Starting phenix.real_space_refine on Wed Nov 13 23:37:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihk_35447/11_2024/8ihk_35447.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihk_35447/11_2024/8ihk_35447.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihk_35447/11_2024/8ihk_35447.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihk_35447/11_2024/8ihk_35447.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihk_35447/11_2024/8ihk_35447.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihk_35447/11_2024/8ihk_35447.cif" } 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. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 2.37, per 1000 atoms: 1.05 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 - 3.00 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: 0.69 Conformation dependent library (CDL) restraints added in 288.6 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... Secondary structure from input PDB file: 12 helices and 1 sheets defined 77.0% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 25 through 28 Processing helix chain 'R' and resid 29 through 55 Processing helix chain 'R' and resid 60 through 78 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 79 through 89 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) removed outlier: 3.521A pdb=" N ARG R 89 " --> pdb=" O ASP R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 128 removed outlier: 3.569A pdb=" N LEU R 102 " --> pdb=" O ILE R 98 " (cutoff:3.500A) 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 134 through 139 removed outlier: 3.640A pdb=" N ILE R 139 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 158 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) removed outlier: 3.603A pdb=" N LEU R 158 " --> pdb=" O ILE R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 165 removed outlier: 4.004A pdb=" N LYS R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS R 165 " --> pdb=" O HIS R 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 160 through 165' Processing helix chain 'R' and resid 187 through 218 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 260 removed outlier: 4.005A pdb=" N ALA R 229 " --> pdb=" O LYS R 225 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 267 through 280 removed outlier: 4.301A pdb=" N SER R 271 " --> pdb=" O GLU R 267 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL R 272 " --> pdb=" O VAL R 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 294 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=AA1, 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) 134 hydrogen bonds defined for protein. 393 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: 0.63 Time building geometry restraints manager: 0.69 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=" 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=" C5 P9X R 501 " pdb=" O3 P9X R 501 " ideal model delta sigma weight residual 1.248 1.307 -0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" C4 P9X R 501 " pdb=" C5 P9X R 501 " ideal model delta sigma weight residual 1.530 1.477 0.053 2.00e-02 2.50e+03 6.99e+00 bond pdb=" C TRP R 142 " pdb=" O TRP R 142 " ideal model delta sigma weight residual 1.236 1.210 0.026 1.15e-02 7.56e+03 5.30e+00 ... (remaining 2317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 3092 1.36 - 2.72: 47 2.72 - 4.08: 14 4.08 - 5.44: 9 5.44 - 6.80: 5 Bond angle restraints: 3167 Sorted by residual: 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 angle pdb=" CA TRP R 142 " pdb=" C TRP R 142 " pdb=" O TRP R 142 " ideal model delta sigma weight residual 120.82 118.41 2.41 1.05e+00 9.07e-01 5.28e+00 ... (remaining 3162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 1157 17.97 - 35.93: 150 35.93 - 53.90: 35 53.90 - 71.86: 2 71.86 - 89.83: 3 Dihedral angle restraints: 1347 sinusoidal: 514 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 1344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 203 0.024 - 0.047: 95 0.047 - 0.071: 43 0.071 - 0.095: 18 0.095 - 0.118: 9 Chirality restraints: 368 Sorted by residual: 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 chirality pdb=" CG LEU R 257 " pdb=" CB LEU R 257 " pdb=" CD1 LEU R 257 " pdb=" CD2 LEU R 257 " both_signs ideal model delta sigma weight residual False -2.59 -2.47 -0.12 2.00e-01 2.50e+01 3.33e-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: 487 2.78 - 3.31: 2224 3.31 - 3.84: 3584 3.84 - 4.37: 4004 4.37 - 4.90: 6994 Nonbonded interactions: 17293 Sorted by model distance: nonbonded pdb=" OD1 ASN R 68 " pdb=" OG SER R 148 " model vdw 2.246 3.040 nonbonded pdb=" NH2 ARG R 111 " pdb=" O2 P9X R 501 " model vdw 2.393 3.120 nonbonded pdb=" NH2 ARG R 101 " pdb=" O LEU R 163 " model vdw 2.396 3.120 nonbonded pdb=" OD1 ASP R 97 " pdb=" N ILE R 98 " model vdw 2.433 3.120 nonbonded pdb=" NE1 TRP R 93 " pdb=" O GLY R 96 " model vdw 2.459 3.120 ... (remaining 17288 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.050 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.630 ------------------------------------------------------------------------------- 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 : 0.003 0.059 2322 Z= 0.253 Angle : 0.569 6.803 3167 Z= 0.287 Chirality : 0.038 0.118 368 Planarity : 0.004 0.046 382 Dihedral : 16.211 89.829 794 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 to be fit. 