Starting phenix.real_space_refine on Mon Sep 23 16:46:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsq_24677/09_2024/7rsq_24677.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsq_24677/09_2024/7rsq_24677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsq_24677/09_2024/7rsq_24677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsq_24677/09_2024/7rsq_24677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsq_24677/09_2024/7rsq_24677.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsq_24677/09_2024/7rsq_24677.cif" } resolution = 3.8 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 13 5.16 5 C 1296 2.51 5 N 349 2.21 5 O 354 1.98 5 H 1958 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3970 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 3970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 3970 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 5, 'TRANS': 240} Chain breaks: 7 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 2.98, per 1000 atoms: 0.75 Number of scatterers: 3970 At special positions: 0 Unit cell: (55.86, 65.66, 104.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 O 354 8.00 N 349 7.00 C 1296 6.00 H 1958 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 577.6 milliseconds 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 478 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 86.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'B' and resid 5 through 20 Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.518A pdb=" N GLU B 44 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 49 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 105 removed outlier: 4.154A pdb=" N ALA B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 107 No H-bonds generated for 'chain 'B' and resid 106 through 107' Processing helix chain 'B' and resid 111 through 111 No H-bonds generated for 'chain 'B' and resid 111 through 111' Processing helix chain 'B' and resid 112 through 127 removed outlier: 4.274A pdb=" N GLU B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 152 removed outlier: 3.932A pdb=" N ASN B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 173 removed outlier: 4.883A pdb=" N ALA B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 221 removed outlier: 3.734A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 239 removed outlier: 3.537A pdb=" N LEU B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 263 removed outlier: 3.970A pdb=" N TRP B 249 " --> pdb=" O HIS B 245 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 254 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 281 removed outlier: 4.148A pdb=" N ARG B 270 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N HIS B 271 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N CYS B 272 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 307 through 325 removed outlier: 3.933A pdb=" N ALA B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 328 No H-bonds generated for 'chain 'B' and resid 326 through 328' Processing helix chain 'B' and resid 391 through 405 removed outlier: 4.613A pdb=" N VAL B 403 " --> pdb=" O GLY B 399 " (cutoff:3.500A) 124 hydrogen bonds defined for protein. 372 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: 1.18 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.40 - 0.69: 2 0.69 - 0.97: 137 0.97 - 1.25: 2124 1.25 - 1.53: 1498 1.53 - 1.81: 252 Warning: very small bond lengths. Bond restraints: 4013 Sorted by residual: bond pdb=" CG MET B 267 " pdb=" HG2 MET B 267 " ideal model delta sigma weight residual 0.970 1.583 -0.613 2.00e-02 2.50e+03 9.41e+02 bond pdb=" N HIS B 241 " pdb=" H HIS B 241 " ideal model delta sigma weight residual 0.860 0.404 0.456 2.00e-02 2.50e+03 5.20e+02 bond pdb=" CB PHE B 266 " pdb=" HB2 PHE B 266 " ideal model delta sigma weight residual 0.970 0.594 0.376 2.00e-02 2.50e+03 3.53e+02 bond pdb=" N LEU B 264 " pdb=" H LEU B 264 " ideal model delta sigma weight residual 0.860 1.128 -0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" CB MET B 267 " pdb=" HB2 MET B 267 " ideal model delta sigma weight residual 0.970 0.741 0.229 2.00e-02 2.50e+03 1.31e+02 ... (remaining 4008 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.94: 7162 13.94 - 27.88: 3 27.88 - 41.82: 3 41.82 - 55.77: 0 55.77 - 69.71: 1 Bond angle restraints: 7169 Sorted by residual: angle pdb=" HB2 PHE B 266 " pdb=" CB PHE B 266 " pdb=" HB3 PHE B 266 " ideal model delta sigma weight residual 110.00 40.29 69.71 3.00e+00 1.11e-01 5.40e+02 angle pdb=" CA PHE B 266 " pdb=" CB PHE B 266 " pdb=" HB2 PHE B 266 " ideal model delta sigma weight residual 109.00 70.58 38.42 3.00e+00 1.11e-01 1.64e+02 angle pdb=" HG2 MET B 267 " pdb=" CG MET B 267 " pdb=" HG3 MET B 267 " ideal model delta sigma weight residual 110.00 138.24 -28.24 3.00e+00 1.11e-01 8.86e+01 angle pdb=" CG