Starting phenix.real_space_refine on Thu Sep 10 21:42:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/26pf_80806/09_2026/26pf_80806.cif Found real_map, /net/cci-nas-00/data/ceres_data/26pf_80806/09_2026/26pf_80806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/26pf_80806/09_2026/26pf_80806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/26pf_80806/09_2026/26pf_80806.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/26pf_80806/09_2026/26pf_80806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/26pf_80806/09_2026/26pf_80806.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 13 5.16 5 C 2423 2.51 5 N 707 2.21 5 O 782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3925 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 638 Classifications: {'peptide': 118} Incomplete info: {'backbone_only': 8, 'truncation_to_alanine': 71} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 359 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'TYR:plan': 6, 'PHE:plan': 2, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 135 Chain: "B" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 689 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 2598 Classifications: {'peptide': 410} Incomplete info: {'backbone_only': 8, 'truncation_to_alanine': 159} Link IDs: {'PTRANS': 25, 'TRANS': 384} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 566 Unresolved non-hydrogen angles: 755 Unresolved non-hydrogen dihedrals: 438 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 10, 'PHE:plan': 7, 'ASN:plan1': 16, 'GLU:plan': 11, 'TYR:plan': 6, 'ASP:plan': 15, 'TRP:plan': 1, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 297 Time building chain proxies: 1.07, per 1000 atoms: 0.27 Number of scatterers: 3925 At special positions: 0 Unit cell: (52.928, 80.219, 114.126, 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 13 16.00 O 782 8.00 N 707 7.00 C 2423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 308 " distance=2.04 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: 0.34 Conformation dependent library (CDL) restraints added in 135.2 milliseconds 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 11 sheets defined 3.3% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'C' and resid 87 through 92 removed outlier: 4.269A pdb=" N PHE C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 288 removed outlier: 4.119A pdb=" N GLY C 287 " --> pdb=" O PHE C 284 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 4.056A pdb=" N ILE A 50 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 229 through 230 removed outlier: 6.845A pdb=" N ALA B 229 " --> pdb=" O THR B 326 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 240 through 241 removed outlier: 5.413A pdb=" N ALA B 294 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N SER B 283 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 264 through 268 removed outlier: 3.779A pdb=" N LEU B 267 " --> pdb=" O TRP B 255 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N TRP B 255 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N TYR B 256 " --> pdb=" O TYR B 306 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN B 258 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 304 " --> pdb=" O GLN B 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 13 through 15 Processing sheet with id=AA6, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.584A pdb=" N VAL C 28 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU C 102 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLU C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU C 97 " --> pdb=" O GLU C 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 61 through 67 removed outlier: 5.981A pdb=" N VAL C 46 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLN C 67 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ALA C 44 " --> pdb=" O GLN C 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 124 through 125 removed outlier: 3.939A pdb=" N VAL C 150 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 173 through 174 removed outlier: 6.123A pdb=" N VAL C 173 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER C 279 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 330 through 331 removed outlier: 3.821A pdb=" N TYR C 331 " --> pdb=" O ILE C 391 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 391 " --> pdb=" O TYR C 331 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 382 " --> pdb=" O ASP C 390 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 349 through 352 removed outlier: 3.693A pdb=" N THR C 349 " --> pdb=" O THR C 406 " (cutoff:3.500A) 49 hydrogen bonds defined for protein. 