Starting phenix.real_space_refine on Sun Mar 10 20:33:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eir_28162/03_2024/8eir_28162.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eir_28162/03_2024/8eir_28162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eir_28162/03_2024/8eir_28162.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eir_28162/03_2024/8eir_28162.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eir_28162/03_2024/8eir_28162.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eir_28162/03_2024/8eir_28162.pdb" } resolution = 2.49 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= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 3080 2.51 5 N 834 2.21 5 O 914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 153": "OD1" <-> "OD2" Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A ASP 263": "OD1" <-> "OD2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "B GLU 14": "OE1" <-> "OE2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B ASP 216": "OD1" <-> "OD2" Residue "B ASP 229": "OD1" <-> "OD2" Residue "B TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 245": "OD1" <-> "OD2" Residue "B ASP 263": "OD1" <-> "OD2" Residue "B GLU 270": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4870 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2366 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain: "B" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2366 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 69 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 69 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Time building chain proxies: 3.21, per 1000 atoms: 0.66 Number of scatterers: 4870 At special positions: 0 Unit cell: (88.065, 70.11, 76.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 914 8.00 N 834 7.00 C 3080 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: 1.65 Conformation dependent library (CDL) restraints added in 869.6 milliseconds 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1156 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 6 sheets defined 28.8% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 13 through 15 No H-bonds generated for 'chain 'A' and resid 13 through 15' Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 53 through 60 removed outlier: 3.542A pdb=" N ARG A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 200 through 214 Processing helix chain 'A' and resid 226 through 237 removed outlier: 3.808A pdb=" N LYS A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'B' and resid 13 through 15 No H-bonds generated for 'chain 'B' and resid 13 through 15' Processing helix chain 'B' and resid 41 through 44 Processing helix chain 'B' and resid 53 through 60 removed outlier: 3.579A pdb=" N ARG B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 66 Processing helix chain 'B' and resid 200 through 214 Processing helix chain 'B' and resid 226 through 237 removed outlier: 3.783A pdb=" N LYS B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR B 237 " --> pdb=" O VAL B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 250 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 292 through 302 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 75 removed outlier: 4.520A pdb=" N VAL A 68 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ASN A 28 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103 removed outlier: 5.550A pdb=" N HIS A 163 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR A 175 " --> pdb=" O HIS A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 129 removed outlier: 6.823A pdb=" N ALA A 116 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL A 125 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A 114 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLN A 127 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE A 112 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 11.351A pdb=" N THR A 111 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE A 152 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL A 148 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY A 149 " --> pdb=" O CYS A 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 75 removed outlier: 4.483A pdb=" N VAL B 68 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASN B 28 " --> pdb=" O PRO B 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 103 removed outlier: 6.982A pdb=" N ALA B 173 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 121 through 129 removed outlier: 6.831A pdb=" N ALA B 116 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL B 125 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL B 114 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN B 127 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE B 112 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 11.358A pdb=" N THR B 111 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ILE B 152 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL B 148 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY B 149 " --> pdb=" O CYS B 160 " (cutoff:3.500A) 191 hydrogen bonds defined for protein. 