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: 0.1537 time to fit residues: 7.5257 Evaluate side-chains 39 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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: 6.9990 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7608 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2322 Z= 0.186 Angle : 0.548 6.654 3167 Z= 0.284 Chirality : 0.042 0.124 368 Planarity : 0.005 0.051 382 Dihedral : 4.588 24.379 325 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.27 % Allowed : 29.66 % Favored : 69.07 % 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: 0.27 (0.52), residues: 281 helix: 0.66 (0.38), residues: 202 sheet: None (None), residues: 0 loop : -0.88 (0.74), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 256 HIS 0.004 0.001 HIS R 253 PHE 0.013 0.001 PHE R 232 TYR 0.007 0.001 TYR R 284 ARG 0.002 0.000 ARG R 218 *********************** 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 40 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.262 Fit side-chains REVERT: R 62 SER cc_start: 0.8967 (t) cc_final: 0.8459 (m) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 0.1345 time to fit residues: 6.4240 Evaluate side-chains 36 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 220 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2322 Z= 0.183 Angle : 0.521 6.660 3167 Z= 0.267 Chirality : 0.041 0.121 368 Planarity : 0.004 0.049 382 Dihedral : 4.160 15.613 325 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.24 % Allowed : 27.97 % 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: 0.49 (0.52), residues: 281 helix: 0.85 (0.38), residues: 203 sheet: None (None), residues: 0 loop : -0.90 (0.74), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 256 HIS 0.002 0.001 HIS R 253 PHE 0.008 0.001 PHE R 117 TYR 0.006 0.001 TYR R 294 ARG 0.001 0.000 ARG R 128 *********************** 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 47 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.238 Fit side-chains REVERT: R 21 PHE cc_start: 0.4414 (m-80) cc_final: 0.3955 (m-80) REVERT: R 62 SER cc_start: 0.8944 (t) cc_final: 0.8502 (m) REVERT: R 101 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.6402 (mtm180) outliers start: 10 outliers final: 6 residues processed: 44 average time/residue: 0.1414 time to fit residues: 7.4701 Evaluate side-chains 43 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 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 77 ILE Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 160 VAL 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: 0.1980 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.7568 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2322 Z= 0.143 Angle : 0.517 8.980 3167 Z= 0.256 Chirality : 0.040 0.116 368 Planarity : 0.004 0.049 382 Dihedral : 3.787 14.344 325 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.24 % Allowed : 28.39 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.53), residues: 281 helix: 1.15 (0.38), residues: 203 sheet: None (None), residues: 0 loop : -0.96 (0.72), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 256 HIS 0.002 0.000 HIS R 253 PHE 0.007 0.001 PHE R 206 TYR 0.005 0.001 TYR R 87 ARG 0.001 0.000 ARG R 216 *********************** 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 47 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: R 21 PHE cc_start: 0.4787 (m-80) cc_final: 0.4275 (m-80) REVERT: R 62 SER cc_start: 0.8829 (t) cc_final: 0.8438 (m) REVERT: R 168 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5667 (mt) REVERT: R 216 ARG cc_start: 0.8296 (ttm-80) cc_final: 0.7712 (mtp85) outliers start: 10 outliers final: 7 residues processed: 44 average time/residue: 0.1474 time to fit residues: 7.7671 Evaluate side-chains 43 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 77 ILE Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 168 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 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: 0.7616 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2322 