111 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: 0.45 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1244 1.33 - 1.45: 564 1.45 - 1.57: 2158 1.57 - 1.69: 0 1.69 - 1.81: 19 Bond restraints: 3985 Sorted by residual: bond pdb=" N PHE C 33 " pdb=" CA PHE C 33 " ideal model delta sigma weight residual 1.455 1.489 -0.034 9.60e-03 1.09e+04 1.25e+01 bond pdb=" N VAL A 92 " pdb=" CA VAL A 92 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.18e+00 bond pdb=" N VAL C 28 " pdb=" CA VAL C 28 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.15e+00 bond pdb=" N VAL C 173 " pdb=" CA VAL C 173 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.27e-02 6.20e+03 8.14e+00 bond pdb=" N VAL A 98 " pdb=" CA VAL A 98 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.11e+00 ... (remaining 3980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 5171 1.57 - 3.14: 239 3.14 - 4.71: 39 4.71 - 6.28: 7 6.28 - 7.85: 2 Bond angle restraints: 5458 Sorted by residual: angle pdb=" N THR A 27 " pdb=" CA THR A 27 " pdb=" C THR A 27 " ideal model delta sigma weight residual 112.93 107.00 5.93 1.33e+00 5.65e-01 1.99e+01 angle pdb=" N PRO C 158 " pdb=" CA PRO C 158 " pdb=" CB PRO C 158 " ideal model delta sigma weight residual 103.25 98.84 4.41 1.05e+00 9.07e-01 1.76e+01 angle pdb=" C TYR C 159 " pdb=" CA TYR C 159 " pdb=" CB TYR C 159 " ideal model delta sigma weight residual 109.65 116.17 -6.52 1.75e+00 3.27e-01 1.39e+01 angle pdb=" CA GLU C 29 " pdb=" C GLU C 29 " pdb=" O GLU C 29 " ideal model delta sigma weight residual 122.37 118.17 4.20 1.15e+00 7.56e-01 1.33e+01 angle pdb=" CA THR A 29 " pdb=" C THR A 29 " pdb=" O THR A 29 " ideal model delta sigma weight residual 121.87 117.78 4.09 1.16e+00 7.43e-01 1.24e+01 ... (remaining 5453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 2084 16.70 - 33.40: 162 33.40 - 50.09: 34 50.09 - 66.79: 7 66.79 - 83.49: 2 Dihedral angle restraints: 2289 sinusoidal: 514 harmonic: 1775 Sorted by residual: dihedral pdb=" CB CYS B 241 " pdb=" SG CYS B 241 " pdb=" SG CYS B 308 " pdb=" CB CYS B 308 " ideal model delta sinusoidal sigma weight residual -86.00 -169.49 83.49 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CA PRO C 78 " pdb=" C PRO C 78 " pdb=" N ARG C 79 " pdb=" CA ARG C 79 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ASN B 271 " pdb=" C ASN B 271 " pdb=" N ASN B 272 " pdb=" CA ASN B 272 " ideal model delta harmonic sigma weight residual 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 2286 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 407 0.041 - 0.082: 157 0.082 - 0.123: 70 0.123 - 0.164: 11 0.164 - 0.205: 3 Chirality restraints: 648 Sorted by residual: chirality pdb=" CA VAL C 157 " pdb=" N VAL C 157 " pdb=" C VAL C 157 " pdb=" CB VAL C 157 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA VAL C 173 " pdb=" N VAL C 173 " pdb=" C VAL C 173 " pdb=" CB VAL C 173 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA VAL A 92 " pdb=" N VAL A 92 " pdb=" C VAL A 92 " pdb=" CB VAL A 92 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 645 not shown) Planarity restraints: 740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 399 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.36e+00 pdb=" N PRO C 400 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 400 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 400 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 423 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C LYS C 423 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS C 423 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA C 424 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 259 " 0.009 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C LEU B 259 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU B 259 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO B 260 " 0.010 2.00e-02 2.50e+03 ... (remaining 737 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 532 2.75 - 3.29: 3943 3.29 - 3.83: 5779 3.83 - 4.36: 6426 4.36 - 4.90: 11429 Nonbonded interactions: 28109 Sorted by model distance: nonbonded pdb=" OG SER B 309 " pdb=" O PHE B 319 " model vdw 2.218 3.040 nonbonded pdb=" NE1 TRP C 366 " pdb=" O SER C 380 " model vdw 2.280 3.120 nonbonded pdb=" OG SER C 237 " pdb=" O VAL C 239 " model vdw 2.280 3.040 nonbonded pdb=" N SER A 56 " pdb=" O MET A 69 " model vdw 2.325 3.120 nonbonded pdb=" NE2 GLN B 257 " pdb=" OD2 ASP B 305 " model vdw 2.327 3.120 ... (remaining 28104 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 3.940 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: 0.010 Set scattering table: 0.010 Process input model: 5.520 Find NCS groups from input model: 0.020 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4659 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 3986 Z= 0.349 Angle : 0.753 7.846 5460 Z= 0.479 Chirality : 0.052 0.205 648 Planarity : 0.004 