507 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: 1.22 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1570 1.34 - 1.45: 705 1.45 - 1.57: 2637 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 4974 Sorted by residual: bond pdb=" CA ASN A 277 " pdb=" CB ASN A 277 " ideal model delta sigma weight residual 1.529 1.558 -0.029 1.62e-02 3.81e+03 3.18e+00 bond pdb=" CB ASN A 277 " pdb=" CG ASN A 277 " ideal model delta sigma weight residual 1.516 1.560 -0.044 2.50e-02 1.60e+03 3.09e+00 bond pdb=" C LEU A 167 " pdb=" N PRO A 168 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.68e+00 bond pdb=" CA ASN A 277 " pdb=" C ASN A 277 " ideal model delta sigma weight residual 1.526 1.541 -0.015 1.29e-02 6.01e+03 1.38e+00 bond pdb=" C LEU B 167 " pdb=" N PRO B 168 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.27e+00 ... (remaining 4969 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.16: 152 107.16 - 113.88: 2720 113.88 - 120.60: 1938 120.60 - 127.31: 1907 127.31 - 134.03: 41 Bond angle restraints: 6758 Sorted by residual: angle pdb=" CA ASN A 277 " pdb=" CB ASN A 277 " pdb=" CG ASN A 277 " ideal model delta sigma weight residual 112.60 116.85 -4.25 1.00e+00 1.00e+00 1.81e+01 angle pdb=" CA MET B 49 " pdb=" CB MET B 49 " pdb=" CG MET B 49 " ideal model delta sigma weight residual 114.10 121.23 -7.13 2.00e+00 2.50e-01 1.27e+01 angle pdb=" C ASN A 277 " pdb=" CA ASN A 277 " pdb=" CB ASN A 277 " ideal model delta sigma weight residual 111.80 116.89 -5.09 1.46e+00 4.69e-01 1.21e+01 angle pdb=" CA ARG B 217 " pdb=" CB ARG B 217 " pdb=" CG ARG B 217 " ideal model delta sigma weight residual 114.10 120.82 -6.72 2.00e+00 2.50e-01 1.13e+01 angle pdb=" CB MET A 17 " pdb=" CG MET A 17 " pdb=" SD MET A 17 " ideal model delta sigma weight residual 112.70 121.99 -9.29 3.00e+00 1.11e-01 9.60e+00 ... (remaining 6753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 2554 16.91 - 33.82: 256 33.82 - 50.73: 86 50.73 - 67.64: 29 67.64 - 84.55: 3 Dihedral angle restraints: 2928 sinusoidal: 1122 harmonic: 1806 Sorted by residual: dihedral pdb=" CA ASP A 245 " pdb=" CB ASP A 245 " pdb=" CG ASP A 245 " pdb=" OD1 ASP A 245 " ideal model delta sinusoidal sigma weight residual -30.00 -86.78 56.78 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA THR A 175 " pdb=" C THR A 175 " pdb=" N ASP A 176 " pdb=" CA ASP A 176 " ideal model delta harmonic sigma weight residual 180.00 163.89 16.11 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA PHE B 181 " pdb=" C PHE B 181 " pdb=" N TYR B 182 " pdb=" CA TYR B 182 " ideal model delta harmonic sigma weight residual 180.00 163.96 16.04 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 2925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 447 0.039 - 0.077: 226 0.077 - 0.116: 81 0.116 - 0.154: 7 0.154 - 0.192: 5 Chirality restraints: 766 Sorted by residual: chirality pdb=" CA HIS A 41 " pdb=" N HIS A 41 " pdb=" C HIS A 41 " pdb=" CB HIS A 41 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CA HIS B 41 " pdb=" N HIS B 41 " pdb=" C HIS B 41 " pdb=" CB HIS B 41 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA PRO A 168 " pdb=" N PRO A 168 " pdb=" C PRO A 168 " pdb=" CB PRO A 168 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.24e-01 ... (remaining 763 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 38 " -0.063 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO A 39 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 231 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C ASN A 231 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN A 231 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU A 232 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 277 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.72e+00 pdb=" C ASN A 277 " -0.033 2.00e-02 2.50e+03 pdb=" O ASN A 277 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY A 278 " 0.011 2.00e-02 2.50e+03 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 4 2.55 - 3.14: 3562 3.14 - 3.72: 7054 3.72 - 4.31: 10414 4.31 - 4.90: 17751 Nonbonded interactions: 38785 Sorted by model distance: nonbonded pdb=" O ASN A 277 " pdb=" ND2 ASN A 277 " model vdw 1.960 2.520 nonbonded pdb=" N ASP B 187 " pdb=" OD1 ASP B 187 " model vdw 2.486 2.520 nonbonded pdb=" N ASP A 187 " pdb=" OD1 ASP A 187 " model vdw 2.488 2.520 nonbonded pdb=" NE2 GLN B 69 " pdb=" OE1 GLN B 74 " model vdw 2.546 2.520 nonbonded pdb=" OE2 GLU A 166 " pdb=" N SER B 1 " model vdw 2.560 2.520 ... (remaining 38780 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.330 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: 6.990 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 17.020 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.005 0.044 4974 Z= 0.323 Angle : 0.813 9.962 6758 Z= 0.441 Chirality : 0.050 0.192 766 Planarity : 0.006 0.095 880 Dihedral : 16.398 84.551 1772 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.24 % Favored : 97.44 % Rotamer: Outliers : 2.61 % Allowed : 20.90 % Favored : 76.49 % 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: -1.27 (0.30), residues: 624 helix: -0.43 (0.36), residues: 168 sheet: -1.09 (0.55), residues: 72 loop : -0.95 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 207 HIS 0.010 0.004 HIS A 41 PHE 0.022 0.003 PHE B 230 TYR 0.025 0.003 TYR A 182 ARG 0.006 0.001 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.6750 (mtm-85) cc_final: 0.6391 (ttp-110) outliers start: 14 outliers final: 3 residues processed: 103 average time/residue: 1.6913 time to fit residues: 179.2485 Evaluate side-chains 86 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 254 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS A 277 ASN B 64 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4974 Z= 0.231 