Starting phenix.real_space_refine on Fri Sep 11 00:02:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21gm_67657/09_2026/21gm_67657.cif Found real_map, /net/cci-nas-00/data/ceres_data/21gm_67657/09_2026/21gm_67657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21gm_67657/09_2026/21gm_67657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21gm_67657/09_2026/21gm_67657.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21gm_67657/09_2026/21gm_67657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21gm_67657/09_2026/21gm_67657.map" } resolution = 3.2 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= 0.006 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 31 5.16 5 C 3536 2.51 5 N 951 2.21 5 O 1090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 5608 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1389 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 164} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1353 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1477 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 183} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'TRP:plan': 1, 'TYR:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 3, 'TRANS': 181} Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 3, 'TYR:plan': 2, 'PHE:plan': 6, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.45, per 1000 atoms: 0.26 Number of scatterers: 5608 At special positions: 0 Unit cell: (67.5, 105.3, 116.64, 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 31 16.00 O 1090 8.00 N 951 7.00 C 3536 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS B 32 " - pdb=" SG CYS B 93 " distance=2.05 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 107 " distance=2.04 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 108 " 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 Links applied NAG-ASN " NAG A 301 " - " ASN A 125 " Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 209.6 milliseconds 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1350 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 11 sheets defined 42.5% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 162 through 225 Processing helix chain 'B' and resid 115 through 121 removed outlier: 3.620A pdb=" N MET B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 195 removed outlier: 4.153A pdb=" N TYR B 150 " --> pdb=" O HIS B 146 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 219 Processing helix chain 'D' and resid 129 through 133 Processing helix chain 'D' and resid 134 through 143 Processing helix chain 'D' and resid 145 through 216 removed outlier: 3.866A pdb=" N ARG D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR D 182 " --> pdb=" O THR D 178 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 42 Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 106 removed outlier: 3.595A pdb=" N GLY A 106 " --> pdb=" O TYR A 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 54 removed outlier: 6.320A pdb=" N MET A 85 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLN A 101 " --> pdb=" O MET A 85 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL A 87 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A 99 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL A 89 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 22 through 25 removed outlier: 7.088A pdb=" N ILE B 105 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 37 removed outlier: 3.554A pdb=" N GLY B 88 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 81 through 83 removed outlier: 3.857A pdb=" N PHE B 82 " --> pdb=" O MET B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 36 through 40 removed outlier: 6.146A pdb=" N VAL C 119 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL C 97 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR C 62 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY C 93 " --> pdb=" O TYR C 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 