PHE B 266 " pdb=" CB PHE B 266 " pdb=" HB2 PHE B 266 " ideal model delta sigma weight residual 108.00 135.95 -27.95 3.00e+00 1.11e-01 8.68e+01 angle pdb=" SD MET B 267 " pdb=" CG MET B 267 " pdb=" HG2 MET B 267 " ideal model delta sigma weight residual 108.00 84.32 23.68 3.00e+00 1.11e-01 6.23e+01 ... (remaining 7164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.64: 1724 12.64 - 25.28: 87 25.28 - 37.92: 43 37.92 - 50.55: 22 50.55 - 63.19: 22 Dihedral angle restraints: 1898 sinusoidal: 997 harmonic: 901 Sorted by residual: dihedral pdb=" CA MET B 223 " pdb=" C MET B 223 " pdb=" N PHE B 224 " pdb=" CA PHE B 224 " ideal model delta harmonic sigma weight residual -180.00 -159.31 -20.69 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" N PHE B 203 " pdb=" CA PHE B 203 " pdb=" CB PHE B 203 " pdb=" CG PHE B 203 " ideal model delta sinusoidal sigma weight residual 60.00 0.25 59.75 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA GLN B 400 " pdb=" CB GLN B 400 " pdb=" CG GLN B 400 " pdb=" CD GLN B 400 " ideal model delta sinusoidal sigma weight residual -180.00 -129.95 -50.05 3 1.50e+01 4.44e-03 8.85e+00 ... (remaining 1895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 230 0.057 - 0.114: 60 0.114 - 0.171: 10 0.171 - 0.229: 0 0.229 - 0.286: 1 Chirality restraints: 301 Sorted by residual: chirality pdb=" CA ASN B 242 " pdb=" N ASN B 242 " pdb=" C ASN B 242 " pdb=" CB ASN B 242 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA PHE B 266 " pdb=" N PHE B 266 " pdb=" C PHE B 266 " pdb=" CB PHE B 266 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA VAL B 403 " pdb=" N VAL B 403 " pdb=" C VAL B 403 " pdb=" CB VAL B 403 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 298 not shown) Planarity restraints: 580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 242 " 0.304 2.00e-02 2.50e+03 3.43e-01 1.76e+03 pdb=" CG ASN B 242 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN B 242 " -0.293 2.00e-02 2.50e+03 pdb=" ND2 ASN B 242 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 242 " -0.506 2.00e-02 2.50e+03 pdb="HD22 ASN B 242 " 0.520 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 400 " -0.184 2.00e-02 2.50e+03 2.10e-01 6.60e+02 pdb=" CD GLN B 400 " 0.014 2.00e-02 2.50e+03 pdb=" OE1 GLN B 400 " 0.175 2.00e-02 2.50e+03 pdb=" NE2 GLN B 400 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN B 400 " -0.319 2.00e-02 2.50e+03 pdb="HE22 GLN B 400 " 0.312 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 262 " -0.160 2.00e-02 2.50e+03 1.60e-01 3.82e+02 pdb=" CG ASN B 262 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN B 262 " 0.153 2.00e-02 2.50e+03 pdb=" ND2 ASN B 262 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 262 " -0.230 2.00e-02 2.50e+03 pdb="HD22 ASN B 262 " 0.225 2.00e-02 2.50e+03 ... (remaining 577 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 303 2.26 - 2.84: 7835 2.84 - 3.43: 9345 3.43 - 4.01: 11655 4.01 - 4.60: 17202 Nonbonded interactions: 46340 Sorted by model distance: nonbonded pdb=" O LYS B 205 " pdb=" HZ2 LYS B 205 " model vdw 1.674 2.450 nonbonded pdb=" O SER B 35 " pdb=" H TYR B 37 " model vdw 1.680 2.450 nonbonded pdb=" HA TYR B 230 " pdb=" HD1 TYR B 230 " model vdw 1.700 2.270 nonbonded pdb=" O ALA B 160 " pdb=" HG SER B 164 " model vdw 1.707 2.450 nonbonded pdb=" O LEU B 17 " pdb=" HG SER B 20 " model vdw 1.727 2.450 ... (remaining 46335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.160 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: 0.070 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.510 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 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 : 0.008 0.042 2055 Z= 0.502 Angle : 0.802 9.818 2768 Z= 0.556 Chirality : 0.053 0.286 301 Planarity : 0.004 0.058 345 Dihedral : 12.745 59.753 744 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.88 % Allowed : 2.40 % Favored : 94.71 % 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: -0.64 (0.51), residues: 230 helix: -0.54 (0.34), residues: 169 sheet: None (None), residues: 0 loop : 0.51 (0.87), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 6 HIS 0.002 0.000 HIS B 105 PHE 0.013 0.001 PHE B 280 TYR 0.010 0.001 TYR B 172 ARG 0.003 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 42 average time/residue: 0.4401 time to fit residues: 20.4432 Evaluate side-chains 24 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 265 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2055 Z= 0.199 Angle : 0.554 4.335 2768 Z= 0.307 Chirality : 0.031 0.119 301 Planarity : 0.005 0.047 345 Dihedral : 5.826 59.873 270 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.92 % Allowed : 5.77 % Favored : 92.31 % 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: 1.51 (0.54), residues: 230 helix: 1.27 (0.37), residues: 163 sheet: None (None), residues: 