Angle : 0.577 8.952 6758 Z= 0.301 Chirality : 0.041 0.134 766 Planarity : 0.005 0.069 880 Dihedral : 4.848 35.383 677 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.08 % Favored : 97.60 % Rotamer: Outliers : 2.99 % Allowed : 21.46 % Favored : 75.56 % 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: -0.24 (0.32), residues: 624 helix: 0.92 (0.40), residues: 174 sheet: -0.62 (0.55), residues: 76 loop : -0.54 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 207 HIS 0.007 0.002 HIS A 64 PHE 0.012 0.001 PHE B 230 TYR 0.007 0.001 TYR A 182 ARG 0.003 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: B 4 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7309 (mmm160) outliers start: 16 outliers final: 9 residues processed: 91 average time/residue: 1.7906 time to fit residues: 167.4597 Evaluate side-chains 83 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 4 ARG Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 301 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 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 64 HIS B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4974 Z= 0.277 Angle : 0.554 8.290 6758 Z= 0.291 Chirality : 0.042 0.130 766 Planarity : 0.005 0.061 880 Dihedral : 4.655 32.422 676 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.24 % Favored : 97.44 % Rotamer: Outliers : 4.66 % Allowed : 19.78 % Favored : 75.56 % 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: -0.19 (0.32), residues: 624 helix: 1.08 (0.41), residues: 174 sheet: -0.27 (0.57), residues: 76 loop : -0.67 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 207 HIS 0.007 0.002 HIS A 41 PHE 0.015 0.002 PHE A 230 TYR 0.008 0.001 TYR B 182 ARG 0.008 0.001 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 73 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: B 279 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7046 (mtp180) outliers start: 25 outliers final: 6 residues processed: 86 average time/residue: 1.6032 time to fit residues: 142.1428 Evaluate side-chains 80 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 304 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4974 Z= 0.168 Angle : 0.492 7.500 6758 Z= 0.255 Chirality : 0.039 0.115 766 Planarity : 0.005 0.054 880 Dihedral : 4.240 20.806 675 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.80 % Allowed : 20.52 % Favored : 76.68 % 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: -0.05 (0.32), residues: 624 helix: 1.19 (0.41), residues: 174 sheet: -0.05 (0.58), residues: 76 loop : -0.61 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 207 HIS 0.006 0.001 HIS A 64 PHE 0.008 0.001 PHE B 230 TYR 0.006 0.001 TYR B 182 ARG 0.009 0.001 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: B 279 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7015 (mtp180) outliers start: 15 outliers final: 4 residues processed: 79 average time/residue: 1.7760 time to fit residues: 144.3312 Evaluate side-chains 78 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 301 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4974 Z= 0.195 Angle : 0.504 7.185 6758 Z= 0.261 Chirality : 0.040 0.117 766 Planarity : 0.005 0.052 880 Dihedral : 4.211 19.025 675 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.73 % Allowed : 20.34 % Favored : 75.93 % 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: -0.02 (0.32), residues: 624 helix: 1.20 (0.42), residues: 174 sheet: 0.05 (0.58), residues: 76 loop : -0.60 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 207 HIS 0.006 0.001 HIS A 64 PHE 0.011 0.001 PHE B 230 TYR 0.007 0.001 TYR B 182 ARG 0.010 0.001 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 71 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: B 49 MET cc_start: 0.7494 (mmt) cc_final: 0.7286 (mmt) REVERT: B 279 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7024 (mtp180) outliers start: 20 outliers final: 7 residues processed: 82 average time/residue: 1.7293 time to fit residues: 146.1034 Evaluate side-chains 79 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 304 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 0.0870 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 4974 Z= 0.559 Angle : 0.657 8.545 6758 Z= 0.348 Chirality : 0.047 0.148 766 Planarity : 0.006 0.055 880 Dihedral : 4.972 38.708 675 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.10 % Allowed : 18.66 % Favored : 77.24 % 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: -0.63 (0.31), residues: 624 helix: 0.86 (0.41), residues: 174 sheet: -0.33 (0.56), residues: 72 loop : -1.08 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 218 HIS 0.011 0.002 HIS A 41 PHE 0.020 0.002 PHE B 230 TYR 0.011 0.002 TYR B 182 ARG 0.012 0.001 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 75 time to evaluate : 0.587 Fit side-chains REVERT: B 49 MET cc_start: 0.7501 (mmt) cc_final: 0.7286 (mmt) REVERT: B 279 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7225 (mtp180) outliers start: 22 outliers final: 6 residues processed: 89 average time/residue: 1.5811 time to fit residues: 145.0376 Evaluate side-chains 74 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 301 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4974 Z= 0.206 Angle : 0.533 7.484 6758 Z= 0.273 Chirality : 0.040 0.116 766 Planarity : 0.005 0.052 880 Dihedral : 4.386 24.595 675 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.43 % Allowed : 20.71 % Favored : 