Starting phenix.real_space_refine on Thu Dec 7 15:48:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqq_32092/12_2023/7vqq_32092.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqq_32092/12_2023/7vqq_32092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqq_32092/12_2023/7vqq_32092.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqq_32092/12_2023/7vqq_32092.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqq_32092/12_2023/7vqq_32092.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqq_32092/12_2023/7vqq_32092.pdb" } resolution = 2.9 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= 0.004 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: 3 Type Number sf(0) Gaussians C 1158 2.51 5 N 327 2.21 5 O 483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 122": "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: 1968 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 656 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 91, 650 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Conformer: "B" Number of residues, atoms: 91, 650 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} bond proxies already assigned to first conformer: 659 Chain: "B" Number of atoms: 656 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 91, 650 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Conformer: "B" Number of residues, atoms: 91, 650 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} bond proxies already assigned to first conformer: 659 Chain: "C" Number of atoms: 656 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 91, 650 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Conformer: "B" Number of residues, atoms: 91, 650 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} bond proxies already assigned to first conformer: 659 Time building chain proxies: 2.18, per 1000 atoms: 1.11 Number of scatterers: 1968 At special positions: 0 Unit cell: (80.3, 83.6, 30.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 483 8.00 N 327 7.00 C 1158 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: 0.77 Conformation dependent library (CDL) restraints added in 834.3 milliseconds 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 444 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 58 removed outlier: 6.676A pdb=" N SER A 56 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER B 56 " --> pdb=" O SER C 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 removed outlier: 6.353A pdb=" N ASN B 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 70 removed outlier: 3.503A pdb=" N SER C 70 " --> pdb=" O GLN B 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 73 through 74 removed outlier: 6.734A pdb=" N GLN A 73 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLN B 73 " --> pdb=" O GLY C 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.345A pdb=" N TYR A 81 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR B 81 " --> pdb=" O GLY C 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 93 through 96 10 hydrogen bonds defined for protein. 30 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: 0.42 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 333 1.28 - 1.35: 322 1.35 - 1.41: 337 1.41 - 1.47: 346 1.47 - 1.54: 681 Bond restraints: 2019 Sorted by residual: bond pdb=" C ALA A 105 " pdb=" N PRO A 106 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.12e-02 7.97e+03 5.02e+00 bond pdb=" C TYR B 91 " pdb=" N GLY B 92 " ideal model delta sigma weight residual 1.330 1.308 0.021 1.31e-02 5.83e+03 2.64e+00 bond pdb=" CA GLY B 92 " pdb=" C GLY B 92 " ideal model delta sigma weight residual 1.517 1.496 0.021 1.43e-02 4.89e+03 2.24e+00 bond pdb=" CA GLN C 118 " pdb=" CB GLN C 118 " ideal model delta sigma weight residual 1.530 1.506 0.024 1.69e-02 3.50e+03 2.04e+00 bond pdb=" N GLY A 65 " pdb=" CA GLY A 65 " ideal model delta sigma weight residual 1.460 1.442 0.018 1.26e-02 6.30e+03 2.03e+00 ... (remaining 2014 not shown) Histogram of bond angle deviations from ideal: 102.21 - 107.61: 55 107.61 - 113.02: 865 113.02 - 118.43: 488 118.43 - 123.83: 1288 123.83 - 129.24: 37 Bond angle restraints: 2733 Sorted by residual: angle pdb=" CA TYR C 38 " pdb=" CB TYR C 38 " pdb=" CG TYR C 38 " ideal model delta sigma weight residual 113.90 108.92 4.98 1.80e+00 3.09e-01 7.64e+00 angle pdb=" CA GLY C 82 " pdb=" C GLY C 82 " pdb=" N SER C 83 " ideal model delta sigma weight residual 115.49 118.02 -2.53 1.03e+00 9.43e-01 6.01e+00 angle pdb=" CA GLY C 76 " pdb=" C GLY C 76 " pdb=" N SER C 77 " ideal model delta sigma weight residual 115.09 118.18 -3.09 1.29e+00 6.01e-01 5.73e+00 angle pdb=" CA TYR A 38 " pdb=" CB TYR A 38 " pdb=" CG TYR A 38 " ideal model delta sigma weight residual 113.90 109.60 4.30 1.80e+00 3.09e-01 5.72e+00 angle pdb=" N GLY A 59 " pdb=" CA GLY A 59 " pdb=" C GLY A 59 " ideal model delta sigma weight residual 113.18 118.73 -5.55 2.37e+00 1.78e-01 5.49e+00 ... (remaining 2728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.17: 1007 13.17 - 26.34: 117 26.34 - 39.51: 19 39.51 - 52.68: 4 52.68 - 65.85: 2 Dihedral angle restraints: 1149 sinusoidal: 390 harmonic: 759 Sorted by residual: dihedral pdb=" CA TYR A 91 " pdb=" C TYR A 91 " pdb=" N GLY A 92 " pdb=" CA GLY A 92 " ideal model delta harmonic sigma weight residual -180.00 -163.21 -16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA TYR C 91 " pdb=" C TYR C 91 " pdb=" N GLY C 92 " pdb=" CA GLY C 92 " ideal model delta harmonic sigma weight residual -180.00 -163.70 -16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA TYR B 58 " pdb=" C TYR B 58 " pdb=" N GLY B 59 " pdb=" CA GLY B 59 " ideal model delta harmonic sigma weight residual 180.00 163.77 16.23 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 