0 loop : 0.59 (0.87), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 249 HIS 0.004 0.001 HIS B 401 PHE 0.016 0.002 PHE B 396 TYR 0.019 0.001 TYR B 317 ARG 0.008 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7619 (tt) outliers start: 4 outliers final: 2 residues processed: 31 average time/residue: 0.3192 time to fit residues: 11.4875 Evaluate side-chains 25 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 203 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7070 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2055 Z= 0.165 Angle : 0.474 4.433 2768 Z= 0.264 Chirality : 0.028 0.116 301 Planarity : 0.004 0.048 345 Dihedral : 5.261 58.488 269 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.44 % Allowed : 9.62 % Favored : 88.94 % 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: 1.87 (0.56), residues: 230 helix: 1.71 (0.39), residues: 175 sheet: None (None), residues: 0 loop : -0.18 (0.89), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 249 HIS 0.002 0.001 HIS B 245 PHE 0.010 0.001 PHE B 396 TYR 0.016 0.001 TYR B 317 ARG 0.008 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 125 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7573 (tt) outliers start: 3 outliers final: 1 residues processed: 25 average time/residue: 0.3140 time to fit residues: 9.2633 Evaluate side-chains 23 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 203 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 0.0970 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.0570 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 overall best weight: 0.5296 ------------------------------------------------------------------------------- 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: 0.7073 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 2055 Z= 0.160 Angle : 0.453 6.529 2768 Z= 0.247 Chirality : 0.028 0.098 301 Planarity : 0.004 0.054 345 Dihedral : 5.150 58.451 269 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.92 % Allowed : 11.54 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.57), residues: 230 helix: 2.33 (0.39), residues: 169 sheet: None (None), residues: 0 loop : -0.40 (0.86), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 249 HIS 0.002 0.001 HIS B 245 PHE 0.007 0.001 PHE B 396 TYR 0.012 0.001 TYR B 317 ARG 0.007 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 125 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7470 (tt) outliers start: 4 outliers final: 1 residues processed: 22 average time/residue: 0.3336 time to fit residues: 8.6040 Evaluate side-chains 21 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 203 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 22 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: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2055 Z= 0.269 Angle : 0.533 3.858 2768 Z= 0.301 Chirality : 0.030 0.101 301 Planarity : 0.005 0.060 345 Dihedral : 5.393 53.019 269 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.44 % Allowed : 14.42 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.55), residues: 230 helix: 1.35 (0.38), residues: 185 sheet: None (None), residues: 0 loop : -0.89 (0.89), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 249 HIS 0.004 0.001 HIS B 105 PHE 0.012 0.002 PHE B 13 TYR 0.026 0.002 TYR B 317 ARG 0.005 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 18 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 125 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7684 (tt) outliers start: 3 outliers final: 2 residues processed: 20 average time/residue: 0.2627 time to fit residues: 6.1700 Evaluate side-chains 21 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 18 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 397 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 0.0970 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2055 Z= 0.148 Angle : 0.430 4.083 2768 Z= 0.236 Chirality : 0.027 0.090 301 Planarity : 0.004 0.065 345 Dihedral : 5.212 55.666 269 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.92 % Allowed : 13.94 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.57), residues: 230 helix: 1.76 (0.40), residues: 186 sheet: None (None), residues: 0 loop : -1.29 (0.83), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 149 HIS 0.003 0.001 HIS B 105 PHE 0.011 0.001 PHE B 396 TYR 0.013 0.001 TYR B 317 ARG 0.010 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 17 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 21 ARG cc_start: 0.7399 (mmm160) cc_final: 0.7173 (tpp80) REVERT: B 125 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7526 (tt) REVERT: B 319 LEU cc_start: 0.8597 (tp) cc_final: 0.8389 (tp) outliers start: 4 outliers final: 2 residues processed: 19 average time/residue: 0.3490 time to fit residues: 7.7937 Evaluate side-chains 20 