Z= 0.174 Angle : 0.525 7.411 3167 Z= 0.263 Chirality : 0.041 0.116 368 Planarity : 0.004 0.049 382 Dihedral : 3.839 14.930 325 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.66 % Allowed : 29.24 % Favored : 66.10 % 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: 0.79 (0.53), residues: 281 helix: 1.13 (0.38), residues: 203 sheet: None (None), residues: 0 loop : -0.97 (0.73), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 256 HIS 0.002 0.001 HIS R 253 PHE 0.008 0.001 PHE R 117 TYR 0.005 0.001 TYR R 87 ARG 0.001 0.000 ARG R 128 *********************** 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 46 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: R 21 PHE cc_start: 0.4748 (m-80) cc_final: 0.4353 (m-80) REVERT: R 62 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.8457 (m) REVERT: R 168 LEU cc_start: 0.6282 (OUTLIER) cc_final: 0.5691 (mt) outliers start: 11 outliers final: 8 residues processed: 43 average time/residue: 0.1417 time to fit residues: 7.3278 Evaluate side-chains 45 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 101 ARG Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 226 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 0.0370 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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: 0.7590 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2322 Z= 0.152 Angle : 0.514 7.829 3167 Z= 0.256 Chirality : 0.040 0.115 368 Planarity : 0.004 0.050 382 Dihedral : 3.699 14.537 325 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.93 % Allowed : 28.39 % 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: 0.84 (0.52), residues: 281 helix: 1.16 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -1.01 (0.72), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 256 HIS 0.002 0.000 HIS R 253 PHE 0.014 0.001 PHE R 232 TYR 0.005 0.001 TYR R 87 ARG 0.005 0.000 ARG R 216 *********************** 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 48 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: R 21 PHE cc_start: 0.4755 (m-80) cc_final: 0.4380 (m-80) REVERT: R 62 SER cc_start: 0.8816 (OUTLIER) cc_final: 0.8431 (m) REVERT: R 168 LEU cc_start: 0.6356 (OUTLIER) cc_final: 0.5754 (mt) REVERT: R 216 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.7634 (mtp85) outliers start: 14 outliers final: 10 residues processed: 43 average time/residue: 0.1412 time to fit residues: 7.2584 Evaluate side-chains 46 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 101 ARG Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 160 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2322 Z= 0.155 Angle : 0.522 8.398 3167 Z= 0.261 Chirality : 0.040 0.114 368 Planarity : 0.004 0.049 382 Dihedral : 3.650 14.359 325 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.93 % Allowed : 28.39 % 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: 0.90 (0.52), residues: 281 helix: 1.20 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -0.97 (0.72), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 256 HIS 0.002 0.000 HIS R 253 PHE 0.007 0.001 PHE R 206 TYR 0.006 0.001 TYR R 87 ARG 0.005 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 to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: R 21 PHE cc_start: 0.4832 (m-80) cc_final: 0.4504 (m-80) REVERT: R 62 SER cc_start: 0.8816 (OUTLIER) cc_final: 0.8430 (m) REVERT: R 168 LEU cc_start: 0.6311 (OUTLIER) cc_final: 0.5725 (mt) outliers start: 14 outliers final: 11 residues processed: 46 average time/residue: 0.1417 time to fit residues: 7.8997 Evaluate side-chains 48 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 101 ARG Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 225 LYS 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: 0.6980 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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: 0.7576 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2322 Z= 0.151 Angle : 0.521 8.469 3167 Z= 0.261 Chirality : 0.040 0.115 368 Planarity : 0.004 0.048 382 Dihedral : 3.573 13.675 325 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 5.93 % Allowed : 28.81 % Favored : 65.25 % 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: 0.97 (0.52), residues: 281 helix: 1.27 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -1.00 (0.72), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP R 142 HIS 0.002 0.000 HIS R 253 PHE 0.007 0.001 PHE R 232 TYR 0.005 0.001 TYR R 87 ARG 0.006 0.000 ARG R 216 *********************** 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 49 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: R 21 PHE cc_start: 0.4893 (m-80) cc_final: 0.4580 (m-80) REVERT: R 62 SER cc_start: 