Starting phenix.real_space_refine on Fri Aug 2 13:43:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbw_38231/08_2024/8xbw_38231.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbw_38231/08_2024/8xbw_38231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbw_38231/08_2024/8xbw_38231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbw_38231/08_2024/8xbw_38231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbw_38231/08_2024/8xbw_38231.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbw_38231/08_2024/8xbw_38231.cif" } resolution = 2.89 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= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 6 5.16 5 C 1573 2.51 5 N 501 2.21 5 O 555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 40": "NH1" <-> "NH2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F ARG 36": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "L ARG 27": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 2671 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 678 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "I" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 366 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "J" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 372 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "L" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 465 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Time building chain proxies: 2.90, per 1000 atoms: 1.09 Number of scatterers: 2671 At special positions: 0 Unit cell: (82.68, 71.02, 77.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 P 36 15.00 O 555 8.00 N 501 7.00 C 1573 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 539.1 milliseconds 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 454 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 2 sheets defined 73.6% alpha, 1.7% beta 18 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.807A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'L' and resid 25 through 31 removed outlier: 3.703A pdb=" N GLU L 29 " --> pdb=" O ILE L 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN L 30 " --> pdb=" O SER L 26 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS L 31 " --> pdb=" O ARG L 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 25 through 31' Processing helix chain 'L' and resid 34 through 45 Processing helix chain 'L' and resid 48 through 54 Processing helix chain 'L' and resid 56 through 62 removed outlier: 4.357A pdb=" N LEU L 60 " --> pdb=" O PRO L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 82 Processing sheet with id=AA1, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.866A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 118 through 119 123 hydrogen bonds defined for protein. 363 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 0.70 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 678 1.33 - 1.45: 614 1.45 - 1.57: 1412 1.57 - 1.69: 71 1.69 - 1.81: 9 Bond restraints: 2784 Sorted by residual: bond pdb=" N ASN F 25 " pdb=" CA ASN F 25 " ideal model delta sigma weight residual 1.455 1.504 -0.049 1.29e-02 6.01e+03 1.46e+01 bond pdb=" CA ASN F 25 " pdb=" CB ASN F 25 " ideal model delta sigma weight residual 1.536 1.578 -0.042 1.42e-02 4.96e+03 8.73e+00 bond pdb=" N ILE F 26 " pdb=" CA ILE F 26 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.71e+00 bond pdb=" CZ ARG F 19 " pdb=" NH2 ARG F 19 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.05e+00 bond pdb=" CZ ARG F 23 " pdb=" NH2 ARG F 23 " ideal model delta sigma weight residual 1.330 1.300 0.030 1.30e-02 5.92e+03 5.28e+00 ... (remaining 2779 not shown) Histogram of bond angle deviations from ideal: 98.36 - 105.69: 207 105.69 - 113.03: 1512 113.03 - 120.36: 1163 120.36 - 127.69: 954 127.69 - 135.03: 60 Bond angle restraints: 3896 Sorted by residual: angle pdb=" CA ASN F 25 " pdb=" CB ASN F 25 " pdb=" CG ASN F 25 " ideal model delta sigma weight residual 112.60 106.96 5.64 1.00e+00 1.00e+00 3.18e+01 angle pdb=" N ASN F 25 " pdb=" CA ASN F 25 " pdb=" C ASN F 25 " ideal model delta sigma weight residual 113.97 121.08 -7.11 1.28e+00 6.10e-01 3.09e+01 angle pdb=" CA ASN F 25 " pdb=" C ASN F 25 " pdb=" N ILE F 26 " ideal model delta sigma weight residual 118.47 125.19 -6.72 1.26e+00 6.30e-01 2.85e+01 angle pdb=" C HIS E 39 " pdb=" CA HIS E 39 " pdb=" CB HIS E 39 " ideal model delta sigma weight residual 109.51 117.73 -8.22 1.71e+00 3.42e-01 2.31e+01 angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.10 108.70 4.40 9.70e-01 1.06e+00 2.05e+01 ... (remaining 3891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 1208 16.98 - 33.96: 184 33.96 - 50.94: 153 50.94 - 67.92: 64 67.92 - 84.90: 3 Dihedral angle restraints: 1612 sinusoidal: 911 