36 through 40 removed outlier: 6.146A pdb=" N VAL C 119 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AB1, first strand: chain 'D' and resid 33 through 36 removed outlier: 3.513A pdb=" N LEU D 121 " --> pdb=" O SER D 61 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 43 through 47 removed outlier: 3.613A pdb=" N LEU D 44 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU D 106 " --> pdb=" O THR D 77 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 1002 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: 0.76 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1887 1.35 - 1.47: 1305 1.47 - 1.59: 2456 1.59 - 1.72: 0 1.72 - 1.84: 54 Bond restraints: 5702 Sorted by residual: bond pdb=" C1 NAG A 301 " pdb=" O5 NAG A 301 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.56e+00 bond pdb=" C5 NAG A 301 " pdb=" O5 NAG A 301 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.33e+00 bond pdb=" CA CYS B 93 " pdb=" CB CYS B 93 " ideal model delta sigma weight residual 1.534 1.509 0.025 2.33e-02 1.84e+03 1.17e+00 bond pdb=" N ASP D 101 " pdb=" CA ASP D 101 " ideal model delta sigma weight residual 1.458 1.473 -0.015 1.35e-02 5.49e+03 1.16e+00 bond pdb=" C3 NAG A 301 " pdb=" O3 NAG A 301 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.71e-01 ... (remaining 5697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 7607 1.97 - 3.94: 77 3.94 - 5.90: 6 5.90 - 7.87: 1 7.87 - 9.84: 1 Bond angle restraints: 7692 Sorted by residual: angle pdb=" CA CYS B 93 " pdb=" CB CYS B 93 " pdb=" SG CYS B 93 " ideal model delta sigma weight residual 114.40 124.24 -9.84 2.30e+00 1.89e-01 1.83e+01 angle pdb=" N GLU B 136 " pdb=" CA GLU B 136 " pdb=" CB GLU B 136 " ideal model delta sigma weight residual 110.39 116.03 -5.64 1.66e+00 3.63e-01 1.16e+01 angle pdb=" C ASN B 135 " pdb=" N GLU B 136 " pdb=" CA GLU B 136 " ideal model delta sigma weight residual 120.72 115.39 5.33 1.67e+00 3.59e-01 1.02e+01 angle pdb=" C PHE B 92 " pdb=" N CYS B 93 " pdb=" CA CYS B 93 " ideal model delta sigma weight residual 122.81 117.84 4.97 1.57e+00 4.06e-01 1.00e+01 angle pdb=" CA CYS C 47 " pdb=" CB CYS C 47 " pdb=" SG CYS C 47 " ideal model delta sigma weight residual 114.40 120.56 -6.16 2.30e+00 1.89e-01 7.18e+00 ... (remaining 7687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 3082 16.94 - 33.87: 295 33.87 - 50.81: 62 50.81 - 67.75: 12 67.75 - 84.68: 7 Dihedral angle restraints: 3458 sinusoidal: 1378 harmonic: 2080 Sorted by residual: dihedral pdb=" CB CYS C 47 " pdb=" SG CYS C 47 " pdb=" SG CYS C 107 " pdb=" CB CYS C 107 " ideal model delta sinusoidal sigma weight residual 93.00 33.68 59.32 1 1.00e+01 1.00e-02 4.70e+01 dihedral pdb=" CB CYS D 43 " pdb=" SG CYS D 43 " pdb=" SG CYS D 108 " pdb=" CB CYS D 108 " ideal model delta sinusoidal sigma weight residual 93.00 54.77 38.23 1 1.00e+01 1.00e-02 2.06e+01 dihedral pdb=" CA PHE B 92 " pdb=" C PHE B 92 " pdb=" N CYS B 93 " pdb=" CA CYS B 93 " ideal model delta harmonic sigma weight residual 180.00 -160.88 -19.12 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 3455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 619 0.035 - 0.069: 178 0.069 - 0.104: 49 0.104 - 0.138: 17 0.138 - 0.173: 3 Chirality restraints: 866 Sorted by residual: chirality pdb=" CA CYS B 93 " pdb=" N CYS B 93 " pdb=" C CYS B 93 " pdb=" CB CYS B 93 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CB ILE B 46 " pdb=" CA ILE B 46 " pdb=" CG1 ILE B 46 " pdb=" CG2 ILE B 46 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.94e-01 chirality pdb=" CA ASP D 101 " pdb=" N ASP D 101 " pdb=" C ASP D 101 " pdb=" CB ASP D 101 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 863 not shown) Planarity restraints: 1000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 91 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO A 92 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 92 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 92 