Starting phenix.real_space_refine on Mon Feb 10 20:22:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihk_35447/02_2025/8ihk_35447.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihk_35447/02_2025/8ihk_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/cci-nas-00/data/ceres_data/8ihk_35447/02_2025/8ihk_35447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihk_35447/02_2025/8ihk_35447.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihk_35447/02_2025/8ihk_35447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihk_35447/02_2025/8ihk_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-5592/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: 2.24, per 1000 atoms: 0.99 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: 0.58 Conformation dependent library (CDL) restraints added in 276.2 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... 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: 0.53 Time building geometry restraints manager: 0.66 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: 0.420 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: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.740 Find NCS groups from input model: 0.030 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.900 ------------------------------------------------------------------------------- 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 : 0.247 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: 0.1511 time to fit residues: 7.4187 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 : 0.223 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.198406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.153858 restraints weight = 2598.800| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.23 r_work: 0.3574 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 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 : 0.252 Fit side-chains REVERT: R 62 SER cc_start: 0.8941 (t) cc_final: 0.8410 (m) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 0.1332 time to fit residues: 6.4013 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 : 0.215 ------------------------------------------------------------------------------- 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 16 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.199095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.156393 restraints weight = 2549.487| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.74 r_work: 0.3559 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2245 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= 0.180 Angle : 0.518 6.630 3167 Z= 0.265 Chirality : 0.041 0.121 368 Planarity : 0.004 0.049 382 Dihedral : 4.124 15.416 325 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.35 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: 0.51 (0.52), residues: 281 helix: 0.86 (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 0.009 0.001 TRP R 256 HIS 0.002 0.001 HIS R 253 PHE 0.007 0.001 PHE R 117 TYR 0.007 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 : 0.246 Fit side-chains REVERT: R 21 PHE cc_start: 0.4477 (m-80) cc_final: 0.3938 (m-80) REVERT: R 62 SER cc_start: 0.8936 (t) cc_final: 0.8474 (m) outliers start: 10 outliers final: 6 residues processed: 44 average time/residue: 0.1472 time to fit residues: 7.7963 Evaluate side-chains 42 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 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 8 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 12 optimal weight: 0.0570 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 7 optimal weight: 0.0970 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.201381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.156679 restraints weight = 2503.086| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.29 r_work: 0.3607 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2585 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= 0.138 Angle : 0.517 9.011 3167 Z= 0.256 Chirality : 0.040 0.116 368 Planarity : 0.004 0.050 382 Dihedral : 3.760 14.181 325 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.39 % Allowed : 28.81 % 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: 0.86 (0.53), residues: 281 helix: 1.19 (0.38), residues: 203 sheet: None (None), residues: 0 loop : -0.97 (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 0.008 0.001 PHE R 206 TYR 0.005 0.001 TYR R 87 ARG 0.005 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 46 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.244 Fit side-chains REVERT: R 21 PHE cc_start: 0.4809 (m-80) cc_final: 0.4250 (m-80) REVERT: R 45 ASN cc_start: 0.7729 (m-40) cc_final: 0.7512 (m110) REVERT: R 62 SER cc_start: 0.8842 (t) cc_final: 0.8425 (m) REVERT: R 216 ARG cc_start: 0.8397 (ttm-80) cc_final: 0.7633 (mtp85) outliers start: 8 outliers final: 6 residues processed: 43 average time/residue: 0.1286 time to fit residues: 6.8503 Evaluate side-chains 43 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 109 MET Chi-restraints excluded: chain R residue 160 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4281 r_free = 0.4281 target = 0.200741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.157230 restraints weight = 2561.020| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.38 r_work: 0.3585 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2620 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 : 0.531 7.160 3167 Z= 0.257 Chirality : 0.040 0.115 368 Planarity : 0.004 0.049 382 Dihedral : 3.747 14.130 325 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % 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: 0.91 (0.53), residues: 281 helix: 1.24 (0.39), residues: 203 sheet: None (None), residues: 0 loop : -1.02 (0.71), residues: 78 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 0.004 0.001 TYR R 87 ARG 0.003 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 45 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.233 Fit side-chains REVERT: R 21 PHE cc_start: 0.4692 (m-80) cc_final: 0.4260 (m-80) REVERT: R 45 ASN cc_start: 0.7666 (m-40) cc_final: 0.7451 (m110) REVERT: R 62 SER cc_start: 0.8868 (OUTLIER) cc_final: 0.8446 (m) outliers start: 10 outliers final: 9 residues processed: 42 average time/residue: 0.1226 time to fit residues: 6.3375 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 : 0.241 ------------------------------------------------------------------------------- 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 109 MET Chi-restraints excluded: chain R residue 160 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.198183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.155030 restraints weight = 2607.074| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.88 r_work: 0.3537 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2641 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= 0.192 Angle : 0.544 7.774 3167 Z= 0.268 Chirality : 0.041 0.116 368 Planarity : 0.004 0.049 382 Dihedral : 3.840 15.391 325 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.24 % Allowed : 28.81 % Favored : 66.95 % 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: 0.80 (0.52), residues: 281 helix: 1.13 (0.38), residues: 204 sheet: None (None), residues: 0 loop : -0.97 (0.71), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 295 ARG 0.006 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 47 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.243 Fit side-chains REVERT: R 21 PHE cc_start: 0.4797 (m-80) cc_final: 0.4426 (m-80) REVERT: R 62 