Starting phenix.real_space_refine on Sun Mar 10 14:40:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihk_35447/03_2024/8ihk_35447_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihk_35447/03_2024/8ihk_35447.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihk_35447/03_2024/8ihk_35447_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihk_35447/03_2024/8ihk_35447_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihk_35447/03_2024/8ihk_35447_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihk_35447/03_2024/8ihk_35447.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihk_35447/03_2024/8ihk_35447.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihk_35447/03_2024/8ihk_35447_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihk_35447/03_2024/8ihk_35447_updated.pdb" } resolution = 3.21 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= 0.002 sd= 0.034 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 1515 2.51 5 N 361 2.21 5 O 360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2253 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2237 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 9, 'TRANS': 273} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'P9X': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.80, per 1000 atoms: 0.80 Number of scatterers: 2253 At special positions: 0 Unit cell: (52.26, 69.42, 73.32, 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 360 8.00 N 361 7.00 C 1515 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=1.63 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: 0.94 Conformation dependent library (CDL) restraints added in 420.2 milliseconds 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 544 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 11 helices and 1 sheets defined 70.7% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'R' and resid 26 through 28 No H-bonds generated for 'chain 'R' and resid 26 through 28' Processing helix chain 'R' and resid 30 through 54 Processing helix chain 'R' and resid 61 through 77 removed outlier: 3.661A pdb=" N PHE R 65 " --> pdb=" O SER R 61 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU R 66 " --> pdb=" O SER R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 88 removed outlier: 3.531A pdb=" N TYR R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR R 87 " --> pdb=" O VAL R 83 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL R 88 " --> pdb=" O MET R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 127 removed outlier: 3.821A pdb=" N PHE R 107 " --> pdb=" O VAL R 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN R 110 " --> pdb=" O MET R 106 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL R 121 " --> pdb=" O PHE R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 138 Processing helix chain 'R' and resid 141 through 157 removed outlier: 3.500A pdb=" N SER R 148 " --> pdb=" O ALA R 144 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL R 156 " --> pdb=" O TRP R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 164 Processing helix chain 'R' and resid 188 through 217 removed outlier: 3.594A pdb=" N LEU R 194 " --> pdb=" O GLU R 190 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Proline residue: R 200 - end of helix removed outlier: 3.546A pdb=" N LEU R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG R 216 " --> pdb=" O ILE R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 259 removed outlier: 3.536A pdb=" N VAL R 235 " --> pdb=" O PHE R 232 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL R 236 " --> pdb=" O ILE R 233 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS R 243 " --> pdb=" O PHE R 240 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE R 244 " --> pdb=" O VAL R 241 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU R 245 " --> pdb=" O ILE R 242 " (cutoff:3.500A) Proline residue: R 246 - end of helix removed outlier: 3.659A pdb=" N VAL R 249 " --> pdb=" O PRO R 246 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL R 250 " --> pdb=" O SER R 247 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE R 252 " --> pdb=" O VAL R 249 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS R 253 " --> pdb=" O VAL R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 293 removed outlier: 4.455A pdb=" N VAL R 272 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER R 281 " --> pdb=" O PHE R 277 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR R 283 " --> pdb=" O THR R 279 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR R 284 " --> pdb=" O LEU R 280 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN R 286 " --> pdb=" O PHE R 282 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET R 288 " --> pdb=" O TYR R 284 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing sheet with id= A, first strand: chain 'R' and resid 169 through 171 removed outlier: 3.633A pdb=" N ILE R 169 " --> pdb=" O VAL R 176 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL R 176 " --> pdb=" O ILE R 169 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA R 174 " --> pdb=" O ASN R 171 " (cutoff:3.500A) 118 hydrogen bonds defined for protein. 285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.52 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 432 1.33 - 1.45: 608 1.45 - 1.57: 1259 1.57 - 1.70: 0 1.70 - 1.82: 23 Bond restraints: 2322 Sorted by residual: bond pdb=" C1 P9X R 501 " pdb=" C6 P9X R 501 " ideal model delta sigma weight residual 1.402 1.524 -0.122 2.00e-02 2.50e+03 3.75e+01 bond pdb=" C1 P9X R 501 " pdb=" O1 P9X R 501 " ideal model delta sigma weight residual 1.578 1.463 0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" CA TRP R 142 " pdb=" CB TRP R 142 " ideal model delta sigma weight residual 1.529 1.477 0.052 1.55e-02 4.16e+03 1.14e+01 bond pdb=" N TRP R 142 " pdb=" CA TRP R 142 " ideal model delta sigma weight residual 1.459 1.423 0.037 1.19e-02 7.06e+03 9.56e+00 bond pdb=" C3 P9X R 501 " pdb=" C4 P9X R 501 " ideal model delta sigma weight residual 1.414 1.361 0.053 2.00e-02 2.50e+03 7.02e+00 ... (remaining 2317 not shown) Histogram of bond angle deviations from ideal: 100.95 - 107.55: 88 107.55 - 114.15: 1333 114.15 - 120.75: 1031 120.75 - 127.35: 681 127.35 - 133.95: 34 Bond angle restraints: 3167 Sorted by residual: angle pdb=" C3 P9X R 501 " pdb=" C4 P9X R 501 " pdb=" C5 P9X R 501 " ideal model delta sigma weight residual 120.00 132.23 -12.23 3.00e+00 1.11e-01 1.66e+01 angle pdb=" N TRP R 142 " pdb=" CA TRP R 142 " pdb=" C TRP R 142 " ideal model delta sigma weight residual 111.07 106.89 4.18 1.07e+00 8.73e-01 1.53e+01 angle pdb=" CA TRP R 142 " pdb=" C TRP R 142 " pdb=" N THR R 143 " ideal model delta sigma weight residual 117.07 120.84 -3.77 1.14e+00 7.69e-01 1.09e+01 angle pdb=" C ASN R 141 " pdb=" N TRP R 142 " pdb=" CA TRP R 142 " ideal model delta sigma weight residual 120.44 117.05 3.39 1.30e+00 5.92e-01 6.80e+00 angle pdb=" N LEU R 167 " pdb=" CA LEU R 167 " pdb=" C LEU R 167 " ideal model delta sigma weight residual 108.34 111.41 -3.07 1.31e+00 5.83e-01 5.51e+00 ... (remaining 3162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 1141 17.97 - 35.93: 151 35.93 - 53.90: 31 53.90 - 71.86: 2 71.86 - 89.83: 3 Dihedral angle restraints: 1328 sinusoidal: 495 harmonic: 833 Sorted by residual: dihedral pdb=" CB CYS R 19 " pdb=" SG CYS R 19 " pdb=" SG CYS R 266 " pdb=" CB CYS R 266 " ideal model delta sinusoidal sigma weight residual 93.00 177.87 -84.87 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS R 100 " pdb=" SG CYS R 100 " pdb=" SG CYS R 177 " pdb=" CB CYS R 177 " ideal model delta sinusoidal sigma weight residual 93.00 127.23 -34.23 1 1.00e+01 1.00e-02 1.66e+01 dihedral pdb=" CA CYS R 100 " pdb=" CB CYS R 100 " pdb=" SG CYS R 100 " pdb=" SG CYS R 177 " ideal model delta sinusoidal sigma weight residual 79.00 12.78 66.22 1 2.00e+01 2.50e-03 1.43e+01 ... (remaining 1325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 211 0.025 - 0.050: 89 0.050 - 0.075: 46 0.075 - 0.100: 17 0.100 - 0.125: 5 Chirality restraints: 368 Sorted by residual: chirality pdb=" C1 P9X R 501 " pdb=" C2 P9X R 501 " pdb=" C6 P9X R 501 " pdb=" O1 P9X R 501 " both_signs ideal model delta sigma weight residual False 2.64 2.77 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA ILE R 178 " pdb=" N ILE R 178 " pdb=" C ILE R 178 " pdb=" CB ILE R 178 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA VAL R 20 " pdb=" N VAL R 20 " pdb=" C VAL R 20 " pdb=" CB VAL R 20 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 365 not shown) Planarity restraints: 382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 98 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO R 99 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO R 99 