1146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 143 0.029 - 0.057: 52 0.057 - 0.086: 28 0.086 - 0.115: 13 0.115 - 0.143: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA TYR B 41 " pdb=" N TYR B 41 " pdb=" C TYR B 41 " pdb=" CB TYR B 41 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA TYR C 41 " pdb=" N TYR C 41 " pdb=" C TYR C 41 " pdb=" CB TYR C 41 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA TYR A 41 " pdb=" N TYR A 41 " pdb=" C TYR A 41 " pdb=" CB TYR A 41 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 240 not shown) Planarity restraints: 381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 71 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.05e+00 pdb=" N PRO A 72 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 71 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO C 72 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 72 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 72 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 103 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO A 104 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " 0.020 5.00e-02 4.00e+02 ... (remaining 378 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 504 2.77 - 3.30: 1610 3.30 - 3.83: 2713 3.83 - 4.37: 3259 4.37 - 4.90: 6117 Nonbonded interactions: 14203 Sorted by model distance: nonbonded pdb=" O SER A 39 " pdb=" OG SER A 39 " model vdw 2.233 2.440 nonbonded pdb=" O SER C 39 " pdb=" OG SER C 39 " model vdw 2.234 2.440 nonbonded pdb=" O THR A 71 " pdb=" OG1 THR A 71 " model vdw 2.396 2.440 nonbonded pdb=" O TYR B 41 " pdb=" OG SER B 44 " model vdw 2.410 2.440 nonbonded pdb=" O THR C 71 " pdb=" OG1 THR C 71 " model vdw 2.417 2.440 ... (remaining 14198 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 34 through 92 or resid 94 through 124)) selection = (chain 'B' and (resid 34 through 92 or resid 94 through 124)) selection = (chain 'C' and (resid 34 through 92 or resid 94 through 124)) } 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=0.00 max=1.00 mean=0.99 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.530 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.960 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 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 : 0.009 0.044 2019 Z= 0.569 Angle : 0.847 5.552 2733 Z= 0.486 Chirality : 0.047 0.143 243 Planarity : 0.006 0.044 381 Dihedral : 11.510 65.851 705 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.36 % Favored : 87.64 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % 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: -6.09 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.64 (0.17), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.003 TYR C 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.214 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1762 time to fit residues: 3.9697 Evaluate side-chains 15 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.212 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN B 88 GLN ** B 93 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN C 88 GLN C 94 GLN C 103 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2019 Z= 0.169 Angle : 0.590 4.413 2733 Z= 0.319 Chirality : 0.038 0.136 243 Planarity : 0.004 0.029 381 Dihedral : 4.421 15.848 315 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.83 % Allowed : 4.57 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.60 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.26 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR C 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 15 time to evaluate : 0.212 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 17 average time/residue: 0.3109 time to fit residues: 5.8642 Evaluate side-chains 17 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 13 time to evaluate : 0.179 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.0187 time to fit residues: 0.2958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 6 optimal weight: 0.0970 chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2019 Z= 0.237 Angle : 0.624 4.851 2733 Z= 0.339 Chirality : 0.039 0.145 243 Planarity : 0.004 0.030 381 Dihedral : 4.429 15.564 315 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.83 % Allowed : 6.85 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.44 (0.24), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.14 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR C 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 13 time to evaluate : 0.217 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 15 average time/residue: 0.2148 time to fit residues: 3.7924 Evaluate side-chains 17 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 13 time to evaluate : 0.217 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.0216 time to fit residues: 0.3501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2019 Z= 0.390 Angle : 0.740 6.061 2733 Z= 0.406 Chirality : 0.044 0.179 243 Planarity : 0.004 0.031 381 Dihedral : 4.786 15.687 315 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 1.83 % Allowed : 8.68 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.42 (0.24), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.13 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.002 TYR C 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 13 time to evaluate : 0.216 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 15 average time/residue: 0.2205 time to fit residues: 3.8784 Evaluate side-chains 17 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 13 time to evaluate : 0.215 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.0215 time to fit residues: 0.3505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 