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 39 " -0.009 2.00e-02 2.50e+03 7.20e-03 1.04e+00 pdb=" CG TYR A 39 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR A 39 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 39 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 39 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 39 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 39 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 39 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 114 " 0.016 5.00e-02 4.00e+02 2.37e-02 8.96e-01 pdb=" N PRO A 115 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " 0.013 5.00e-02 4.00e+02 ... (remaining 997 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1507 2.81 - 3.33: 5517 3.33 - 3.86: 9243 3.86 - 4.38: 9992 4.38 - 4.90: 18110 Nonbonded interactions: 44369 Sorted by model distance: nonbonded pdb=" NE2 GLN C 50 " pdb=" O PRO C 51 " model vdw 2.288 3.120 nonbonded pdb=" OE2 GLU C 87 " pdb=" NE2 HIS C 95 " model vdw 2.302 3.120 nonbonded pdb=" N GLY B 40 " pdb=" O ALA B 84 " model vdw 2.337 3.120 nonbonded pdb=" NE ARG B 74 " pdb=" O MET B 98 " model vdw 2.350 3.120 nonbonded pdb=" ND2 ASN B 96 " pdb=" O THR B 102 " model vdw 2.351 3.120 ... (remaining 44364 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: 9.470 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: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.950 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 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 : 0.004 0.030 5707 Z= 0.180 Angle : 0.528 9.838 7703 Z= 0.296 Chirality : 0.039 0.173 866 Planarity : 0.003 0.056 999 Dihedral : 14.214 84.681 2096 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.11 (0.35), residues: 704 helix: 4.45 (0.26), residues: 280 sheet: -1.23 (0.40), residues: 199 loop : -2.41 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 154 TYR 0.017 0.001 TYR A 39 PHE 0.009 0.001 PHE C 112 TRP 0.010 0.001 TRP A 187 HIS 0.004 0.001 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 ( 5702) covalent geometry : angle 0.52313 / 0.29 ( 7692) SS BOND : bond 0.01229 / 0.60 ( 4) SS BOND : angle 2.32759 / 0.92 ( 8) hydrogen bonds : bond 0.16000 / 9.60 ( 343) hydrogen bonds : angle 5.86284 / 4.17 ( 1002) link_NAG-ASN : bond 0.00051 / 0.03 ( 1) link_NAG-ASN : angle 0.72410 / 0.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 40 PHE cc_start: 0.7160 (p90) cc_final: 0.6862 (p90) REVERT: B 60 GLU cc_start: 0.6793 (tm-30) cc_final: 0.6404 (tm-30) REVERT: B 75 GLU cc_start: 0.5629 (tp30) cc_final: 0.5293 (mt-10) REVERT: B 98 MET cc_start: 0.6042 (ttm) cc_final: 0.5835 (ttm) REVERT: B 147 GLU cc_start: 0.6425 (tt0) cc_final: 0.6199 (tm-30) REVERT: C 52 MET cc_start: 0.7207 (tpp) cc_final: 0.6835 (mmm) REVERT: C 123 GLU cc_start: 0.7785 (tt0) cc_final: 0.7239 (tt0) REVERT: D 41 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7263 (ttp80) REVERT: D 111 SER cc_start: 0.7660 (p) cc_final: 0.7394 (p) REVERT: D 150 GLU cc_start: 0.7497 (tp30) cc_final: 0.7154 (mm-30) REVERT: D 152 ARG cc_start: 0.6638 (tpp80) cc_final: 0.6270 (tpp80) REVERT: D 156 ASP cc_start: 0.6595 (m-30) cc_final: 0.6236 (m-30) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.0635 time to fit residues: 11.7364 Evaluate side-chains 114 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.0370 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN D 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.174158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131394 restraints weight = 6287.506| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.22 r_work: 0.3354 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 5707 Z= 0.286 Angle : 0.690 10.713 7703 Z= 0.376 Chirality : 0.044 0.216 866 Planarity : 0.004 0.062 999 Dihedral : 4.704 29.193 784 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.23 % Allowed : 8.90 % Favored : 88.87 % 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: 0.53 (0.34), residues: 704 