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 99 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 31 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.29e+00 pdb=" N PRO R 32 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO R 32 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 32 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 30 " -0.019 5.00e-02 4.00e+02 2.80e-02 1.25e+00 pdb=" N PRO R 31 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO R 31 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 31 " -0.016 5.00e-02 4.00e+02 ... (remaining 379 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 488 2.78 - 3.31: 2241 3.31 - 3.84: 3581 3.84 - 4.37: 4045 4.37 - 4.90: 7002 Nonbonded interactions: 17357 Sorted by model distance: nonbonded pdb=" OD1 ASN R 68 " pdb=" OG SER R 148 " model vdw 2.246 2.440 nonbonded pdb=" NH2 ARG R 111 " pdb=" O2 P9X R 501 " model vdw 2.393 2.520 nonbonded pdb=" NH2 ARG R 101 " pdb=" O LEU R 163 " model vdw 2.396 2.520 nonbonded pdb=" OD1 ASP R 97 " pdb=" N ILE R 98 " model vdw 2.433 2.520 nonbonded pdb=" NE1 TRP R 93 " pdb=" O GLY R 96 " model vdw 2.459 2.520 ... (remaining 17352 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 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: 2.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.270 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 2322 Z= 0.372 Angle : 0.616 12.230 3167 Z= 0.298 Chirality : 0.039 0.125 368 Planarity : 0.004 0.046 382 Dihedral : 16.217 89.829 775 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 27.97 % Favored : 72.03 % 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 (0.49), residues: 281 helix: -0.13 (0.38), residues: 191 sheet: None (None), residues: 0 loop : -1.61 (0.63), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP R 142 HIS 0.001 0.000 HIS R 161 PHE 0.012 0.001 PHE R 21 TYR 0.011 0.001 TYR R 87 ARG 0.001 0.000 ARG R 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.252 Fit side-chains REVERT: R 192 MET cc_start: 0.6068 (ttp) cc_final: 0.5770 (tmm) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1528 time to fit residues: 7.4482 Evaluate side-chains 39 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 0.0570 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2322 Z= 0.150 Angle : 0.509 6.680 3167 Z= 0.258 Chirality : 0.041 0.121 368 Planarity : 0.005 0.048 382 Dihedral : 4.741 33.361 306 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.12 % Allowed : 26.69 % Favored : 71.19 % 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: -0.58 (0.49), residues: 281 helix: 0.06 (0.36), residues: 195 sheet: None (None), residues: 0 loop : -1.20 (0.68), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 50 HIS 0.002 0.000 HIS R 55 PHE 0.014 0.001 PHE R 232 TYR 0.008 0.001 TYR R 87 ARG 0.001 0.000 ARG R 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.244 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 42 average time/residue: 0.1236 time to fit residues: 6.3740 Evaluate side-chains 38 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.0040 chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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: 0.7598 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2322 Z= 0.128 Angle : 0.504 9.995 3167 Z= 0.243 Chirality : 0.039 0.119 368 Planarity : 0.004 0.045 382 Dihedral : 4.266 28.543 306 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.54 % Allowed : 29.66 % Favored : 67.80 % 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: -0.38 (0.50), residues: 281 helix: 0.23 (0.38), residues: 196 sheet: None (None), residues: 0 loop : -1.18 (0.67), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP R 142 HIS 0.002 0.000 HIS R 253 PHE 0.007 0.001 PHE R 206 TYR 0.005 0.001 TYR R 284 ARG 0.001 0.000 ARG R 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.279 Fit side-chains REVERT: R 21 PHE cc_start: 0.4631 (m-80) cc_final: 0.4092 (m-80) outliers start: 6 outliers final: 6 residues processed: 44 average time/residue: 0.1101 time to fit residues: 6.0524 Evaluate side-chains 44 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 226 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 0.0020 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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: 0.7636 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2322 Z= 