Starting phenix.real_space_refine on Tue Feb 13 08:48:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb2_24961/02_2024/7sb2_24961.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb2_24961/02_2024/7sb2_24961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb2_24961/02_2024/7sb2_24961.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb2_24961/02_2024/7sb2_24961.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb2_24961/02_2024/7sb2_24961.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb2_24961/02_2024/7sb2_24961.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 2956 2.51 5 N 787 2.21 5 O 955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 207": "OD1" <-> "OD2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4715 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2357 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 5, 'TRANS': 293} Chain: "B" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2358 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 6, 'TRANS': 292} Time building chain proxies: 2.79, per 1000 atoms: 0.59 Number of scatterers: 4715 At special positions: 0 Unit cell: (69.216, 64.272, 118.656, 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 17 16.00 O 955 8.00 N 787 7.00 C 2956 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: 2.01 Conformation dependent library (CDL) restraints added in 769.4 milliseconds 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1090 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 8 sheets defined 52.7% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 32 through 66 Processing helix chain 'A' and resid 67 through 104 removed outlier: 3.561A pdb=" N PHE A 71 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLU A 73 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ALA A 74 " --> pdb=" O GLN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 Processing helix chain 'A' and resid 130 through 152 Processing helix chain 'A' and resid 159 through 169 Processing helix chain 'A' and resid 183 through 190 Processing helix chain 'A' and resid 193 through 229 Processing helix chain 'B' and resid 33 through 67 Processing helix chain 'B' and resid 67 through 103 removed outlier: 5.493A pdb=" N GLU B 73 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA B 74 " --> pdb=" O GLN B 70 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 103 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 132 through 151 Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 183 through 189 Processing helix chain 'B' and resid 193 through 228 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 237 Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA5, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA6, first strand: chain 'B' and resid 174 through 175 Processing sheet with id=AA7, first strand: chain 'B' and resid 233 through 238 removed outlier: 3.562A pdb=" N GLU B 238 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 253 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 267 through 269 299 hydrogen bonds defined for protein. 870 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: 1.36 Time building geometry restraints manager: 2.15 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: 1598 1.34 - 1.46: 796 1.46 - 1.57: 2358 1.57 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 4786 Sorted by residual: bond pdb=" CB VAL B 81 " pdb=" CG1 VAL B 81 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.91e+00 bond pdb=" C LEU B 307 " pdb=" N TYR B 308 " ideal model delta sigma weight residual 1.331 1.314 0.017 1.44e-02 4.82e+03 1.37e+00 bond pdb=" CA LEU B 291 " pdb=" CB LEU B 291 " ideal model delta sigma weight residual 1.526 1.509 0.018 1.53e-02 4.27e+03 1.33e+00 bond pdb=" CG GLU B 47 " pdb=" CD GLU B 47 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.27e+00 bond pdb=" N VAL A 174 " pdb=" CA VAL A 174 " ideal model delta sigma weight residual 1.458 1.444 0.014 1.24e-02 6.50e+03 1.22e+00 ... (remaining 4781 not shown) Histogram of bond angle deviations from ideal: 97.84 - 105.06: 46 105.06 - 112.29: 2306 112.29 - 119.52: 1631 119.52 - 126.74: 2423 126.74 - 133.97: 21 Bond angle restraints: 6427 Sorted by residual: angle pdb=" N LYS A 288 " pdb=" CA LYS A 288 " pdb=" C LYS A 288 " ideal model delta sigma weight residual 110.59 106.09 4.50 1.45e+00 4.76e-01 9.63e+00 angle pdb=" N VAL B 268 " pdb=" CA VAL B 268 " pdb=" CB VAL B 268 " ideal model delta sigma weight residual 112.65 109.59 3.06 1.00e+00 1.00e+00 9.34e+00 angle pdb=" N GLU B 47 " pdb=" CA GLU B 47 " pdb=" CB GLU B 47 " ideal model delta sigma weight residual 110.12 114.50 -4.38 1.47e+00 4.63e-01 8.86e+00 