 5 C 2122 2.51 5 N 490 2.21 5 O 574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3206 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1562 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "B" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1562 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Time building chain proxies: 2.24, per 1000 atoms: 0.70 Number of scatterers: 3206 At special positions: 0 Unit cell: (63.3, 59.924, 91.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 4 15.00 O 574 8.00 N 490 7.00 C 2122 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: 1.31 Conformation dependent library (CDL) restraints added in 529.8 milliseconds 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 10 helices and 4 sheets defined 46.1% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 43 through 62 Processing helix chain 'A' and resid 68 through 99 removed outlier: 4.095A pdb=" N SER A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 133 Processing helix chain 'A' and resid 137 through 140 No H-bonds generated for 'chain 'A' and resid 137 through 140' Processing helix chain 'A' and resid 220 through 223 No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'B' and resid 43 through 62 Processing helix chain 'B' and resid 68 through 99 removed outlier: 4.095A pdb=" N SER B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 133 Processing helix chain 'B' and resid 137 through 140 No H-bonds generated for 'chain 'B' and resid 137 through 140' Processing helix chain 'B' and resid 220 through 223 No H-bonds generated for 'chain 'B' and resid 220 through 223' Processing sheet with id= A, first strand: chain 'A' and resid 155 through 160 removed outlier: 6.214A pdb=" N HIS A 150 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N CYS A 200 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE A 232 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR A 217 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE A 230 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 183 through 186 Processing sheet with id= C, first strand: chain 'B' and resid 155 through 160 removed outlier: 6.214A pdb=" N HIS B 150 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N CYS B 200 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE B 232 " --> pdb=" O TYR B 215 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR B 217 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE B 230 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 183 through 186 190 hydrogen bonds defined for protein. 450 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: 0.80 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 464 1.31 - 1.44: 1042 1.44 - 1.57: 1764 1.57 - 1.69: 8 1.69 - 1.82: 18 Bond restraints: 3296 Sorted by residual: bond pdb=" C10 PEE B 402 " pdb=" O2 PEE B 402 " ideal model delta sigma weight residual 1.332 1.423 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C10 PEE A 401 " pdb=" O2 PEE A 401 " ideal model delta sigma weight residual 1.332 1.423 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C10 PEE B 401 " pdb=" O2 PEE B 401 " ideal model delta sigma weight residual 1.332 1.421 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C10 PEE A 402 " pdb=" O2 PEE A 402 " ideal model delta sigma weight residual 1.332 1.421 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C30 PEE B 402 " pdb=" O3 PEE B 402 " ideal model delta sigma weight residual 1.327 1.410 -0.083 2.00e-02 2.50e+03 1.74e+01 ... (remaining 3291 not shown) Histogram of bond angle deviations from ideal: 100.84 - 107.47: 98 107.47 - 114.10: 1900 114.10 - 120.72: 1386 120.72 - 127.35: 1060 127.35 - 133.98: 44 Bond angle restraints: 4488 Sorted by residual: angle pdb=" O3P PEE A 401 " pdb=" P PEE A 401 " pdb=" O4P PEE A 401 " ideal model delta sigma weight residual 92.91 110.27 -17.36 3.00e+00 1.11e-01 3.35e+01 angle pdb=" O3P PEE B 402 " pdb=" P PEE B 402 " pdb=" O4P PEE B 402 " ideal model delta sigma weight residual 92.91 110.27 -17.36 3.00e+00 1.11e-01 3.35e+01 angle pdb=" O3P PEE B 401 " pdb=" P PEE B 401 " pdb=" O4P PEE B 401 " ideal model delta sigma weight residual 92.91 109.90 -16.99 3.00e+00 1.11e-01 3.21e+01 angle pdb=" O3P PEE A 402 " pdb=" P PEE A 402 " pdb=" O4P PEE A 402 " ideal model delta sigma weight residual 92.91 109.90 -16.99 3.00e+00 1.11e-01 3.21e+01 angle pdb=" O1P PEE A 401 " pdb=" P PEE A 401 " pdb=" O2P PEE A 401 " ideal model delta sigma weight residual 119.43 108.94 10.49 3.00e+00 1.11e-01 1.22e+01 ... (remaining 4483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.38: 1822 29.38 - 58.76: 34 58.76 - 88.14: 10 88.14 - 117.52: 6 117.52 - 146.90: 