helix: 3.84 (0.26), residues: 281 sheet: -1.53 (0.37), residues: 213 loop : -2.62 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 178 TYR 0.022 0.002 TYR A 39 PHE 0.018 0.002 PHE B 94 TRP 0.015 0.001 TRP A 187 HIS 0.009 0.002 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.29 ( 5702) covalent geometry : angle 0.67232 / 0.37 ( 7692) SS BOND : bond 0.01616 / 0.81 ( 4) SS BOND : angle 4.32507 / 2.05 ( 8) hydrogen bonds : bond 0.05013 / 3.33 ( 343) hydrogen bonds : angle 4.54022 / 3.20 ( 1002) link_NAG-ASN : bond 0.00601 / 0.32 ( 1) link_NAG-ASN : angle 3.58113 / 1.44 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: B 60 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7071 (tm-30) REVERT: B 91 LYS cc_start: 0.7594 (ttpt) cc_final: 0.7367 (ttmt) REVERT: B 147 GLU cc_start: 0.8067 (tt0) cc_final: 0.7775 (tp30) REVERT: B 151 MET cc_start: 0.8096 (ptm) cc_final: 0.7657 (ptm) REVERT: C 123 GLU cc_start: 0.8725 (tt0) cc_final: 0.8492 (tt0) REVERT: D 41 ARG cc_start: 0.8482 (ttp80) cc_final: 0.7801 (ttp80) REVERT: D 150 GLU cc_start: 0.8459 (tp30) cc_final: 0.7806 (mm-30) REVERT: D 156 ASP cc_start: 0.8092 (m-30) cc_final: 0.7777 (m-30) outliers start: 13 outliers final: 10 residues processed: 113 average time/residue: 0.0710 time to fit residues: 10.7463 Evaluate side-chains 110 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 100 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 0 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 128 HIS ** 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 = 0.4047 r_free = 0.4047 target = 0.176811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.138664 restraints weight = 6282.891| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 3.18 r_work: 0.3382 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 5707 Z= 0.197 Angle : 0.610 9.298 7703 Z= 0.331 Chirality : 0.041 0.194 866 Planarity : 0.004 0.078 999 Dihedral : 4.472 28.318 784 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.40 % Allowed : 12.33 % Favored : 85.27 % 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: 0.56 (0.34), residues: 704 helix: 3.89 (0.26), residues: 280 sheet: -1.49 (0.37), residues: 213 loop : -2.63 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 154 TYR 0.015 0.001 TYR A 39 PHE 0.012 0.002 PHE C 106 TRP 0.015 0.001 TRP A 187 HIS 0.006 0.001 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 ( 5702) covalent geometry : angle 0.59269 / 0.33 ( 7692) SS BOND : bond 0.01560 / 0.80 ( 4) SS BOND : angle 3.63985 / 1.77 ( 8) hydrogen bonds : bond 0.04408 / 2.94 ( 343) hydrogen bonds : angle 4.22290 / 2.97 ( 1002) link_NAG-ASN : bond 0.00601 / 0.32 ( 1) link_NAG-ASN : angle 4.30589 / 1.74 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 GLU cc_start: 0.7604 (tm-30) cc_final: 0.6276 (tm-30) REVERT: B 151 MET cc_start: 0.7926 (ptm) cc_final: 0.7347 (ptm) REVERT: C 52 MET cc_start: 0.8037 (mmm) cc_final: 0.7783 (mmm) REVERT: D 41 ARG cc_start: 0.8536 (ttp80) cc_final: 0.7958 (ttp80) REVERT: D 150 GLU cc_start: 0.8425 (tp30) cc_final: 0.7788 (mm-30) REVERT: D 156 ASP cc_start: 0.7987 (m-30) cc_final: 0.7730 (m-30) outliers start: 14 outliers final: 11 residues processed: 112 average time/residue: 0.0695 time to fit residues: 10.5717 Evaluate side-chains 109 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 100 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 5 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 41 optimal weight: 0.0980 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 50 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 28 HIS C 128 ASN ** D 128 HIS ** 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 = 0.4117 r_free = 0.4117 target = 0.184797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.145920 restraints weight = 6099.696| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 3.21 r_work: 0.3494 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 5707 Z= 0.123 Angle : 0.535 11.246 