angle pdb=" C PHE B 282 " pdb=" N GLN B 283 " pdb=" CA GLN B 283 " ideal model delta sigma weight residual 121.54 127.07 -5.53 1.91e+00 2.74e-01 8.39e+00 angle pdb=" CB MET B 38 " pdb=" CG MET B 38 " pdb=" SD MET B 38 " ideal model delta sigma weight residual 112.70 104.52 8.18 3.00e+00 1.11e-01 7.44e+00 ... (remaining 6422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 2528 16.50 - 33.00: 306 33.00 - 49.49: 51 49.49 - 65.99: 12 65.99 - 82.49: 8 Dihedral angle restraints: 2905 sinusoidal: 1191 harmonic: 1714 Sorted by residual: dihedral pdb=" CA PHE B 282 " pdb=" C PHE B 282 " pdb=" N GLN B 283 " pdb=" CA GLN B 283 " ideal model delta harmonic sigma weight residual 180.00 -152.34 -27.66 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA ALA A 279 " pdb=" C ALA A 279 " pdb=" N SER A 280 " pdb=" CA SER A 280 " ideal model delta harmonic sigma weight residual -180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA MET A 230 " pdb=" C MET A 230 " pdb=" N THR A 231 " pdb=" CA THR A 231 " ideal model delta harmonic sigma weight residual 180.00 161.46 18.54 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 2902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 380 0.030 - 0.061: 191 0.061 - 0.091: 76 0.091 - 0.122: 21 0.122 - 0.152: 11 Chirality restraints: 679 Sorted by residual: chirality pdb=" CA ARG B 275 " pdb=" N ARG B 275 " pdb=" C ARG B 275 " pdb=" CB ARG B 275 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CG LEU A 236 " pdb=" CB LEU A 236 " pdb=" CD1 LEU A 236 " pdb=" CD2 LEU A 236 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA VAL B 318 " pdb=" N VAL B 318 " pdb=" C VAL B 318 " pdb=" CB VAL B 318 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 676 not shown) Planarity restraints: 859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 244 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C TYR B 244 " -0.025 2.00e-02 2.50e+03 pdb=" O TYR B 244 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR B 245 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 213 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C GLN A 213 " -0.024 2.00e-02 2.50e+03 pdb=" O GLN A 213 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU A 214 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 72 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.70e+00 pdb=" C ALA A 72 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA A 72 " -0.008 2.00e-02 2.50e+03 pdb=" N GLU A 73 " -0.008 2.00e-02 2.50e+03 ... (remaining 856 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 415 2.72 - 3.27: 5638 3.27 - 3.81: 8488 3.81 - 4.36: 10038 4.36 - 4.90: 16378 Nonbonded interactions: 40957 Sorted by model distance: nonbonded pdb=" OE1 GLU B 212 " pdb=" OH TYR B 216 " model vdw 2.178 2.440 nonbonded pdb=" O GLU B 98 " pdb=" NE2 GLN B 102 " model vdw 2.182 2.520 nonbonded pdb=" O GLU A 248 " pdb=" ND2 ASN B 297 " model vdw 2.185 2.520 nonbonded pdb=" NZ LYS A 154 " pdb=" OD2 ASP A 166 " model vdw 2.193 2.520 nonbonded pdb=" O GLN B 223 " pdb=" OG SER B 226 " model vdw 2.222 2.440 ... (remaining 40952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 30 through 325) selection = (chain 'B' and resid 30 through 325) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 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: 2.220 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.240 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 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 : 0.007 0.046 4786 Z= 0.434 Angle : 0.787 8.184 6427 Z= 0.436 Chirality : 0.044 0.152 679 Planarity : 0.004 0.030 859 Dihedral : 14.924 82.489 1815 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 23.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.42 % Favored : 91.41 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: -0.29 (0.34), residues: 594 helix: 1.69 (0.29), residues: 296 sheet: -0.99 (0.57), residues: 82 loop : -2.68 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 184 HIS 0.001 0.001 HIS B 301 PHE 0.019 0.002 PHE B 136 TYR 0.021 0.002 TYR A 158 ARG 0.019 0.002 ARG B 275 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8736 (tp) cc_final: 0.8417 (tp) REVERT: B 233 TYR cc_start: 0.7285 (m-80) cc_final: 0.6726 (m-80) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1737 time to fit residues: 11.3961 Evaluate side-chains 43 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 0.0040 chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4786 Z= 0.175 Angle : 0.624 7.485 6427 Z= 0.326 Chirality : 0.041 0.136 679 Planarity : 0.003 0.047 859 Dihedral : 5.157 29.281 640 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % 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: 0.41 (0.35), residues: 594 helix: 2.32 (0.28), residues: 300 sheet: -0.97 (0.58), residues: 80 loop : -2.37 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 184 HIS 0.003 0.001 HIS B 301 PHE 0.012 0.002 PHE B 136 TYR 0.012 0.001 TYR B 245 ARG 0.005 0.001 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.525 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1603 time to fit residues: 11.1059 Evaluate side-chains 42 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.0870 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 0.0060 chunk 14 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.4774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 172 ASN B 146 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4786 Z= 0.150 Angle : 0.577 7.897 6427 Z= 0.302 Chirality : 0.040 0.132 679 Planarity : 0.003 0.031 859 Dihedral : 4.796 29.383 640 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.59 % Allowed : 13.27 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.35), residues: 594 helix: 2.60 (0.28), residues: 300 sheet: -0.92 (0.57), residues: 79 loop : -2.20 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 184 HIS 0.002 0.001 HIS B 301 PHE 0.013 0.001 PHE B 136 TYR 0.014 0.001 TYR B 245 ARG 0.006 0.001 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 203 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7235 (mtp) REVERT: B 38 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7839 (mmm) REVERT: B 233 TYR cc_start: 0.7074 (m-80) cc_final: 0.6710 (m-80) outliers start: 3 outliers final: 0 residues processed: 57 average time/residue: 0.1939 time to fit residues: 14.2440 Evaluate side-chains 44 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain B residue 38 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 50 optimal weight: 0.0470 chunk 15 optimal weight: 8.9990 chunk 46 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4786 Z= 0.166 Angle : 0.576 8.097 6427 Z= 0.303 Chirality : 0.040 0.132 679 Planarity : 0.003 0.031 859 Dihedral : 4.656 28.386 640 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.19 % Allowed : 14.06 % Favored : 84.75 % 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: 0.87 (0.35), residues: 594 helix: 2.69 (0.28), residues: 300 sheet: -0.89 (0.57), residues: 79 loop : -2.06 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 184 HIS 0.001 0.001 HIS B 301 PHE 0.013 0.001 PHE B 136 TYR 0.014 0.001 TYR B 245 ARG 0.006 0.001 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7304 (mtp) REVERT: A 233 TYR cc_start: 0.7529 (m-80) cc_final: 0.7327 (m-80) REVERT: B 38 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7769 (mmm) outliers start: 6 outliers final: 2 residues processed: 50 average time/residue: 0.1678 time to fit residues: 11.0953 Evaluate side-chains 44 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 203 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 14 optimal weight: 0.0870 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4786 Z= 0.153 Angle : 0.580 7.542 6427 Z= 0.300 Chirality : 0.040 0.132 679 Planarity : 0.003 0.030 859 Dihedral : 4.557 27.914 640 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.39 % Allowed : 16.04 % Favored : 82.57 % 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: 0.99 (0.35), residues: 594 helix: 2.74 (0.28), residues: 300 sheet: -0.88 (0.57), residues: 79 loop : -1.91 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 184 HIS 0.001 0.000 HIS B 301 PHE 0.013 0.001 PHE B 136 TYR 0.014 0.001 TYR B 245 ARG 0.006 0.001 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7197 (mtp) REVERT: A 233 TYR cc_start: 0.7595 (m-80) cc_final: 0.7356 (m-80) REVERT: B 38 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7595 (mmm) outliers start: 7 outliers final: 4 residues processed: 50 average time/residue: 0.1474 time to fit residues: 10.1503 Evaluate side-chains 47 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4786 Z= 0.166 Angle : 0.573 7.253 6427 Z= 0.301 Chirality : 0.040 0.172 679 Planarity : 0.003 0.029 859 Dihedral : 4.502 27.392 640 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.78 % Allowed : 17.82 % Favored : 80.40 % 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: 1.01 (0.35), residues: 594 helix: 2.64 (0.28), residues: 302 sheet: -0.90 (0.57), residues: 79 loop : -1.73 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 184 HIS 0.001 0.001 HIS B 301 PHE 0.013 0.001 PHE B 136 TYR 0.023 0.001 TYR A 158 ARG 0.007 0.001 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 203 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7151 (mtp) REVERT: B 38 