0.063 740 Dihedral : 13.402 76.912 1156 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.85 % Favored : 86.15 % Rotamer: Outliers : 0.00 % Allowed : 26.85 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.02 (0.29), residues: 628 helix: None (None), residues: 0 sheet: -3.42 (0.40), residues: 150 loop : -3.60 (0.24), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 107 TYR 0.013 0.001 TYR C 159 PHE 0.011 0.001 PHE C 351 TRP 0.010 0.002 TRP C 140 HIS 0.001 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.35 ( 3985) covalent geometry : angle 0.75276 / 0.48 ( 5458) SS BOND : bond 0.00512 / 0.27 ( 1) SS BOND : angle 0.79620 / 0.42 ( 2) hydrogen bonds : bond 0.30420 / 22.66 ( 49) hydrogen bonds : angle 14.95146 / 11.19 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0689 time to fit residues: 5.4090 Evaluate side-chains 36 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 56 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 ASN C 59 HIS ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.162993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.150909 restraints weight = 10594.488| |-----------------------------------------------------------------------------| r_work (start): 0.4620 rms_B_bonded: 3.81 r_work: 0.4541 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5543 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3986 Z= 0.155 Angle : 0.637 7.239 5460 Z= 0.345 Chirality : 0.047 0.146 648 Planarity : 0.004 0.038 740 Dihedral : 5.082 20.537 650 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.90 % Favored : 87.10 % Rotamer: Outliers : 6.23 % Allowed : 25.29 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.76 (0.30), residues: 628 helix: None (None), residues: 0 sheet: -3.59 (0.40), residues: 147 loop : -3.28 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 273 TYR 0.015 0.002 TYR C 76 PHE 0.021 0.002 PHE C 132 TRP 0.008 0.002 TRP A 35 HIS 0.002 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 ( 3985) covalent geometry : angle 0.63697 / 0.34 ( 5458) SS BOND : bond 0.00262 / 0.14 ( 1) SS BOND : angle 0.26472 / 0.11 ( 2) hydrogen bonds : bond 0.04028 / 3.01 ( 49) hydrogen bonds : angle 9.85271 / 7.43 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.168 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 48 average time/residue: 0.0426 time to fit residues: 2.9465 Evaluate side-chains 37 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 416 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 34 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 51 ASN C 59 HIS C 60 GLN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.156188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.143150 restraints weight = 10418.277| |-----------------------------------------------------------------------------| r_work (start): 0.4523 rms_B_bonded: 3.92 r_work: 0.4439 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5840 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3986 Z= 0.181 Angle : 0.668 5.118 5460 Z= 0.366 Chirality : 0.049 0.238 648 Planarity : 0.004 0.035 740 Dihedral : 5.559 20.383 650 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.85 % Favored : 86.15 % Rotamer: Outliers : 7.39 % Allowed : 24.90 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.68 (0.30), residues: 628 helix: None (None), residues: 0 sheet: -3.12 (0.42), residues: 151 loop : -3.38 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 273 TYR 0.026 0.002 TYR B 269 PHE 0.029 0.003 PHE C 383 TRP 0.031 0.003 TRP C 366 HIS 0.003 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 ( 3985) covalent geometry : angle 0.66771 / 0.37 ( 5458) SS BOND : bond 0.00116 / 0.06 ( 1) SS BOND : angle 0.92244 / 0.36 ( 2) hydrogen bonds : bond 0.04659 / 3.45 ( 49) hydrogen bonds : angle 9.24695 / 6.94 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 30 time to evaluate : 0.148 Fit side-chains REVERT: C 284 PHE cc_start: 0.6768 (OUTLIER) cc_final: 0.6104 (t80) outliers start: 19 outliers final: 13 residues processed: 46 average time/residue: 0.0487 time to fit residues: 3.0223 Evaluate side-chains 44 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 284 PHE Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 377 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 0.0040 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 272 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.156769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.143894 restraints weight = 10337.519| |-----------------------------------------------------------------------------| r_work (start): 0.4539 rms_B_bonded: 3.86 r_work: 0.4454 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5797 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3986 Z= 0.136 Angle : 0.590 