7703 Z= 0.292 Chirality : 0.039 0.187 866 Planarity : 0.004 0.071 999 Dihedral : 4.132 24.277 784 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.25 % Allowed : 12.84 % Favored : 83.90 % 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: 0.76 (0.34), residues: 704 helix: 4.03 (0.26), residues: 288 sheet: -1.34 (0.37), residues: 200 loop : -2.76 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 154 TYR 0.009 0.001 TYR A 39 PHE 0.012 0.002 PHE C 122 TRP 0.014 0.001 TRP A 187 HIS 0.004 0.001 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 5702) covalent geometry : angle 0.52121 / 0.29 ( 7692) SS BOND : bond 0.01616 / 0.82 ( 4) SS BOND : angle 3.54270 / 1.63 ( 8) hydrogen bonds : bond 0.03801 / 2.52 ( 343) hydrogen bonds : angle 3.87299 / 2.74 ( 1002) link_NAG-ASN : bond 0.00294 / 0.15 ( 1) link_NAG-ASN : angle 2.26486 / 0.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 67 GLN cc_start: 0.5786 (tp40) cc_final: 0.5221 (tt0) REVERT: A 142 ASP cc_start: 0.7561 (t0) cc_final: 0.6727 (p0) REVERT: B 60 GLU cc_start: 0.7444 (tm-30) cc_final: 0.6699 (tm-30) REVERT: B 151 MET cc_start: 0.7782 (ptm) cc_final: 0.7193 (ptm) REVERT: C 52 MET cc_start: 0.8030 (mmm) cc_final: 0.7626 (mmm) REVERT: D 41 ARG cc_start: 0.8570 (ttp80) cc_final: 0.8000 (ttp80) REVERT: D 150 GLU cc_start: 0.8326 (tp30) cc_final: 0.7669 (mm-30) REVERT: D 156 ASP cc_start: 0.7867 (m-30) cc_final: 0.7592 (m-30) outliers start: 19 outliers final: 12 residues processed: 114 average time/residue: 0.0663 time to fit residues: 10.1523 Evaluate side-chains 109 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 77 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 20 optimal weight: 0.0060 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 60 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 68 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 128 ASN ** D 128 HIS ** 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 = 0.4119 r_free = 0.4119 target = 0.185166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.146327 restraints weight = 6195.563| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 3.22 r_work: 0.3477 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 5707 Z= 0.134 Angle : 0.552 13.786 7703 Z= 0.299 Chirality : 0.040 0.192 866 Planarity : 0.004 0.064 999 Dihedral : 4.010 17.753 784 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.08 % Allowed : 15.24 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.73 (0.34), residues: 704 helix: 3.96 (0.26), residues: 290 sheet: -1.38 (0.36), residues: 219 loop : -2.82 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 154 TYR 0.021 0.001 TYR B 189 PHE 0.011 0.002 PHE C 122 TRP 0.012 0.001 TRP A 187 HIS 0.004 0.001 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 5702) covalent geometry : angle 0.53712 / 0.29 ( 7692) SS BOND : bond 0.01627 / 0.82 ( 4) SS BOND : angle 3.87502 / 1.69 ( 8) hydrogen bonds : bond 0.03787 / 2.52 ( 343) hydrogen bonds : angle 3.79752 / 2.68 ( 1002) link_NAG-ASN : bond 0.00197 / 0.10 ( 1) link_NAG-ASN : angle 1.56237 / 0.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.7616 (t0) cc_final: 0.6786 (p0) REVERT: B 60 GLU cc_start: 0.7423 (tm-30) cc_final: 0.6874 (tm-30) REVERT: B 147 GLU cc_start: 0.8103 (tp30) cc_final: 0.7728 (tp30) REVERT: B 151 MET cc_start: 0.7784 (ptm) cc_final: 0.7060 (ptm) REVERT: C 52 MET cc_start: 0.7902 (mmm) cc_final: 0.7416 (mmm) REVERT: D 41 ARG cc_start: 0.8561 (ttp80) cc_final: 0.7901 (ttp80) REVERT: D 150 GLU cc_start: 0.8331 (tp30) cc_final: 0.7688 (mm-30) REVERT: D 156 ASP cc_start: 0.7876 (m-30) cc_final: 0.7605 (m-30) outliers start: 18 outliers final: 15 residues processed: 117 average time/residue: 0.0618 time to fit residues: 9.8334 Evaluate side-chains 118 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 126 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 64 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 128 ASN ** D 128 HIS ** 