76.87 % 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: -0.33 (0.32), residues: 624 helix: 1.11 (0.42), residues: 174 sheet: -0.06 (0.56), residues: 76 loop : -0.92 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 218 HIS 0.006 0.001 HIS B 64 PHE 0.009 0.001 PHE A 230 TYR 0.007 0.001 TYR A 182 ARG 0.012 0.001 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.568 Fit side-chains REVERT: B 49 MET cc_start: 0.7555 (mmt) cc_final: 0.7339 (mmt) REVERT: B 279 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7086 (mtp180) outliers start: 13 outliers final: 6 residues processed: 73 average time/residue: 1.7429 time to fit residues: 131.1446 Evaluate side-chains 73 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 301 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 57 optimal weight: 0.4980 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4974 Z= 0.176 Angle : 0.514 7.132 6758 Z= 0.261 Chirality : 0.039 0.117 766 Planarity : 0.005 0.057 880 Dihedral : 4.138 17.931 675 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.80 % Allowed : 20.52 % Favored : 76.68 % 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: -0.20 (0.33), residues: 624 helix: 1.29 (0.42), residues: 174 sheet: 0.02 (0.56), residues: 76 loop : -0.88 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 218 HIS 0.006 0.001 HIS B 64 PHE 0.008 0.001 PHE A 230 TYR 0.007 0.001 TYR A 182 ARG 0.014 0.001 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 66 time to evaluate : 0.560 Fit side-chains REVERT: B 49 MET cc_start: 0.7576 (mmt) cc_final: 0.7373 (mmt) REVERT: B 279 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7031 (mtp180) outliers start: 15 outliers final: 7 residues processed: 73 average time/residue: 1.6358 time to fit residues: 123.0350 Evaluate side-chains 74 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 301 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.0020 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4974 Z= 0.161 Angle : 0.503 7.132 6758 Z= 0.255 Chirality : 0.039 0.116 766 Planarity : 0.005 0.062 880 Dihedral : 4.008 16.754 675 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.68 % Allowed : 21.64 % Favored : 76.68 % 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: -0.12 (0.33), residues: 624 helix: 1.42 (0.42), residues: 174 sheet: 0.01 (0.56), residues: 76 loop : -0.84 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 218 HIS 0.007 0.001 HIS A 64 PHE 0.007 0.001 PHE A 230 TYR 0.007 0.001 TYR A 182 ARG 0.015 0.001 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.618 Fit side-chains REVERT: B 4 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7500 (mmm160) REVERT: B 49 MET cc_start: 0.7585 (mmt) cc_final: 0.7385 (mmt) REVERT: B 279 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7021 (mtp180) outliers start: 9 outliers final: 5 residues processed: 72 average time/residue: 1.7415 time to fit residues: 129.2500 Evaluate side-chains 73 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 4 ARG Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 301 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 0.0980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 HIS B 164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4974 Z= 0.174 Angle : 0.517 7.955 6758 Z= 0.263 Chirality : 0.039 0.117 766 Planarity : 0.005 0.063 880 Dihedral : 3.972 17.619 674 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.24 % Allowed : 21.46 % Favored : 76.31 % 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: -0.10 (0.33), residues: 624 helix: 1.47 (0.42), residues: 174 sheet: 0.01 (0.56), residues: 76 loop : -0.84 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 218 HIS 0.007 0.001 HIS B 64 PHE 0.010 0.001 PHE B 223 TYR 0.007 0.001 TYR A 182 ARG 0.015 0.001 ARG A 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.567 Fit side-chains REVERT: B 4 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7484 (mmm160) REVERT: B 279 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7031 (mtp180) outliers start: 12 outliers final: 5 residues processed: 72 average time/residue: 1.6382 time to fit residues: 121.6236 Evaluate side-chains 72 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 4 ARG Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 279 ARG Chi-restraints excluded: chain B residue 301 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 43 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 56 optimal weight: 0.5980 chunk 33 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.089039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.069361 restraints weight = 8446.587| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.64 r_work: 0.2764 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4974 Z= 0.160 Angle : 0.511 7.604 6758 Z= 0.260 Chirality : 0.039 0.117 766 Planarity : 0.005 0.063 880 Dihedral : 3.878 15.930 674 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.24 % Allowed : 21.46 % Favored : 76.31 % 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: -0.05 (0.33), residues: 624 helix: 1.53 (0.42), residues: 174 sheet: 0.01 (0.56), residues: 76 loop : -0.82 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 218 HIS 0.007 0.001 HIS A 64 PHE 0.007 0.001 PHE B 223 TYR 0.006 0.001 TYR A 182 ARG 0.015 0.001 ARG A 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2706.32 seconds wall clock time: 48 minutes 16.86 seconds (2896.86 seconds total)