harmonic: 701 Sorted by residual: dihedral pdb=" CA GLY L 32 " pdb=" C GLY L 32 " pdb=" N ILE L 33 " pdb=" CA ILE L 33 " ideal model delta harmonic sigma weight residual 180.00 155.24 24.76 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA ARG F 19 " pdb=" C ARG F 19 " pdb=" N LYS F 20 " pdb=" CA LYS F 20 " ideal model delta harmonic sigma weight residual 180.00 159.26 20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" C HIS E 39 " pdb=" N HIS E 39 " pdb=" CA HIS E 39 " pdb=" CB HIS E 39 " ideal model delta harmonic sigma weight residual -122.60 -131.94 9.34 0 2.50e+00 1.60e-01 1.40e+01 ... (remaining 1609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 424 0.102 - 0.204: 18 0.204 - 0.305: 1 0.305 - 0.407: 0 0.407 - 0.509: 1 Chirality restraints: 444 Sorted by residual: chirality pdb=" P DA J 97 " pdb=" OP1 DA J 97 " pdb=" OP2 DA J 97 " pdb=" O5' DA J 97 " both_signs ideal model delta sigma weight residual True 2.35 -2.85 -0.51 2.00e-01 2.50e+01 6.48e+00 chirality pdb=" P DA I 51 " pdb=" OP1 DA I 51 " pdb=" OP2 DA I 51 " pdb=" O5' DA I 51 " both_signs ideal model delta sigma weight residual True 2.35 -2.64 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA ASN F 25 " pdb=" N ASN F 25 " pdb=" C ASN F 25 " pdb=" CB ASN F 25 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 441 not shown) Planarity restraints: 371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 51 " -0.076 2.00e-02 2.50e+03 3.09e-02 2.62e+01 pdb=" N9 DA I 51 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DA I 51 " 0.023 2.00e-02 2.50e+03 pdb=" N7 DA I 51 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DA I 51 " 0.012 2.00e-02 2.50e+03 pdb=" C6 DA I 51 " -0.009 2.00e-02 2.50e+03 pdb=" N6 DA I 51 " -0.041 2.00e-02 2.50e+03 pdb=" N1 DA I 51 " -0.007 2.00e-02 2.50e+03 pdb=" C2 DA I 51 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DA I 51 " 0.025 2.00e-02 2.50e+03 pdb=" C4 DA I 51 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 39 " -0.043 2.00e-02 2.50e+03 3.59e-02 1.93e+01 pdb=" CG HIS E 39 " 0.058 2.00e-02 2.50e+03 pdb=" ND1 HIS E 39 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS E 39 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 HIS E 39 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS E 39 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN L 23 " 0.060 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO L 24 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO L 24 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO L 24 " 0.048 5.00e-02 4.00e+02 ... (remaining 368 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 1 1.90 - 2.65: 54 2.65 - 3.40: 3563 3.40 - 4.15: 7271 4.15 - 4.90: 11510 Nonbonded interactions: 22399 Sorted by model distance: nonbonded pdb=" NH2 ARG E 40 " pdb=" O2 DT J 90 " model vdw 1.155 3.120 nonbonded pdb=" NH2 ARG E 40 " pdb=" C2 DT J 90 " model vdw 2.155 3.340 nonbonded pdb=" O GLN L 23 " pdb=" N VAL L 49 " model vdw 2.220 3.120 nonbonded pdb=" OD1 ASP E 77 " pdb=" NZ LYS L 73 " model vdw 2.273 3.120 nonbonded pdb=" NZ LYS L 57 " pdb=" OD1 ASP L 72 " model vdw 2.299 3.120 ... (remaining 22394 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.850 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 2784 Z= 0.376 Angle : 1.060 8.216 3896 Z= 0.729 Chirality : 0.054 0.509 444 Planarity : 0.009 0.089 371 Dihedral : 23.744 84.903 1158 Min Nonbonded Distance : 1.155 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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: -0.65 (0.47), residues: 236 helix: -0.12 (0.36), residues: 159 sheet: None (None), residues: 0 loop : -0.82 (0.62), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.025 0.004 HIS E 39 PHE 0.009 0.001 PHE F 61 TYR 0.016 0.002 TYR F 51 ARG 0.006 0.001 ARG L 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 ASP cc_start: 0.9230 (m-30) cc_final: 0.8979 (p0) REVERT: F 43 VAL cc_start: 0.7864 (t) cc_final: 0.7433 (t) REVERT: L 73 LYS cc_start: 0.6764 (mttt) cc_final: 0.6412 (tppt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 1.1723 time to fit residues: 137.6091 Evaluate side-chains 74 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 7 optimal weight: 0.0030 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS E 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 2784 Z= 0.257 Angle : 0.847 13.532 3896 Z= 0.453 Chirality : 0.044 0.183 444 Planarity : 0.006 0.043 371 Dihedral : 26.446 62.566 663 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 26.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 7.43 % Allowed : 29.21 % Favored : 63.