Starting phenix.real_space_refine on Mon Sep 23 11:46:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqq_32092/09_2024/7vqq_32092.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqq_32092/09_2024/7vqq_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_32092/09_2024/7vqq_32092.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqq_32092/09_2024/7vqq_32092.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqq_32092/09_2024/7vqq_32092.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqq_32092/09_2024/7vqq_32092.cif" } 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. Time to flip 30 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 2.41, per 1000 atoms: 1.22 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 491.6 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: 0.22 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: 0.36 Time building geometry restraints manager: 0.97 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: 0.00 - 1.11: 2352 1.11 - 2.22: 306 2.22 - 3.33: 57 3.33 - 4.44: 14 4.44 - 5.55: 4 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 3.040 nonbonded pdb=" O SER C 39 " pdb=" OG SER C 39 " model vdw 2.234 3.040 nonbonded pdb=" O THR A 71 " pdb=" OG1 THR A 71 " model vdw 2.396 3.040 nonbonded pdb=" O TYR B 41 " pdb=" OG SER B 44 " model vdw 2.410 3.040 nonbonded pdb=" O THR C 71 " pdb=" OG1 THR C 71 " model vdw 2.417 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.540 Find NCS groups from input model: 0.080 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:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.450 ------------------------------------------------------------------------------- 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 : 0.210 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1785 time to fit residues: 3.9960 Evaluate side-chains 15 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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: 5.9990 chunk 20 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.0010 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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 A 103 GLN B 88 GLN B 93 GLN B B 103 GLN C 88 GLN C 94 GLN C 103 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1500 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= 0.115 Angle : 0.538 4.016 2733 Z= 0.289 Chirality : 0.037 0.126 243 Planarity : 0.004 0.026 381 Dihedral : 4.052 15.164 315 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.37 % Allowed : 5.48 % Favored : 93.15 % 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: -5.46 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.16 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR A 97 *********************** 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: 3 poor density : 16 time to evaluate : 0.213 Fit side-chains REVERT: B 103 GLN cc_start: 0.7864 (mt0) cc_final: 0.7634 (mt0) outliers start: 3 outliers final: 3 residues processed: 18 average time/residue: 0.2984 time to fit residues: 5.9822 Evaluate side-chains 17 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 14 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER 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: 9.9990 chunk 20 optimal weight: 0.2980 chunk 16 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 overall best weight: 5.8588 ------------------------------------------------------------------------------- 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: 0.8407 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 2019 Z= 0.483 Angle : 0.781 6.040 2733 Z= 0.430 Chirality : 0.045 0.167 243 Planarity : 0.005 0.035 381 Dihedral : 4.949 15.759 315 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 2.74 % Allowed : 8.22 % Favored : 89.04 % 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: -5.54 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.21 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.003 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 21 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 15 time to evaluate : 0.198 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 18 average time/residue: 0.1805 time to fit residues: 3.8271 Evaluate side-chains 20 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 14 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- 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: 0.8352 moved from start: 0.1263 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= 0.201 Angle : 0.604 4.757 2733 Z= 0.326 Chirality : 0.040 0.150 243 Planarity : 0.004 0.028 381 Dihedral : 4.352 15.502 315 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.74 % Allowed : 8.68 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.29 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 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 19 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 13 time to evaluate : 0.217 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 16 average time/residue: 0.1963 time to fit residues: 3.7160 Evaluate side-chains 19 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 13 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.0020 chunk 10 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 overall best weight: 3.7794 ------------------------------------------------------------------------------- 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: 0.8377 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2019 Z= 0.314 Angle : 0.677 5.631 2733 Z= 0.368 Chirality : 0.042 0.166 243 Planarity : 0.004 0.029 381 Dihedral : 4.561 15.504 315 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.74 % Allowed : 8.68 % Favored : 88.58 % 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: -5.27 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.01 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.002 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 19 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 13 time to evaluate : 0.212 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 16 average time/residue: 0.1765 time to fit residues: 3.3431 Evaluate side-chains 19 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 13 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.8335 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2019 Z= 0.163 Angle : 0.569 4.359 2733 Z= 0.305 Chirality : 0.038 0.136 243 Planarity : 0.003 0.023 381 Dihedral : 4.101 14.851 315 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.74 % Allowed : 9.59 % 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: -5.07 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR C 38 *********************** 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 19 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 13 time to evaluate : 0.186 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 16 average time/residue: 0.2005 time to fit residues: 3.7521 Evaluate side-chains 18 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 13 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2019 Z= 0.285 Angle : 0.650 5.263 2733 Z= 0.352 Chirality : 0.040 0.155 243 Planarity : 0.004 0.026 381 Dihedral : 4.396 14.917 315 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.74 % Allowed : 10.05 % 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: -5.09 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR C 38 *********************** 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 19 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 13 time to evaluate : 0.219 Fit side-chains REVERT: C 91 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.7475 (m-80) outliers start: 6 outliers final: 5 residues processed: 15 average time/residue: 0.2244 time to fit residues: 3.9077 Evaluate side-chains 19 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 13 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 0.0030 chunk 12 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.6794 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2019 Z= 0.158 Angle : 0.562 4.281 2733 Z= 0.300 Chirality : 0.037 0.133 243 Planarity : 0.003 0.022 381 Dihedral : 3.988 14.681 315 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.83 % Allowed : 10.96 % 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: -4.95 (0.24), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR B 97 *********************** 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 17 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 13 time to evaluate : 0.232 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 15 average time/residue: 0.2117 time to fit residues: 3.7220 Evaluate side-chains 17 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 13 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 109 THR 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: 10.0000 chunk 21 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 3 optimal weight: 0.0050 overall best weight: 3.0002 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2019 Z= 0.253 Angle : 0.625 5.004 2733 Z= 0.338 Chirality : 0.039 0.150 243 Planarity : 0.003 0.024 381 Dihedral : 4.262 14.705 315 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.74 % Allowed : 10.50 % 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: -4.98 (0.24), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR C 38 *********************** 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 19 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 13 time to evaluate : 0.197 Fit side-chains REVERT: C 91 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.7461 (m-80) outliers start: 6 outliers final: 5 residues processed: 15 average time/residue: 0.2150 time to fit residues: 3.7678 Evaluate side-chains 19 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 13 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 109 THR 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: 2.9990 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 0.2980 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1734 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= 0.129 Angle : 0.533 3.986 2733 Z= 0.284 Chirality : 0.036 0.119 243 Planarity : 0.003 0.019 381 Dihedral : 3.793 14.040 315 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.28 % Allowed : 10.50 % 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: -4.82 (0.24), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.18), 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 18 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 13 time to evaluate : 0.214 Fit side-chains REVERT: C 90 SER cc_start: 0.8369 (OUTLIER) cc_final: 0.8160 (p) outliers start: 5 outliers final: 4 residues processed: 15 average time/residue: 0.1931 time to fit residues: 3.4453 Evaluate side-chains 17 residues out of total 213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 12 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 0.1980 chunk 3 optimal weight: 3.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.100854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.077604 restraints weight = 9789.969| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 4.03 r_work: 0.3040 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1514 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= 0.210 Angle : 0.590 4.715 2733 Z= 0.317 Chirality : 0.038 0.136 243 Planarity : 0.003 0.021 381 Dihedral : 4.049 14.013 315 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.74 % Allowed : 10.50 % 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: -4.84 (0.24), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR C 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 951.61 seconds wall clock time: 21 minutes 34.80 seconds (1294.80 seconds total)