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 17 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 397 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.0670 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.0970 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2055 Z= 0.124 Angle : 0.398 4.071 2768 Z= 0.217 Chirality : 0.027 0.088 301 Planarity : 0.003 0.044 345 Dihedral : 5.012 56.608 269 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.92 % Allowed : 12.98 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.58), residues: 230 helix: 1.97 (0.40), residues: 191 sheet: None (None), residues: 0 loop : -1.28 (0.81), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 314 HIS 0.002 0.000 HIS B 105 PHE 0.006 0.001 PHE B 396 TYR 0.009 0.001 TYR B 317 ARG 0.006 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 17 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 20 average time/residue: 0.3452 time to fit residues: 8.1546 Evaluate side-chains 17 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 397 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.3980 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.6215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2055 Z= 0.163 Angle : 0.438 3.964 2768 Z= 0.235 Chirality : 0.027 0.087 301 Planarity : 0.004 0.052 345 Dihedral : 4.985 55.247 269 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.40 % Allowed : 12.02 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.58), residues: 230 helix: 1.95 (0.40), residues: 191 sheet: None (None), residues: 0 loop : -1.43 (0.80), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 314 HIS 0.002 0.001 HIS B 105 PHE 0.011 0.001 PHE B 396 TYR 0.015 0.001 TYR B 317 ARG 0.006 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 17 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 21 average time/residue: 0.3284 time to fit residues: 8.1813 Evaluate side-chains 20 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 15 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 397 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.6323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2055 Z= 0.182 Angle : 0.463 4.302 2768 Z= 0.249 Chirality : 0.027 0.089 301 Planarity : 0.003 0.030 345 Dihedral : 5.070 54.982 269 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.44 % Allowed : 13.94 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.58), residues: 230 helix: 1.95 (0.40), residues: 190 sheet: None (None), residues: 0 loop : -1.65 (0.76), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 314 HIS 0.003 0.001 HIS B 105 PHE 0.013 0.001 PHE B 396 TYR 0.016 0.001 TYR B 317 ARG 0.002 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 17 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 20 average time/residue: 0.3516 time to fit residues: 8.4809 Evaluate side-chains 19 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 397 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.6482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2055 Z= 0.161 Angle : 0.443 4.159 2768 Z= 0.236 Chirality : 0.027 0.086 301 Planarity : 0.002 0.024 345 Dihedral : 5.021 55.595 269 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.44 % Allowed : 13.94 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.58), residues: 230 helix: 2.15 (0.40), residues: 186 sheet: None (None), residues: 0 loop : -1.83 (0.73), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 314 HIS 0.002 0.001 HIS B 105 PHE 0.012 0.001 PHE B 396 TYR 0.014 0.001 TYR B 317 ARG 0.002 0.000 ARG B 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 19 average time/residue: 0.3516 time to fit residues: 7.9040 Evaluate side-chains 18 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 397 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.114272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.099578 restraints weight = 15688.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.102847 restraints weight = 6695.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.104863 restraints weight = 3703.396| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.6562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2055 Z= 0.178 Angle : 0.458 3.940 2768 Z= 0.248 Chirality : 0.027 0.093 301 Planarity : 0.002 0.021 345 Dihedral : 5.077 55.103 269 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.96 % Allowed : 14.90 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.58), residues: 230 helix: 2.12 (0.40), residues: 187 sheet: None (None), residues: 0 loop : -2.17 (0.71), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 314 HIS 0.003 0.001 HIS B 105 PHE 0.015 0.002 PHE B 396 TYR 0.016 0.001 TYR B 317 ARG 0.001 0.000 ARG B 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1679.00 seconds wall clock time: 33 minutes 14.27 seconds (1994.27 seconds total)