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.50), residues: 236 helix: 0.32 (0.37), residues: 174 sheet: None (None), residues: 0 loop : -1.53 (0.61), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS E 39 PHE 0.018 0.003 PHE F 61 TYR 0.024 0.003 TYR E 99 ARG 0.005 0.001 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 104 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8776 (t80) REVERT: E 105 GLU cc_start: 0.9144 (tp30) cc_final: 0.8918 (mm-30) REVERT: F 88 TYR cc_start: 0.8461 (m-10) cc_final: 0.8153 (m-10) REVERT: F 90 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8173 (mm) REVERT: L 61 ILE cc_start: 0.8575 (pp) cc_final: 0.8355 (pp) outliers start: 15 outliers final: 4 residues processed: 94 average time/residue: 1.0005 time to fit residues: 96.3300 Evaluate side-chains 74 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 90 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.7057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 2784 Z= 0.272 Angle : 0.891 11.150 3896 Z= 0.466 Chirality : 0.047 0.223 444 Planarity : 0.006 0.047 371 Dihedral : 25.969 67.731 663 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 24.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 6.93 % Allowed : 35.15 % Favored : 57.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.51), residues: 236 helix: 0.03 (0.38), residues: 175 sheet: None (None), residues: 0 loop : -1.89 (0.65), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 47 PHE 0.010 0.002 PHE F 61 TYR 0.040 0.003 TYR E 99 ARG 0.005 0.001 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 ASP cc_start: 0.9186 (m-30) cc_final: 0.8877 (p0) REVERT: E 104 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8760 (t80) REVERT: E 109 LEU cc_start: 0.8869 (mm) cc_final: 0.8658 (mm) REVERT: F 62 LEU cc_start: 0.9156 (mt) cc_final: 0.8918 (pp) REVERT: F 88 TYR cc_start: 0.8563 (m-10) cc_final: 0.8281 (m-10) REVERT: L 46 PHE cc_start: 0.5644 (m-80) cc_final: 0.5323 (m-80) REVERT: L 70 LYS cc_start: 0.7667 (mttt) cc_final: 0.7369 (tptp) outliers start: 14 outliers final: 7 residues processed: 88 average time/residue: 0.8387 time to fit residues: 76.1095 Evaluate side-chains 77 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain L residue 47 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.8637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 2784 Z= 0.321 Angle : 0.975 15.961 3896 Z= 0.494 Chirality : 0.050 0.276 444 Planarity : 0.006 0.046 371 Dihedral : 25.510 73.428 663 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 27.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 8.42 % Allowed : 32.18 % Favored : 59.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.48), residues: 236 helix: -0.31 (0.36), residues: 166 sheet: None (None), residues: 0 loop : -1.51 (0.61), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 39 PHE 0.017 0.003 PHE E 67 TYR 0.017 0.003 TYR F 72 ARG 0.012 0.001 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8042 (mt) REVERT: E 104 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.8916 (t80) REVERT: F 92 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7804 (tmt170) REVERT: L 46 PHE cc_start: 0.5709 (m-80) cc_final: 0.5468 (m-80) REVERT: L 70 LYS cc_start: 0.7774 (mttt) cc_final: 0.7410 (tptt) REVERT: L 74 ILE cc_start: 0.7169 (pp) cc_final: 0.6403 (pp) outliers start: 17 outliers final: 5 residues processed: 89 average time/residue: 0.7201 time to fit residues: 66.2744 Evaluate side-chains 76 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 92 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 6 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.9238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 2784 Z= 0.275 Angle : 0.963 13.089 3896 Z= 0.485 Chirality : 0.051 0.277 444 Planarity : 0.006 0.048 371 Dihedral : 25.448 77.084 663 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 23.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 6.44 % Allowed : 39.11 % Favored : 54.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.46), residues: 236 helix: -0.35 (0.35), residues: 164 sheet: None (None), residues: 0 loop : -1.72 (0.60), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 39 PHE 0.023 0.002 PHE F 61 TYR 0.040 0.003 TYR E 99 ARG 0.004 0.000 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 ARG cc_start: 0.9002 (mtp180) cc_final: 0.8294 (ptp-110) REVERT: E 82 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8218 (mt) REVERT: E 99 TYR cc_start: 0.8808 (t80) cc_final: 0.8199 (t80) REVERT: E 104 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8656 (t80) REVERT: F 58 LEU cc_start: 0.9249 (tp) cc_final: 0.8883 (mm) REVERT: F 92 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7753 (tmt170) REVERT: L 43 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8426 (pp20) REVERT: L 46 PHE cc_start: 0.5907 (m-80) cc_final: 0.5700 (m-80) REVERT: L 50 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8423 (tp30) REVERT: L 70 LYS cc_start: 0.7894 (mttt) cc_final: 0.7554 (tptm) REVERT: L 74 ILE cc_start: 0.7227 (pp) cc_final: 0.6548 (pp) outliers start: 13 outliers final: 7 residues processed: 81 average time/residue: 0.8140 time to fit residues: 67.9844 Evaluate side-chains 79 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 47 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 0.4980 chunk 8 optimal weight: 0.0570 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.9574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 2784 Z= 0.257 Angle : 0.991 14.374 3896 Z= 0.493 Chirality : 0.053 0.352 444 Planarity : 0.005 0.056 371 Dihedral : 25.339 77.437 663 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 5.94 % Allowed : 41.58 % Favored : 52.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.47), residues: 236 helix: -0.38 (0.36), residues: 164 sheet: None (None), residues: 0 loop : -1.62 (0.62), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 39 PHE 0.014 0.002 PHE F 61 TYR 0.018 0.003 TYR E 99 ARG 0.008 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 104 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8775 (t80) REVERT: E 131 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8988 (ttt180) REVERT: F 60 VAL cc_start: 0.9106 (m) cc_final: 0.8747 (p) REVERT: F 81 VAL cc_start: 0.8750 (OUTLIER) cc_final: 0.8438 (t) REVERT: L 43 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8497 (pp20) REVERT: L 50 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8425 (tp30) REVERT: L 70 LYS cc_start: 0.7877 (mttt) cc_final: 0.7516 (tptm) REVERT: L 74 ILE cc_start: 0.7383 (pp) cc_final: 0.6704 (pp) outliers start: 12 outliers final: 3 residues processed: 76 average time/residue: 0.8290 time to fit residues: 64.9737 Evaluate side-chains 70 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 47 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 14 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 0.0870 chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 23 optimal weight: 0.0970 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.9969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 2784 Z= 0.262 Angle : 1.008 15.552 3896 Z= 0.500 Chirality : 0.052 0.414 444 Planarity : 0.005 0.053 371 Dihedral : 25.270 77.048 663 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 5.45 % Allowed : 41.09 % Favored : 53.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.48), residues: 236 helix: -0.27 (0.37), residues: 162 sheet: None (None), residues: 0 loop : -1.45 (0.61), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS E 39 PHE 0.012 0.002 PHE E 67 TYR 0.025 0.002 TYR E 99 ARG 0.004 0.000 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 104 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8709 (t80) REVERT: E 131 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.8961 (ttt180) REVERT: F 46 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.8019 (pt) REVERT: F 92 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7849 (tmt170) REVERT: L 50 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8567 (mm-30) REVERT: L 60 LEU cc_start: 0.8989 (pp) cc_final: 0.8785 (pt) REVERT: L 70 LYS cc_start: 0.8070 (mttt) cc_final: 0.7735 (tptm) REVERT: L 74 ILE cc_start: 0.7414 (pp) cc_final: 0.6664 (pp) outliers start: 11 outliers final: 4 residues processed: 85 average time/residue: 0.7884 time to fit residues: 69.2349 Evaluate side-chains 80 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 47 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.0970 chunk 20 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 1.0443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 2784 Z= 0.308 Angle : 1.110 16.322 3896 Z= 0.545 Chirality : 0.056 0.410 444 Planarity : 0.006 0.047 371 Dihedral : 25.193 78.077 663 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 26.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 5.94 % Allowed : 44.06 % Favored : 50.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.48), residues: 236 helix: -0.64 (0.37), residues: 164 sheet: None (None), residues: 0 loop : -1.70 (0.58), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 39 PHE 0.027 0.003 PHE F 61 TYR 0.051 0.003 TYR E 99 ARG 0.006 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8090 (ttt180) REVERT: L 43 GLU cc_start: 0.7794 (pp20) cc_final: 0.7433 (pp20) REVERT: L 50 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8786 (mm-30) REVERT: L 60 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8699 (pt) REVERT: L 70 LYS cc_start: 0.8073 (mttt) cc_final: 0.7759 (tptm) REVERT: L 74 ILE cc_start: 0.7392 (pp) cc_final: 0.6794 (pp) outliers start: 12 outliers final: 3 residues processed: 76 average time/residue: 0.8614 time to fit residues: 67.4680 Evaluate side-chains 72 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 60 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.0170 chunk 19 optimal weight: 0.0030 chunk 2 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.3828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 1.