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8468 (m) outliers start: 10 outliers final: 7 residues processed: 43 average time/residue: 0.1255 time to fit residues: 6.6610 Evaluate side-chains 44 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 109 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 226 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4274 r_free = 0.4274 target = 0.199913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.157778 restraints weight = 2624.715| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.80 r_work: 0.3546 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2711 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= 0.157 Angle : 0.528 8.553 3167 Z= 0.260 Chirality : 0.040 0.115 368 Planarity : 0.004 0.049 382 Dihedral : 3.767 14.586 325 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.24 % Allowed : 28.81 % Favored : 66.95 % 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: 0.83 (0.52), residues: 281 helix: 1.14 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -0.96 (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 0.015 0.001 PHE R 232 TYR 0.005 0.001 TYR R 87 ARG 0.006 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 45 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.254 Fit side-chains REVERT: R 21 PHE cc_start: 0.4833 (m-80) cc_final: 0.4453 (m-80) REVERT: R 62 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8443 (m) REVERT: R 216 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.7617 (mtp85) outliers start: 10 outliers final: 8 residues processed: 42 average time/residue: 0.1280 time to fit residues: 6.6022 Evaluate side-chains 44 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 109 MET Chi-restraints excluded: chain R residue 160 VAL 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 15 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 overall best weight: 0.4198 ------------------------------------------------------------------------------- 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 = 0.4281 r_free = 0.4281 target = 0.201122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.156394 restraints weight = 2672.419| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.31 r_work: 0.3580 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2857 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= 0.139 Angle : 0.520 8.735 3167 Z= 0.257 Chirality : 0.039 0.113 368 Planarity : 0.004 0.049 382 Dihedral : 3.537 13.603 325 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.39 % Allowed : 30.51 % 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: 1.00 (0.52), residues: 281 helix: 1.31 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -1.05 (0.71), 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 206 TYR 0.005 0.001 TYR R 87 ARG 0.004 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 45 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.266 Fit side-chains REVERT: R 21 PHE cc_start: 0.4848 (m-80) cc_final: 0.4489 (m-80) REVERT: R 62 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8430 (m) REVERT: R 216 ARG cc_start: 0.8379 (ttm-80) cc_final: 0.7542 (mtp85) REVERT: R 220 MET cc_start: 0.8412 (ttm) cc_final: 0.7979 (mtp) outliers start: 8 outliers final: 5 residues processed: 42 average time/residue: 0.1261 time to fit residues: 6.5207 Evaluate side-chains 42 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 109 MET Chi-restraints excluded: chain R residue 183 CYS 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 25 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.0170 chunk 15 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 = 0.4271 r_free = 0.4271 target = 0.200141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.154983 restraints weight = 2573.833| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.36 r_work: 0.3587 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2961 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 : 0.528 8.994 3167 Z= 0.258 Chirality : 0.040 0.115 368 Planarity : 0.004 0.049 382 Dihedral : 3.491 13.172 325 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.24 % Allowed : 30.51 % 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: 1.02 (0.52), residues: 281 helix: 1.34 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -1.10 (0.70), residues: 76 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 0.027 0.002 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 46 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.259 Fit side-chains REVERT: R 21 PHE cc_start: 0.4897 (m-80) cc_final: 0.4527 (m-80) REVERT: R 45 ASN cc_start: 0.7760 (m-40) cc_final: 0.7506 (m110) REVERT: R 62 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8447 (m) REVERT: R 216 ARG cc_start: 0.8356 (ttm-80) cc_final: 0.7578 (mtp85) REVERT: R 220 MET cc_start: 0.8370 (ttm) cc_final: 0.8016 (mtp) outliers start: 10 outliers final: 9 residues processed: 43 average time/residue: 0.1047 time to fit residues: 5.7506 Evaluate side-chains 46 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 160 VAL 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 20 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4248 r_free = 0.4248 target = 0.198005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.153239 restraints weight = 2559.306| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.28 r_work: 0.3543 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2911 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= 0.175 Angle : 0.546 8.748 3167 Z= 0.269 Chirality : 0.041 0.115 368 Planarity : 0.004 0.048 382 Dihedral : 3.640 13.947 325 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.24 % Allowed : 30.08 % 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: 0.86 (0.52), residues: 281 helix: 1.23 (0.38), residues: 205 sheet: None (None), residues: 0 loop : -1.16 (0.70), residues: 76 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 117 TYR 0.027 0.002 TYR R 86 ARG 0.005 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 47 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.225 Fit side-chains REVERT: R 21 PHE cc_start: 0.4964 (m-80) cc_final: 0.4600 (m-80) REVERT: R 62 SER cc_start: 0.8843 (OUTLIER) cc_final: 0.8449 (m) REVERT: R 220 MET cc_start: 0.8366 (ttm) cc_final: 0.7922 (mtp) outliers start: 10 outliers final: 8 residues processed: 43 average time/residue: 0.1209 time to fit residues: 6.4317 Evaluate side-chains 46 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 109 MET Chi-restraints excluded: chain R residue 160 VAL 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 22 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.4263 r_free = 0.4263 target = 0.199462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.154671 restraints weight = 2574.083| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.34 r_work: 0.3562 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2966 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= 0.153 Angle : 0.538 9.452 3167 Z= 0.263 Chirality : 0.040 0.115 368 Planarity : 0.004 0.049 382 Dihedral : 3.624 13.928 325 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % 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: 0.91 (0.52), residues: 281 helix: 1.21 (0.38), residues: 208 sheet: None (None), residues: 0 loop : -1.06 (0.73), 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 0.014 0.001 PHE R 232 TYR 0.027 0.002 TYR R 86 ARG 0.004 0.000 ARG R 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1546.56 seconds wall clock time: 28 minutes 30.51 seconds (1710.51 seconds total)