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 = 0.4057 r_free = 0.4057 target = 0.179016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.136122 restraints weight = 6156.400| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.22 r_work: 0.3361 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 5707 Z= 0.209 Angle : 0.626 15.129 7703 Z= 0.339 Chirality : 0.043 0.208 866 Planarity : 0.004 0.072 999 Dihedral : 4.254 20.742 784 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.11 % Allowed : 16.10 % Favored : 79.79 % 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: 0.60 (0.33), residues: 704 helix: 3.83 (0.26), residues: 288 sheet: -1.36 (0.36), residues: 212 loop : -2.87 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 154 TYR 0.020 0.002 TYR A 39 PHE 0.013 0.002 PHE B 92 TRP 0.011 0.001 TRP A 187 HIS 0.007 0.001 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 ( 5702) covalent geometry : angle 0.61171 / 0.33 ( 7692) SS BOND : bond 0.01615 / 0.81 ( 4) SS BOND : angle 4.12303 / 1.86 ( 8) hydrogen bonds : bond 0.04118 / 2.75 ( 343) hydrogen bonds : angle 3.91952 / 2.74 ( 1002) link_NAG-ASN : bond 0.00180 / 0.09 ( 1) link_NAG-ASN : angle 1.36588 / 0.48 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 ASP cc_start: 0.8321 (p0) cc_final: 0.8084 (p0) REVERT: B 60 GLU cc_start: 0.7510 (tm-30) cc_final: 0.6720 (tm-30) REVERT: B 147 GLU cc_start: 0.8087 (tp30) cc_final: 0.7710 (tp30) REVERT: B 151 MET cc_start: 0.7719 (ptm) cc_final: 0.7013 (ptm) REVERT: C 52 MET cc_start: 0.7992 (mmm) cc_final: 0.7570 (mmm) REVERT: D 41 ARG cc_start: 0.8527 (ttp80) cc_final: 0.7762 (ttp80) REVERT: D 156 ASP cc_start: 0.7853 (m-30) cc_final: 0.7602 (m-30) outliers start: 24 outliers final: 18 residues processed: 110 average time/residue: 0.0681 time to fit residues: 10.0614 Evaluate side-chains 116 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 126 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 128 HIS ** 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 = 0.4096 r_free = 0.4096 target = 0.182821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.144679 restraints weight = 6221.105| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.19 r_work: 0.3413 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 5707 Z= 0.156 Angle : 0.587 15.406 7703 Z= 0.317 Chirality : 0.041 0.204 866 Planarity : 0.004 0.072 999 Dihedral : 4.120 21.384 784 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.60 % Allowed : 17.12 % Favored : 79.28 % 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: 0.66 (0.33), residues: 704 helix: 3.90 (0.26), residues: 288 sheet: -1.38 (0.36), residues: 205 loop : -2.77 (0.38), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 154 TYR 0.020 0.001 TYR B 189 PHE 0.012 0.002 PHE C 122 TRP 0.014 0.001 TRP A 187 HIS 0.005 0.001 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 5702) covalent geometry : angle 0.57431 / 0.31 ( 7692) SS BOND : bond 0.01677 / 0.85 ( 4) SS BOND : angle 3.75832 / 1.74 ( 8) hydrogen bonds : bond 0.03881 / 2.59 ( 343) hydrogen bonds : angle 3.79604 / 2.67 ( 1002) link_NAG-ASN : bond 0.00196 / 0.10 ( 1) link_NAG-ASN : angle 1.33077 / 0.47 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.7579 (t0) cc_final: 0.6677 (p0) REVERT: B 56 ASP cc_start: 0.8319 (p0) cc_final: 0.8051 (p0) REVERT: B 60 GLU cc_start: 0.7453 (tm-30) cc_final: 0.6870 (tm-30) REVERT: B 147 GLU cc_start: 0.8049 (tp30) cc_final: 0.7677 (tp30) REVERT: B 151 MET cc_start: 0.7681 (ptm) cc_final: 0.6964 (ptm) REVERT: D 41 ARG cc_start: 0.8562 (ttp80) cc_final: 0.7780 (ttp80) REVERT: D 150 GLU cc_start: 0.8348 (tp30) cc_final: 0.7750 (mm-30) REVERT: D 156 ASP cc_start: 0.7785 (m-30) cc_final: 0.7501 (m-30) outliers start: 21 outliers final: 19 residues processed: 112 average time/residue: 0.0670 time to fit residues: 10.1887 Evaluate side-chains 119 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 126 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 