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7576 (mmm) outliers start: 9 outliers final: 3 residues processed: 50 average time/residue: 0.1464 time to fit residues: 10.1192 Evaluate side-chains 46 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4786 Z= 0.177 Angle : 0.605 13.258 6427 Z= 0.308 Chirality : 0.040 0.138 679 Planarity : 0.003 0.027 859 Dihedral : 4.491 27.362 640 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.39 % Allowed : 18.81 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.35), residues: 594 helix: 2.62 (0.28), residues: 302 sheet: -0.88 (0.57), residues: 79 loop : -1.73 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 184 HIS 0.001 0.001 HIS B 301 PHE 0.014 0.001 PHE B 136 TYR 0.022 0.001 TYR A 158 ARG 0.007 0.001 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 203 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.7156 (mtp) REVERT: B 38 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7574 (mmm) outliers start: 7 outliers final: 3 residues processed: 52 average time/residue: 0.1501 time to fit residues: 10.5746 Evaluate side-chains 48 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 53 optimal weight: 0.0170 chunk 48 optimal weight: 0.4980 chunk 52 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4786 Z= 0.160 Angle : 0.628 11.599 6427 Z= 0.315 Chirality : 0.040 0.134 679 Planarity : 0.003 0.028 859 Dihedral : 4.442 27.740 640 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.39 % Allowed : 19.41 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.35), residues: 594 helix: 2.65 (0.28), residues: 302 sheet: -0.78 (0.57), residues: 79 loop : -1.73 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 184 HIS 0.001 0.000 HIS B 301 PHE 0.013 0.001 PHE B 136 TYR 0.017 0.001 TYR A 158 ARG 0.008 0.001 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: B 38 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7480 (mmm) outliers start: 7 outliers final: 4 residues processed: 51 average time/residue: 0.1788 time to fit residues: 11.8890 Evaluate side-chains 48 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4786 Z= 0.247 Angle : 0.691 12.790 6427 Z= 0.346 Chirality : 0.041 0.135 679 Planarity : 0.003 0.033 859 Dihedral : 4.581 28.484 640 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.19 % Allowed : 20.20 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.35), residues: 594 helix: 2.61 (0.28), residues: 303 sheet: -0.75 (0.59), residues: 79 loop : -1.81 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 184 HIS 0.002 0.001 HIS B 301 PHE 0.015 0.001 PHE B 136 TYR 0.018 0.001 TYR A 158 ARG 0.010 0.001 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.592 Fit side-chains REVERT: A 203 MET cc_start: 0.7954 (ttp) cc_final: 0.7064 (mtp) outliers start: 6 outliers final: 4 residues processed: 50 average time/residue: 0.1641 time to fit residues: 11.1031 Evaluate side-chains 49 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4786 Z= 0.176 Angle : 0.692 12.927 6427 Z= 0.343 Chirality : 0.041 0.142 679 Planarity : 0.003 0.027 859 Dihedral : 4.491 27.731 640 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.79 % Allowed : 20.00 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.35), residues: 594 helix: 2.54 (0.28), residues: 304 sheet: -0.71 (0.58), residues: 79 loop : -1.74 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 184 HIS 0.001 0.001 HIS B 301 PHE 0.013 0.001 PHE B 136 TYR 0.016 0.001 TYR A 158 ARG 0.006 0.001 ARG B 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.540 Fit side-chains REVERT: A 203 MET cc_start: 0.7766 (ttp) cc_final: 0.7466 (mtp) outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 0.1548 time to fit residues: 10.3114 Evaluate side-chains 47 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.059938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.044853 restraints weight = 19804.894| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 4.43 r_work: 0.2842 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4786 Z= 0.174 Angle : 0.683 12.871 6427 Z= 0.337 Chirality : 0.041 0.135 679 Planarity : 0.003 0.026 859 Dihedral : 4.415 27.100 640 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.79 % Allowed : 20.20 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.35), residues: 594 helix: 2.59 (0.28), residues: 303 sheet: -0.71 (0.58), residues: 79 loop : -1.69 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 184 HIS 0.001 0.001 HIS B 301 PHE 0.013 0.001 PHE B 136 TYR 0.016 0.001 TYR A 158 ARG 0.006 0.001 ARG B 264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1241.47 seconds wall clock time: 23 minutes 18.39 seconds (1398.39 seconds total)