0.150 Angle : 0.495 7.999 3167 Z= 0.242 Chirality : 0.040 0.118 368 Planarity : 0.004 0.045 382 Dihedral : 4.297 30.191 306 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.66 % Allowed : 27.54 % Favored : 67.80 % 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: -0.52 (0.50), residues: 281 helix: 0.11 (0.38), residues: 195 sheet: None (None), residues: 0 loop : -1.20 (0.68), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 142 HIS 0.002 0.001 HIS R 253 PHE 0.015 0.001 PHE R 232 TYR 0.005 0.001 TYR R 284 ARG 0.001 0.000 ARG R 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 0.221 Fit side-chains REVERT: R 21 PHE cc_start: 0.4722 (m-80) cc_final: 0.4267 (m-80) REVERT: R 51 ILE cc_start: 0.7921 (mm) cc_final: 0.7707 (mm) REVERT: R 168 LEU cc_start: 0.6248 (OUTLIER) cc_final: 0.5661 (mt) outliers start: 11 outliers final: 7 residues processed: 45 average time/residue: 0.1205 time to fit residues: 6.7059 Evaluate side-chains 45 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 226 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 0.0870 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 0.0010 overall best weight: 0.5164 ------------------------------------------------------------------------------- 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: 0.7612 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2322 Z= 0.126 Angle : 0.489 7.574 3167 Z= 0.240 Chirality : 0.039 0.115 368 Planarity : 0.004 0.045 382 Dihedral : 4.198 27.518 306 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.81 % Allowed : 30.51 % Favored : 65.68 % 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: -0.45 (0.51), residues: 281 helix: 0.25 (0.38), residues: 194 sheet: None (None), residues: 0 loop : -1.37 (0.64), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP R 142 HIS 0.002 0.000 HIS R 253 PHE 0.007 0.001 PHE R 206 TYR 0.005 0.001 TYR R 284 ARG 0.001 0.000 ARG R 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.240 Fit side-chains REVERT: R 21 PHE cc_start: 0.4774 (m-80) cc_final: 0.4393 (m-80) REVERT: R 51 ILE cc_start: 0.7912 (mm) cc_final: 0.7684 (mm) REVERT: R 168 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.5643 (mt) outliers start: 9 outliers final: 7 residues processed: 45 average time/residue: 0.1167 time to fit residues: 6.4976 Evaluate side-chains 46 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 277 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7647 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2322 Z= 0.160 Angle : 0.491 6.988 3167 Z= 0.243 Chirality : 0.040 0.116 368 Planarity : 0.004 0.045 382 Dihedral : 4.332 30.781 306 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 5.08 % Allowed : 30.51 % Favored : 64.41 % 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: -0.46 (0.51), residues: 281 helix: 0.19 (0.38), residues: 195 sheet: None (None), residues: 0 loop : -1.25 (0.67), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 142 HIS 0.003 0.001 HIS R 253 PHE 0.014 0.001 PHE R 232 TYR 0.006 0.001 TYR R 295 ARG 0.001 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.267 Fit side-chains REVERT: R 21 PHE cc_start: 0.4853 (m-80) cc_final: 0.4524 (m-80) REVERT: R 168 LEU cc_start: 0.6257 (OUTLIER) cc_final: 0.5644 (mt) outliers start: 12 outliers final: 8 residues processed: 48 average time/residue: 0.1192 time to fit residues: 7.0201 Evaluate side-chains 47 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 183 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.0060 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.0370 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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: 0.7624 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2322 Z= 0.137 Angle : 0.488 7.166 3167 Z= 0.238 Chirality : 0.039 0.114 368 Planarity : 0.004 0.045 382 Dihedral : 4.231 29.616 306 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.24 % Allowed : 30.93 % Favored : 64.83 % 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: -0.38 (0.51), residues: 281 helix: 0.27 (0.38), residues: 195 sheet: None (None), residues: 0 loop : -1.28 (0.67), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP R 142 HIS 0.002 0.000 HIS R 253 PHE 0.013 0.001 PHE R 232 TYR 0.005 0.001 TYR R 284 ARG 0.001 0.000 ARG R 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.237 Fit side-chains REVERT: R 21 PHE cc_start: 0.4844 (m-80) cc_final: 0.4538 (m-80) REVERT: R 168 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5639 (mt) outliers start: 10 outliers final: 9 residues processed: 48 average time/residue: 0.1224 time to fit residues: 7.1375 Evaluate side-chains 50 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 277 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7629 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2322 Z= 0.140 Angle : 0.491 7.538 3167 Z= 0.241 Chirality : 0.039 0.115 368 Planarity : 0.004 0.044 382 Dihedral : 4.198 29.979 306 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.66 % Allowed : 30.93 % Favored : 64.41 % 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: -0.37 (0.51), residues: 281 helix: 0.28 (0.38), residues: 196 sheet: None (None), residues: 0 loop : -1.31 (0.68), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP R 142 HIS 0.002 0.001 HIS R 253 PHE 0.014 0.001 PHE R 232 TYR 0.005 0.001 TYR R 284 ARG 0.001 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.277 Fit side-chains REVERT: R 168 LEU cc_start: 0.6236 (OUTLIER) cc_final: 0.5616 (mt) outliers start: 11 outliers final: 10 residues processed: 48 average time/residue: 0.1173 time to fit residues: 6.9593 Evaluate side-chains 50 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 277 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 4.9990 chunk 23 optimal weight: 0.2980 chunk 6 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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: 0.7634 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2322 Z= 0.151 Angle : 0.502 7.181 3167 Z= 0.249 Chirality : 0.039 0.114 368 Planarity : 0.004 0.044 382 Dihedral : 4.265 26.696 306 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.66 % Allowed : 31.36 % Favored : 63.98 % 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: -0.38 (0.51), residues: 281 helix: 0.29 (0.38), residues: 195 sheet: None (None), residues: 0 loop : -1.34 (0.67), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP R 142 HIS 0.004 0.001 HIS R 253 PHE 0.014 0.001 PHE R 232 TYR 0.006 0.001 TYR R 86 ARG 0.001 0.000 ARG R 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.237 Fit side-chains REVERT: R 168 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5623 (mt) outliers start: 11 outliers final: 10 residues processed: 48 average time/residue: 0.1212 time to fit residues: 7.1854 Evaluate side-chains 51 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 277 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7647 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2322 Z= 0.162 Angle : 0.509 7.430 3167 Z= 0.252 Chirality : 0.040 0.115 368 Planarity : 0.004 0.044 382 Dihedral : 4.348 29.461 306 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.66 % Allowed : 31.78 % Favored : 63.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.51), residues: 281 helix: 0.22 (0.38), residues: 196 sheet: None (None), residues: 0 loop : -1.29 (0.68), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP R 142 HIS 0.004 0.001 HIS R 253 PHE 0.015 0.001 PHE R 232 TYR 0.006 0.001 TYR R 86 ARG 0.001 0.000 ARG R 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.276 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 47 average time/residue: 0.1244 time to fit residues: 7.1314 Evaluate side-chains 48 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 277 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.196488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.152372 restraints weight = 2539.292| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.26 r_work: 0.3556 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2322 Z= 0.143 Angle : 0.540 8.955 3167 Z= 0.258 Chirality : 0.040 0.115 368 Planarity : 0.004 0.044 382 Dihedral : 4.290 27.713 306 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.24 % Allowed : 31.36 % Favored : 64.41 % 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: -0.36 (0.51), residues: 281 helix: 0.29 (0.38), residues: 196 sheet: None (None), residues: 0 loop : -1.32 (0.68), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP R 142 HIS 0.004 0.001 HIS R 253 PHE 0.006 0.001 PHE R 206 TYR 0.005 0.001 TYR R 284 ARG 0.001 0.000 ARG R 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 956.70 seconds wall clock time: 18 minutes 28.73 seconds (1108.73 seconds total)