0.0980 chunk 6 optimal weight: 0.3980 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2019 Z= 0.187 Angle : 0.594 4.597 2733 Z= 0.320 Chirality : 0.039 0.142 243 Planarity : 0.003 0.027 381 Dihedral : 4.251 15.108 315 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.37 % Allowed : 9.13 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.22 (0.24), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR C 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 13 time to evaluate : 0.228 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 15 average time/residue: 0.2174 time to fit residues: 3.8409 Evaluate side-chains 16 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 13 time to evaluate : 0.211 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0180 time to fit residues: 0.2436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.2980 chunk 26 optimal weight: 8.9990 chunk 21 optimal weight: 0.0770 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 93 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2019 Z= 0.102 Angle : 0.492 3.895 2733 Z= 0.261 Chirality : 0.035 0.117 243 Planarity : 0.003 0.024 381 Dihedral : 3.558 13.862 315 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.37 % Allowed : 9.13 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.88 (0.25), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR B 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 14 time to evaluate : 0.223 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 16 average time/residue: 0.2059 time to fit residues: 3.8980 Evaluate side-chains 14 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.218 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0225 time to fit residues: 0.3258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 0.0010 chunk 24 optimal weight: 2.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2019 Z= 0.160 Angle : 0.544 4.192 2733 Z= 0.291 Chirality : 0.036 0.111 243 Planarity : 0.003 0.027 381 Dihedral : 3.856 14.544 315 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.46 % Allowed : 11.42 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.82 (0.25), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR B 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.225 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 14 average time/residue: 0.2396 time to fit residues: 3.8968 Evaluate side-chains 14 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.162 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.1988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 6.9990 chunk 24 optimal weight: 0.1980 chunk 14 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2019 Z= 0.206 Angle : 0.589 4.652 2733 Z= 0.317 Chirality : 0.038 0.139 243 Planarity : 0.003 0.026 381 Dihedral : 4.058 14.557 315 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.37 % Allowed : 10.50 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.83 (0.25), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR C 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 13 time to evaluate : 0.295 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 14 average time/residue: 0.2314 time to fit residues: 3.7999 Evaluate side-chains 15 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 13 time to evaluate : 0.218 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0218 time to fit residues: 0.3176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 62 GLN ** A 93 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2019 Z= 0.197 Angle : 0.582 4.876 2733 Z= 0.312 Chirality : 0.038 0.135 243 Planarity : 0.003 0.023 381 Dihedral : 4.028 14.412 315 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.46 % Allowed : 11.87 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.81 (0.24), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR B 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.197 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 14 average time/residue: 0.2307 time to fit residues: 3.7964 Evaluate side-chains 14 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.216 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.2800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 62 GLN ** A 93 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2019 Z= 0.151 Angle : 0.549 4.652 2733 Z= 0.293 Chirality : 0.036 0.121 243 Planarity : 0.003 0.022 381 Dihedral : 3.839 14.003 315 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.46 % Allowed : 12.79 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (0.25), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR B 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.227 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 14 average time/residue: 0.2437 time to fit residues: 4.0066 Evaluate side-chains 14 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.226 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.2976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 62 GLN ** A 93 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.097869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.074296 restraints weight = 9854.928| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 4.06 r_work: 0.2979 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2019 Z= 0.410 Angle : 0.737 6.201 2733 Z= 0.402 Chirality : 0.043 0.174 243 Planarity : 0.004 0.023 381 Dihedral : 4.592 15.124 315 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.91 % Allowed : 11.87 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.97 (0.24), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR C 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 974.61 seconds wall clock time: 23 minutes 32.93 seconds (1412.93 seconds total)