128 HIS ** 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 = 0.4029 r_free = 0.4029 target = 0.176218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.136157 restraints weight = 6172.998| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.37 r_work: 0.3344 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 5707 Z= 0.236 Angle : 0.656 15.473 7703 Z= 0.352 Chirality : 0.043 0.211 866 Planarity : 0.004 0.077 999 Dihedral : 4.402 22.519 784 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.11 % Allowed : 16.61 % Favored : 79.28 % 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: 0.51 (0.33), residues: 704 helix: 3.70 (0.26), residues: 288 sheet: -1.39 (0.36), residues: 212 loop : -2.85 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 154 TYR 0.022 0.002 TYR A 39 PHE 0.014 0.002 PHE B 92 TRP 0.012 0.001 TRP A 187 HIS 0.008 0.002 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.23 ( 5702) covalent geometry : angle 0.64211 / 0.35 ( 7692) SS BOND : bond 0.01734 / 0.88 ( 4) SS BOND : angle 4.10493 / 1.89 ( 8) hydrogen bonds : bond 0.04212 / 2.83 ( 343) hydrogen bonds : angle 3.96276 / 2.77 ( 1002) link_NAG-ASN : bond 0.00197 / 0.10 ( 1) link_NAG-ASN : angle 1.26980 / 0.43 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 ASP cc_start: 0.8355 (p0) cc_final: 0.8105 (p0) REVERT: B 60 GLU cc_start: 0.7565 (tm-30) cc_final: 0.6197 (tm-30) REVERT: B 147 GLU cc_start: 0.8099 (tp30) cc_final: 0.7739 (tp30) REVERT: B 151 MET cc_start: 0.7688 (ptm) cc_final: 0.6979 (ptm) REVERT: C 61 GLU cc_start: 0.8492 (tt0) cc_final: 0.7856 (tp30) REVERT: D 41 ARG cc_start: 0.8497 (ttp80) cc_final: 0.8274 (ptm-80) REVERT: D 104 MET cc_start: 0.7981 (mtp) cc_final: 0.7779 (mtp) REVERT: D 156 ASP cc_start: 0.7798 (m-30) cc_final: 0.7528 (m-30) outliers start: 24 outliers final: 22 residues processed: 115 average time/residue: 0.0729 time to fit residues: 11.1384 Evaluate side-chains 121 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 126 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 128 HIS ** 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 = 0.4028 r_free = 0.4028 target = 0.175355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.134317 restraints weight = 6162.166| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 3.02 r_work: 0.3419 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 5707 Z= 0.179 Angle : 0.636 15.944 7703 Z= 0.340 Chirality : 0.042 0.225 866 Planarity : 0.004 0.075 999 Dihedral : 4.237 20.409 784 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.94 % Allowed : 16.78 % Favored : 79.28 % 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: 0.49 (0.33), residues: 704 helix: 3.76 (0.26), residues: 288 sheet: -1.50 (0.36), residues: 206 loop : -2.84 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 154 TYR 0.019 0.002 TYR B 189 PHE 0.013 0.002 PHE B 92 TRP 0.014 0.001 TRP A 187 HIS 0.005 0.001 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 ( 5702) covalent geometry : angle 0.62096 / 0.33 ( 7692) SS BOND : bond 0.01782 / 0.89 ( 4) SS BOND : angle 4.24984 / 1.84 ( 8) hydrogen bonds : bond 0.04030 / 2.70 ( 343) hydrogen bonds : angle 3.85740 / 2.70 ( 1002) link_NAG-ASN : bond 0.00215 / 0.11 ( 1) link_NAG-ASN : angle 1.26749 / 0.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 ASP cc_start: 0.8380 (p0) cc_final: 0.8127 (p0) REVERT: B 60 GLU cc_start: 0.7425 (tm-30) cc_final: 0.6621 (tm-30) REVERT: B 147 GLU cc_start: 0.8058 (tp30) cc_final: 0.7700 (tp30) REVERT: B 151 MET cc_start: 0.7714 (ptm) cc_final: 0.7012 (ptm) REVERT: C 52 MET cc_start: 0.7891 (mmm) cc_final: 0.7630 (mmm) REVERT: C 158 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8377 (tp30) REVERT: D 41 ARG cc_start: 0.8516 (ttp80) cc_final: 0.8213 (ptm-80) REVERT: D 104 MET cc_start: 0.7912 (mtp) cc_final: 0.7697 (mtp) REVERT: D 156 ASP cc_start: 0.7823 (m-30) cc_final: 0.7546 (m-30) outliers start: 23 outliers final: 21 residues processed: 109 average