6 Dihedral angle restraints: 1878 sinusoidal: 740 harmonic: 1138 Sorted by residual: dihedral pdb=" C4 PEE A 401 " pdb=" O4P PEE A 401 " pdb=" P PEE A 401 " pdb=" O2P PEE A 401 " ideal model delta sinusoidal sigma weight residual -75.78 71.12 -146.90 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C4 PEE B 402 " pdb=" O4P PEE B 402 " pdb=" P PEE B 402 " pdb=" O2P PEE B 402 " ideal model delta sinusoidal sigma weight residual -75.78 71.12 -146.90 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C3 PEE B 401 " pdb=" C1 PEE B 401 " pdb=" C2 PEE B 401 " pdb=" O3P PEE B 401 " ideal model delta sinusoidal sigma weight residual 62.73 -79.00 141.73 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 1875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 446 0.065 - 0.129: 54 0.129 - 0.193: 0 0.193 - 0.258: 0 0.258 - 0.322: 4 Chirality restraints: 504 Sorted by residual: chirality pdb=" C2 PEE B 402 " pdb=" C1 PEE B 402 " pdb=" C3 PEE B 402 " pdb=" O2 PEE B 402 " both_signs ideal model delta sigma weight residual False -2.33 -2.65 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C2 PEE A 401 " pdb=" C1 PEE A 401 " pdb=" C3 PEE A 401 " pdb=" O2 PEE A 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.65 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C2 PEE B 401 " pdb=" C1 PEE B 401 " pdb=" C3 PEE B 401 " pdb=" O2 PEE B 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.64 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 501 not shown) Planarity restraints: 530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 79 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.78e+00 pdb=" C PHE B 79 " 0.023 2.00e-02 2.50e+03 pdb=" O PHE B 79 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL B 80 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 79 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.78e+00 pdb=" C PHE A 79 " -0.023 2.00e-02 2.50e+03 pdb=" O PHE A 79 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL A 80 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 87 " 0.006 2.00e-02 2.50e+03 1.22e-02 1.49e+00 pdb=" C PHE A 87 " -0.021 2.00e-02 2.50e+03 pdb=" O PHE A 87 " 0.008 2.00e-02 2.50e+03 pdb=" N VAL A 88 " 0.007 2.00e-02 2.50e+03 ... (remaining 527 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 345 2.75 - 3.29: 3206 3.29 - 3.83: 5425 3.83 - 4.36: 6184 4.36 - 4.90: 10492 Nonbonded interactions: 25652 Sorted by model distance: nonbonded pdb=" O THR B 89 " pdb=" OG SER B 92 " model vdw 2.213 2.440 nonbonded pdb=" O THR A 89 " pdb=" OG SER A 92 " model vdw 2.213 2.440 nonbonded pdb=" O PRO B 42 " pdb=" OH TYR B 91 " model vdw 2.232 2.440 nonbonded pdb=" O PRO A 42 " pdb=" OH TYR A 91 " model vdw 2.232 2.440 nonbonded pdb=" OG1 THR A 151 " pdb=" O TYR A 154 " model vdw 2.248 2.440 ... (remaining 25647 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 238 or (resid 401 through 402 and (name N or na \ me C1 or name C10 or name C11 or name C2 or name C3 or name C30 or name C31 or n \ ame C4 or name C5 or name O1P or name O2 or name O2P or name O3 or name O3P or n \ ame O4 or name O4P or name O5 or name P )))) selection = (chain 'B' and (resid 40 through 238 or (resid 401 through 402 and (name N or na \ me C1 or name C10 or name C11 or name C2 or name C3 or name C30 or name C31 or n \ ame C4 or name C5 or name O1P or name O2 or name O2P or name O3 or name O3P or n \ ame O4 or name O4P or name O5 or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 3.420 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.600 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 : 0.006 0.091 3296 Z= 0.438 Angle : 0.888 17.361 4488 Z= 0.355 Chirality : 0.046 0.322 504 Planarity : 0.004 0.026 530 Dihedral : 17.012 146.900 1150 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.40), residues: 374 helix: 1.18 (0.37), residues: 164 sheet: 0.65 (0.56), residues: 90 loop : -0.77 (0.48), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 149 HIS 0.003 0.001 HIS A 204 PHE 0.005 0.001 PHE B 114 TYR 0.006 0.001 TYR B 156 ARG 0.001 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.355 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1476 time to fit residues: 31.2692 Evaluate side-chains 82 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.353 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN B 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3296 Z= 0.226 Angle : 0.528 4.838 4488 Z= 0.293 Chirality : 0.040 0.127 504 Planarity : 0.006 0.022 530 Dihedral : 17.847 148.106 480 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.62 % Allowed : 17.34 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.41), residues: 