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 2784 Z= 0.291 Angle : 1.169 19.261 3896 Z= 0.575 Chirality : 0.057 0.373 444 Planarity : 0.005 0.030 371 Dihedral : 25.232 78.620 663 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 24.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.96 % Allowed : 46.04 % Favored : 50.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.47), residues: 236 helix: -0.58 (0.36), residues: 165 sheet: None (None), residues: 0 loop : -1.68 (0.57), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 39 PHE 0.023 0.003 PHE F 61 TYR 0.055 0.002 TYR E 99 ARG 0.004 0.001 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 65 LEU cc_start: 0.8399 (pt) cc_final: 0.8170 (pp) REVERT: E 67 PHE cc_start: 0.7580 (t80) cc_final: 0.6752 (t80) REVERT: E 104 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8887 (t80) REVERT: F 46 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8158 (pt) REVERT: F 92 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8041 (tmt170) REVERT: L 43 GLU cc_start: 0.7867 (pp20) cc_final: 0.7519 (pp20) REVERT: L 50 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8735 (tp30) REVERT: L 60 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8706 (pt) REVERT: L 70 LYS cc_start: 0.8119 (mttt) cc_final: 0.7769 (tptm) REVERT: L 74 ILE cc_start: 0.7447 (pp) cc_final: 0.6794 (pp) outliers start: 8 outliers final: 2 residues processed: 71 average time/residue: 0.7078 time to fit residues: 52.1645 Evaluate side-chains 71 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 60 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 14 optimal weight: 0.1980 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS F 25 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 1.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 2784 Z= 0.299 Angle : 1.186 18.661 3896 Z= 0.583 Chirality : 0.057 0.366 444 Planarity : 0.005 0.024 371 Dihedral : 25.199 78.530 663 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 23.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.95 % Allowed : 46.53 % Favored : 48.51 % 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: -2.03 (0.46), residues: 236 helix: -0.99 (0.36), residues: 166 sheet: None (None), residues: 0 loop : -1.87 (0.57), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 39 PHE 0.030 0.003 PHE F 61 TYR 0.057 0.003 TYR E 99 ARG 0.006 0.001 ARG E 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 52 ARG cc_start: 0.8734 (pmm-80) cc_final: 0.8362 (pmm-80) REVERT: E 65 LEU cc_start: 0.8374 (pt) cc_final: 0.8137 (pp) REVERT: F 92 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7993 (ttt180) REVERT: L 43 GLU cc_start: 0.7823 (pp20) cc_final: 0.7436 (pp20) REVERT: L 47 HIS cc_start: 0.4782 (m90) cc_final: 0.4579 (m-70) REVERT: L 50 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8781 (tp30) REVERT: L 60 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8706 (pt) REVERT: L 70 LYS cc_start: 0.8048 (mttt) cc_final: 0.7705 (tptt) REVERT: L 74 ILE cc_start: 0.7459 (pp) cc_final: 0.6851 (pp) outliers start: 10 outliers final: 4 residues processed: 71 average time/residue: 0.8191 time to fit residues: 60.0306 Evaluate side-chains 69 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 60 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 0.0980 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.072870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.051408 restraints weight = 11924.074| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.84 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 1.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 2784 Z= 0.309 Angle : 1.227 19.226 3896 Z= 0.599 Chirality : 0.059 0.390 444 Planarity : 0.005 0.027 371 Dihedral : 25.219 79.271 663 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 27.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.48 % Allowed : 49.01 % Favored : 48.51 % 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: -2.17 (0.47), residues: 236 helix: -1.06 (0.36), residues: 167 sheet: None (None), residues: 0 loop : -2.07 (0.60), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 39 PHE 0.038 0.003 PHE F 61 TYR 0.068 0.003 TYR E 99 ARG 0.004 0.000 ARG E 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1732.60 seconds wall clock time: 31 minutes 2.38 seconds (1862.38 seconds total)