time/residue: 0.0677 time to fit residues: 9.9446 Evaluate side-chains 121 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 126 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 38 optimal weight: 0.0010 chunk 50 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 128 HIS ** 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 = 0.4103 r_free = 0.4103 target = 0.183684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.144809 restraints weight = 6223.691| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 3.21 r_work: 0.3473 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 5707 Z= 0.134 Angle : 0.585 15.322 7703 Z= 0.315 Chirality : 0.041 0.206 866 Planarity : 0.004 0.070 999 Dihedral : 4.037 19.631 784 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.42 % Allowed : 16.95 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.66 (0.33), residues: 704 helix: 3.89 (0.26), residues: 288 sheet: -1.36 (0.36), residues: 212 loop : -2.82 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 154 TYR 0.011 0.001 TYR C 49 PHE 0.012 0.001 PHE C 106 TRP 0.014 0.001 TRP A 187 HIS 0.003 0.001 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 5702) covalent geometry : angle 0.57094 / 0.31 ( 7692) SS BOND : bond 0.01756 / 0.88 ( 4) SS BOND : angle 3.91924 / 1.73 ( 8) hydrogen bonds : bond 0.03722 / 2.49 ( 343) hydrogen bonds : angle 3.70246 / 2.60 ( 1002) link_NAG-ASN : bond 0.00222 / 0.12 ( 1) link_NAG-ASN : angle 1.21265 / 0.47 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 142 ASP cc_start: 0.7526 (t0) cc_final: 0.6632 (p0) REVERT: B 56 ASP cc_start: 0.8351 (p0) cc_final: 0.8068 (p0) REVERT: B 60 GLU cc_start: 0.7363 (tm-30) cc_final: 0.6559 (tm-30) REVERT: B 147 GLU cc_start: 0.8029 (tp30) cc_final: 0.7657 (tp30) REVERT: B 151 MET cc_start: 0.7679 (ptm) cc_final: 0.6966 (ptm) REVERT: C 52 MET cc_start: 0.7851 (mmm) cc_final: 0.7397 (mmm) REVERT: C 61 GLU cc_start: 0.8367 (tt0) cc_final: 0.7639 (tp30) REVERT: C 158 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8382 (mm-30) REVERT: D 41 ARG cc_start: 0.8510 (ttp80) cc_final: 0.7746 (ttp80) REVERT: D 104 MET cc_start: 0.7839 (mtp) cc_final: 0.7584 (mtp) REVERT: D 150 GLU cc_start: 0.8255 (tp30) cc_final: 0.7762 (mm-30) REVERT: D 156 ASP cc_start: 0.7810 (m-30) cc_final: 0.7515 (m-30) outliers start: 20 outliers final: 20 residues processed: 109 average time/residue: 0.0633 time to fit residues: 9.4963 Evaluate side-chains 119 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 126 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 51 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 187 GLN ** D 128 HIS ** 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 = 0.4016 r_free = 0.4016 target = 0.174379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132474 restraints weight = 6136.795| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.10 r_work: 0.3345 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.005 0.069 5707 Z= 0.218 Angle : 0.652 15.892 7703 Z= 0.351 Chirality : 0.043 0.223 866 Planarity : 0.004 0.071 999 Dihedral : 4.289 21.952 784 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.94 % Allowed : 16.44 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.50 (0.33), residues: 704 helix: 3.72 (0.26), residues: 288 sheet: -1.42 (0.36), residues: 208 loop : -2.85 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 154 TYR 0.020 0.002 TYR B 189 PHE 0.017 0.002 PHE B 92 TRP 0.012 0.001 TRP A 187 HIS 0.008 0.001 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 ( 5702) covalent geometry : angle 0.63727 / 0.34 ( 7692) SS BOND : bond 0.01936 / 0.97 ( 4) SS BOND : angle 4.28028 / 1.88 ( 8) hydrogen bonds : bond 0.04101 / 2.75 ( 343) hydrogen bonds : angle 3.87312 / 2.71 ( 1002) link_NAG-ASN : bond 0.00197 / 0.10 ( 1) link_NAG-ASN : angle 1.11836 / 0.39 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1487.47 seconds wall clock time: 26 minutes 16.80 seconds (1576.80 seconds total)