374 helix: 2.24 (0.38), residues: 166 sheet: 0.77 (0.57), residues: 86 loop : -1.10 (0.44), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 193 HIS 0.007 0.002 HIS A 78 PHE 0.026 0.002 PHE A 230 TYR 0.008 0.001 TYR A 154 ARG 0.001 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.390 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 106 average time/residue: 0.1614 time to fit residues: 20.5344 Evaluate side-chains 95 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.340 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0329 time to fit residues: 1.2531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 0.0060 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3296 Z= 0.189 Angle : 0.454 4.514 4488 Z= 0.251 Chirality : 0.039 0.122 504 Planarity : 0.005 0.022 530 Dihedral : 16.946 143.417 480 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.45 % Allowed : 21.68 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.42), residues: 374 helix: 2.25 (0.41), residues: 166 sheet: 0.68 (0.56), residues: 86 loop : -1.23 (0.42), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 193 HIS 0.007 0.002 HIS B 227 PHE 0.012 0.002 PHE A 230 TYR 0.015 0.001 TYR A 154 ARG 0.000 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.397 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 90 average time/residue: 0.1735 time to fit residues: 18.6210 Evaluate side-chains 83 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.374 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0410 time to fit residues: 0.5918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS B 182 HIS B 204 HIS B 227 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3296 Z= 0.196 Angle : 0.461 5.438 4488 Z= 0.256 Chirality : 0.039 0.125 504 Planarity : 0.004 0.021 530 Dihedral : 16.361 141.679 480 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.16 % Allowed : 22.83 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.42), residues: 374 helix: 2.28 (0.41), residues: 166 sheet: 0.48 (0.56), residues: 86 loop : -1.26 (0.43), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 193 HIS 0.003 0.001 HIS A 78 PHE 0.010 0.002 PHE B 56 TYR 0.006 0.001 TYR B 233 ARG 0.001 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 0.366 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 104 average time/residue: 0.1708 time to fit residues: 21.1304 Evaluate side-chains 78 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0357 time to fit residues: 0.6098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.0050 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3296 Z= 0.148 Angle : 0.439 4.712 4488 Z= 0.247 Chirality : 0.039 0.130 504 Planarity : 0.004 0.021 530 Dihedral : 16.134 149.466 480 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.73 % Allowed : 21.97 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.42), residues: 374 helix: 2.46 (0.41), residues: 166 sheet: 0.45 (0.55), residues: 86 loop : -1.35 (0.43), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 193 HIS 0.003 0.001 HIS A 78 PHE 0.011 0.001 PHE A 43 TYR 0.010 0.001 TYR B 154 ARG 0.001 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.307 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 93 average time/residue: 0.1727 time to fit residues: 19.0467 Evaluate side-chains 78 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.315 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0306 time to fit residues: 0.5186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 0.0030 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.0870 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 0.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS A 144 ASN B 78 HIS B 144 ASN B 213 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3296 Z= 0.143 Angle : 0.452 5.098 4488 Z= 0.252 Chirality : 0.039 0.126 504 Planarity : 0.004 0.021 530 Dihedral : 15.889 152.660 480 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.73 % Allowed : 22.25 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.42), residues: 374 helix: 2.49 (0.41), residues: 166 sheet: 0.22 (0.54), residues: 90 loop : -1.12 (0.45), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 193 HIS 0.002 0.001 HIS A 182 PHE 0.011 0.001 PHE A 43 TYR 0.009 0.001 TYR A 154 ARG 0.001 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 88 average time/residue: 0.1717 time to fit residues: 17.8942 Evaluate side-chains 78 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0317 time to fit residues: 0.5815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 78 HIS ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN B 78 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3296 