6.882 5460 Z= 0.318 Chirality : 0.049 0.277 648 Planarity : 0.004 0.046 740 Dihedral : 5.186 19.214 650 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.01 % Favored : 85.99 % Rotamer: Outliers : 7.00 % Allowed : 25.29 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.61 (0.30), residues: 628 helix: None (None), residues: 0 sheet: -3.20 (0.42), residues: 154 loop : -3.28 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 273 TYR 0.016 0.002 TYR C 10 PHE 0.016 0.002 PHE B 319 TRP 0.042 0.003 TRP C 366 HIS 0.009 0.002 HIS C 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 3985) covalent geometry : angle 0.58937 / 0.32 ( 5458) SS BOND : bond 0.00016 / 0.01 ( 1) SS BOND : angle 1.02080 / 0.42 ( 2) hydrogen bonds : bond 0.03092 / 2.33 ( 49) hydrogen bonds : angle 8.81942 / 6.56 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 29 time to evaluate : 0.134 Fit side-chains REVERT: C 284 PHE cc_start: 0.6857 (OUTLIER) cc_final: 0.6287 (t80) REVERT: C 366 TRP cc_start: 0.6292 (m-10) cc_final: 0.5995 (m-10) outliers start: 18 outliers final: 11 residues processed: 44 average time/residue: 0.0471 time to fit residues: 2.8544 Evaluate side-chains 38 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 26 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 159 TYR Chi-restraints excluded: chain C residue 284 PHE Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 377 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 11 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 272 ASN C 51 ASN C 59 HIS C 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.151229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.138549 restraints weight = 10464.688| |-----------------------------------------------------------------------------| r_work (start): 0.4478 rms_B_bonded: 3.88 r_work: 0.4395 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 0.6517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3986 Z= 0.199 Angle : 0.692 7.250 5460 Z= 0.375 Chirality : 0.049 0.183 648 Planarity : 0.004 0.039 740 Dihedral : 5.969 23.477 650 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.15 % Favored : 81.85 % Rotamer: Outliers : 8.95 % Allowed : 24.90 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.73 (0.30), residues: 628 helix: None (None), residues: 0 sheet: -3.05 (0.44), residues: 141 loop : -3.47 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 273 TYR 0.021 0.002 TYR B 269 PHE 0.022 0.003 PHE C 65 TRP 0.046 0.003 TRP C 366 HIS 0.002 0.001 HIS C 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 ( 3985) covalent geometry : angle 0.69130 / 0.38 ( 5458) SS BOND : bond 0.00237 / 0.12 ( 1) SS BOND : angle 1.39941 / 0.59 ( 2) hydrogen bonds : bond 0.03251 / 2.41 ( 49) hydrogen bonds : angle 9.21701 / 6.75 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 32 time to evaluate : 0.092 Fit side-chains REVERT: A 36 MET cc_start: 0.6112 (mtt) cc_final: 0.5865 (mtt) REVERT: C 284 PHE cc_start: 0.6961 (OUTLIER) cc_final: 0.6650 (t80) outliers start: 23 outliers final: 15 residues processed: 50 average time/residue: 0.0316 time to fit residues: 2.3086 Evaluate side-chains 46 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 30 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 284 PHE Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 377 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 272 ASN C 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.155044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.142812 restraints weight = 10389.236| |-----------------------------------------------------------------------------| r_work (start): 0.4528 rms_B_bonded: 3.65 r_work: 0.4437 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.6642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3986 Z= 0.142 Angle : 0.621 9.169 5460 Z= 0.333 Chirality : 0.048 0.167 648 Planarity : 0.004 0.029 740 Dihedral : 5.418 20.874 650 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.33 % Favored : 85.67 % Rotamer: Outliers : 7.39 % Allowed : 25.68 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.65 (0.31), residues: 628 helix: None (None), residues: 0 sheet: -3.15 (0.42), residues: 156 loop : -3.34 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 273 TYR 0.018 0.002 TYR C 10 PHE 0.018 0.002 PHE B 319 TRP 0.058 0.003 TRP C 366 HIS 0.009 0.002 HIS C 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 3985) covalent geometry : angle 0.62121 / 0.33 ( 5458) SS BOND : bond 0.00009 / 0.00 ( 1) SS BOND : angle 1.01193 / 0.44 ( 2) hydrogen bonds : bond 0.02799 / 2.11 ( 49) hydrogen bonds : angle 8.55949 / 6.26 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 30 time to evaluate : 0.189 Fit side-chains REVERT: A 36 MET cc_start: 0.5940 (mtt) cc_final: 0.5639 (mtt) REVERT: C 366 TRP cc_start: 0.6443 (m-10) cc_final: 0.5899 (m-10) outliers start: 19 outliers final: 15 residues processed: 44 average time/residue: 0.0346 time to fit residues: 2.2759 Evaluate side-chains 42 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 27 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 71 HIS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 377 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 0.0770 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 0.0270 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.154398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.141446 restraints weight = 10498.746| |-----------------------------------------------------------------------------| r_work (start): 0.4533 rms_B_bonded: 3.90 r_work: 0.4448 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 moved from start: 0.6808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3986 Z= 0.122 Angle : 0.582 8.301 5460 Z= 0.312 Chirality : 0.047 0.157 648 Planarity : 0.003 0.028 740 Dihedral : 5.018 22.715 650 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.61 % Favored : 84.39 % Rotamer: Outliers : 7.00 % Allowed : 24.90 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.52 (0.31), residues: 628 helix: None (None), residues: 0 sheet: -3.14 (0.42), residues: 157 loop : -3.20 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 273 TYR 0.016 0.001 TYR C 10 PHE 0.020 0.002 PHE B 319 TRP 0.042 0.002 TRP C 366 HIS 0.002 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 3985) covalent geometry : angle 0.58236 / 0.31 ( 5458) SS BOND : bond 0.00051 / 0.03 ( 1) SS BOND : angle 0.85234 / 0.33 ( 2) hydrogen bonds : bond 0.02626 / 1.97 ( 49) hydrogen bonds : angle 8.18368 / 5.94 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 30 time to evaluate : 0.153 Fit side-chains REVERT: A 36 MET cc_start: 0.5898 (mtt) cc_final: 0.5601 (mtt) REVERT: C 59 HIS cc_start: 0.6865 (t-170) cc_final: 0.6478 (m170) REVERT: C 410 THR cc_start: 0.6007 (m) cc_final: 0.5740 (p) outliers start: 18 outliers final: 15 residues processed: 44 average time/residue: 0.0346 time to fit residues: 2.3580 Evaluate side-chains 40 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 25 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 71 HIS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 377 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 0.0570 chunk 51 optimal weight: 0.0050 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.151905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.139181 restraints weight = 10413.514| |-----------------------------------------------------------------------------| r_work (start): 0.4502 rms_B_bonded: 3.86 r_work: 0.4417 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 moved from start: 0.7270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3986 Z= 0.152 Angle : 0.610 5.452 5460 Z= 0.331 Chirality : 0.048 0.156 648 Planarity : 0.004 0.028 740 Dihedral : 5.272 26.214 650 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.04 % Favored : 82.96 % Rotamer: Outliers : 8.56 % Allowed : 24.51 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.59 (0.30), residues: 628 helix: None (None), residues: 0 sheet: -3.20 (0.41), residues: 147 loop : -3.27 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 107 TYR 0.019 0.002 TYR B 269 PHE 0.018 0.002 PHE B 319 TRP 0.037 0.003 TRP C 366 HIS 0.002 0.001 HIS C 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 3985) covalent geometry : angle 0.60927 / 0.33 ( 5458) SS BOND : bond 0.00073 / 0.04 ( 1) SS BOND : angle 1.09177 / 0.48 ( 2) hydrogen bonds : bond 0.02792 / 2.12 ( 49) hydrogen bonds : angle 8.34057 / 6.09 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 27 time to evaluate : 0.128 Fit side-chains REVERT: C 410 THR cc_start: 0.5876 (m) cc_final: 0.5599 (p) outliers start: 22 outliers final: 18 residues processed: 44 average time/residue: 0.0471 time to fit residues: 2.9091 Evaluate side-chains 45 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 27 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 TRP Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 71 HIS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 377 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.141873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.129467 restraints weight = 10849.449| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 3.81 r_work: 0.4267 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.8767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 3986 Z= 0.389 Angle : 0.951 9.327 5460 Z= 0.520 Chirality : 0.056 0.273 648 Planarity : 0.006 0.040 740 Dihedral : 7.628 35.307 650 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.04 % Favored : 75.96 % Rotamer: Outliers : 7.00 % Allowed : 25.29 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.99 (0.29), residues: 628 helix: None (None), residues: 0 sheet: -3.15 (0.42), residues: 136 loop : -3.70 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 273 TYR 0.026 0.004 TYR B 269 PHE 0.025 0.003 PHE C 132 TRP 0.053 0.005 TRP C 366 HIS 0.002 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00821 / 0.39 ( 3985) covalent geometry : angle 0.94992 / 0.52 ( 5458) SS BOND : bond 0.00314 / 0.17 ( 1) SS BOND : angle 2.67278 / 1.29 ( 2) hydrogen bonds : bond 0.04719 / 3.61 ( 49) hydrogen bonds : angle 9.84407 / 7.29 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 30 time to evaluate : 0.155 Fit side-chains REVERT: C 58 LYS cc_start: 0.6571 (mtpp) cc_final: 0.6121 (ttpt) REVERT: C 202 MET cc_start: 0.5404 (mtt) cc_final: 0.5184 (mtt) outliers start: 18 outliers final: 15 residues processed: 45 average time/residue: 0.0550 time to fit residues: 3.4476 Evaluate side-chains 42 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 27 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 TRP Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 71 HIS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 377 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 51 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 41 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.147227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.135398 restraints weight = 10757.748| |-----------------------------------------------------------------------------| r_work (start): 0.4417 rms_B_bonded: 3.66 r_work: 0.4335 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.8767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3986 Z= 0.205 Angle : 0.728 8.112 5460 Z= 0.393 Chirality : 0.050 0.207 648 Planarity : 0.004 0.033 740 Dihedral : 6.263 26.262 650 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.99 % Favored : 82.01 % Rotamer: Outliers : 6.61 % Allowed : 27.63 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.77 (0.30), residues: 628 helix: None (None), residues: 0 sheet: -2.95 (0.41), residues: 151 loop : -3.54 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 387 TYR 0.017 0.002 TYR B 269 PHE 0.022 0.002 PHE B 319 TRP 0.040 0.003 TRP C 366 HIS 0.003 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 ( 3985) covalent geometry : angle 0.72723 / 0.39 ( 5458) SS BOND : bond 0.00025 / 0.01 ( 1) SS BOND : angle 1.68920 / 0.81 ( 2) hydrogen bonds : bond 0.03148 / 2.35 ( 49) hydrogen bonds : angle 9.06300 / 6.69 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 27 time to evaluate : 0.182 Fit side-chains REVERT: C 58 LYS cc_start: 0.6545 (mtpp) cc_final: 0.6261 (ttpt) REVERT: C 202 MET cc_start: 0.5073 (mtt) cc_final: 0.4845 (mtt) REVERT: C 410 THR cc_start: 0.6220 (m) cc_final: 0.6010 (p) outliers start: 17 outliers final: 16 residues processed: 41 average time/residue: 0.0493 time to fit residues: 2.9636 Evaluate side-chains 42 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 26 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 35 TRP Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 71 HIS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 377 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 38 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 0.0270 chunk 12 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 43 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.146837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.135171 restraints weight = 10709.506| |-----------------------------------------------------------------------------| r_work (start): 0.4444 rms_B_bonded: 3.60 r_work: 0.4364 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6059 moved from start: 0.8891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3986 Z= 0.160 Angle : 0.653 6.895 5460 Z= 0.351 Chirality : 0.049 0.169 648 Planarity : 0.004 0.028 740 Dihedral : 5.540 26.893 650 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.59 % Favored : 80.41 % Rotamer: Outliers : 7.00 % Allowed : 27.24 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.73 (0.30), residues: 628 helix: None (None), residues: 0 sheet: -3.05 (0.40), residues: 163 loop : -3.44 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 273 TYR 0.018 0.002 TYR B 269 PHE 0.019 0.002 PHE B 319 TRP 0.036 0.003 TRP C 366 HIS 0.003 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 ( 3985) covalent geometry : angle 0.65256 / 0.35 ( 5458) SS BOND : bond 0.00016 / 0.01 ( 1) SS BOND : angle 1.08057 / 0.49 ( 2) hydrogen bonds : bond 0.02717 / 2.06 ( 49) hydrogen bonds : angle 8.61865 / 6.38 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1173.72 seconds wall clock time: 21 minutes 9.15 seconds (1269.15 seconds total)