0.8804 (OUTLIER) cc_final: 0.8427 (m) REVERT: R 168 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.5748 (mt) REVERT: R 216 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.7737 (mtp85) REVERT: R 220 MET cc_start: 0.8196 (ttm) cc_final: 0.7821 (mtp) outliers start: 14 outliers final: 11 residues processed: 44 average time/residue: 0.1394 time to fit residues: 7.3580 Evaluate side-chains 48 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 95 PHE Chi-restraints excluded: chain R residue 101 ARG 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 225 LYS 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: 7.9990 chunk 23 optimal weight: 0.0060 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 0.0970 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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: 0.7569 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2322 Z= 0.144 Angle : 0.520 8.997 3167 Z= 0.256 Chirality : 0.040 0.115 368 Planarity : 0.004 0.048 382 Dihedral : 3.559 13.279 325 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.51 % Allowed : 30.08 % 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: 0.97 (0.53), residues: 281 helix: 1.22 (0.38), residues: 208 sheet: None (None), residues: 0 loop : -0.93 (0.74), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP R 142 HIS 0.002 0.000 HIS R 253 PHE 0.007 0.001 PHE R 206 TYR 0.006 0.001 TYR R 86 ARG 0.005 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 49 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: R 21 PHE cc_start: 0.4937 (m-80) cc_final: 0.4623 (m-80) REVERT: R 62 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8405 (m) REVERT: R 168 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.5788 (mt) REVERT: R 216 ARG cc_start: 0.8462 (ttm-80) cc_final: 0.7673 (mtp85) REVERT: R 220 MET cc_start: 0.8197 (ttm) cc_final: 0.7821 (mtp) outliers start: 13 outliers final: 11 residues processed: 44 average time/residue: 0.1425 time to fit residues: 7.5363 Evaluate side-chains 49 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 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 88 VAL Chi-restraints excluded: chain R residue 95 PHE Chi-restraints excluded: chain R residue 101 ARG 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 225 LYS 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: 5.9990 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2322 Z= 0.156 Angle : 0.528 8.792 3167 Z= 0.261 Chirality : 0.040 0.115 368 Planarity : 0.004 0.049 382 Dihedral : 3.580 13.354 325 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.51 % Allowed : 30.51 % 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: 0.95 (0.52), residues: 281 helix: 1.19 (0.38), residues: 208 sheet: None (None), residues: 0 loop : -0.89 (0.74), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 93 HIS 0.002 0.000 HIS R 253 PHE 0.007 0.001 PHE R 232 TYR 0.017 0.001 TYR R 86 ARG 0.006 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 48 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: R 21 PHE cc_start: 0.4974 (m-80) cc_final: 0.4648 (m-80) REVERT: R 62 SER cc_start: 0.8803 (OUTLIER) cc_final: 0.8426 (m) REVERT: R 168 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.5764 (mt) REVERT: R 216 ARG cc_start: 0.8481 (ttm-80) cc_final: 0.7702 (mtp85) REVERT: R 220 MET cc_start: 0.8218 (ttm) cc_final: 0.7869 (mtp) outliers start: 13 outliers final: 11 residues processed: 43 average time/residue: 0.1472 time to fit residues: 7.6400 Evaluate side-chains 48 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 95 PHE Chi-restraints excluded: chain R residue 101 ARG 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 225 LYS 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 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4257 r_free = 0.4257 target = 0.198855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.154980 restraints weight = 2557.607| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.23 r_work: 0.3571 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2322 Z= 0.170 Angle : 0.534 8.668 3167 Z= 0.265 Chirality : 0.041 0.115 368 Planarity : 0.004 0.048 382 Dihedral : 3.723 14.137 325 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.93 % Allowed : 30.51 % 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: 0.88 (0.52), residues: 281 helix: 1.14 (0.38), residues: 208 sheet: None (None), residues: 0 loop : -0.91 (0.74), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 142 HIS 0.002 0.001 HIS R 253 PHE 0.008 0.001 PHE R 232 TYR 0.017 0.002 TYR R 86 ARG 0.005 0.000 ARG R 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1000.30 seconds wall clock time: 18 minutes 42.03 seconds (1122.03 seconds total)