Z= 0.201 Angle : 0.493 6.078 4488 Z= 0.275 Chirality : 0.039 0.130 504 Planarity : 0.004 0.021 530 Dihedral : 15.997 156.240 480 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.02 % Allowed : 22.54 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.42), residues: 374 helix: 2.37 (0.40), residues: 168 sheet: 0.20 (0.53), residues: 90 loop : -0.94 (0.46), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 193 HIS 0.001 0.000 HIS B 78 PHE 0.012 0.001 PHE A 43 TYR 0.005 0.001 TYR A 154 ARG 0.001 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.364 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 91 average time/residue: 0.1754 time to fit residues: 18.8953 Evaluate side-chains 85 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.359 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0335 time to fit residues: 0.8237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.0770 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN A 150 HIS A 227 HIS ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 150 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3296 Z= 0.157 Angle : 0.503 7.268 4488 Z= 0.281 Chirality : 0.039 0.129 504 Planarity : 0.004 0.020 530 Dihedral : 15.838 159.174 480 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.58 % Allowed : 24.57 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.42), residues: 374 helix: 2.28 (0.41), residues: 166 sheet: 0.44 (0.53), residues: 90 loop : -1.19 (0.45), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 149 HIS 0.002 0.001 HIS A 78 PHE 0.012 0.001 PHE B 43 TYR 0.006 0.001 TYR B 91 ARG 0.000 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.364 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 84 average time/residue: 0.1791 time to fit residues: 17.7874 Evaluate side-chains 79 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.373 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 0.0470 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3296 Z= 0.160 Angle : 0.475 4.514 4488 Z= 0.266 Chirality : 0.039 0.128 504 Planarity : 0.004 0.020 530 Dihedral : 15.769 161.795 480 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.16 % Allowed : 23.70 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.42), residues: 374 helix: 2.24 (0.41), residues: 166 sheet: 0.50 (0.53), residues: 90 loop : -1.11 (0.45), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 149 HIS 0.002 0.001 HIS A 78 PHE 0.012 0.001 PHE A 43 TYR 0.004 0.001 TYR A 91 ARG 0.001 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.368 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 87 average time/residue: 0.1895 time to fit residues: 19.8618 Evaluate side-chains 81 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.407 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0370 time to fit residues: 0.6182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3296 Z= 0.212 Angle : 0.517 6.248 4488 Z= 0.283 Chirality : 0.040 0.137 504 Planarity : 0.004 0.021 530 Dihedral : 15.936 164.219 480 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.29 % Allowed : 25.72 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.42), residues: 374 helix: 2.18 (0.41), residues: 166 sheet: 0.68 (0.53), residues: 88 loop : -1.26 (0.45), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 193 HIS 0.002 0.001 HIS B 78 PHE 0.012 0.001 PHE A 43 TYR 0.005 0.001 TYR A 91 ARG 0.000 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.376 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.1884 time to fit residues: 17.6927 Evaluate side-chains 77 residues out of total 346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.371 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.0270 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.099884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.074845 restraints weight = 6581.186| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 4.04 r_work: 0.2797 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3296 Z= 0.177 Angle : 0.513 7.885 4488 Z= 0.279 Chirality : 0.040 0.171 504 Planarity : 0.004 0.020 530 Dihedral : 15.867 164.280 480 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 26.88 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.42), residues: 374 helix: 2.13 (0.41), residues: 166 sheet: 0.65 (0.52), residues: 88 loop : -1.31 (0.45), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 193 HIS 0.002 0.001 HIS B 150 PHE 0.012 0.001 PHE A 43 TYR 0.004 0.001 TYR A 91 ARG 0.000 0.000 ARG A 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1249.50 seconds wall clock time: 23 minutes 18.46 seconds (1398.46 seconds total)