Starting phenix.real_space_refine on Wed Sep 17 03:52:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xwn_38739/09_2025/8xwn_38739.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xwn_38739/09_2025/8xwn_38739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xwn_38739/09_2025/8xwn_38739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xwn_38739/09_2025/8xwn_38739.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xwn_38739/09_2025/8xwn_38739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xwn_38739/09_2025/8xwn_38739.map" } resolution = 3.29 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= 1.000 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 24 5.16 5 C 2296 2.51 5 N 586 2.21 5 O 590 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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3496 Number of models: 1 Model: "" Number of chains: 3 Chain: "R" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2421 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 291} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 575 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 68} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 500 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 1.13, per 1000 atoms: 0.32 Number of scatterers: 3496 At special positions: 0 Unit cell: (69.5125, 74.7, 104.787, 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 24 16.00 O 590 8.00 N 586 7.00 C 2296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 39 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS D 41 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 57 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS E 41 " distance=2.03 Simple disulfide: pdb=" SG CYS E 16 " - pdb=" SG CYS E 57 " distance=2.03 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: 0.30 Conformation dependent library (CDL) restraints added in 115.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 848 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 2 sheets defined 64.6% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'R' and resid 45 through 76 removed outlier: 4.415A pdb=" N SER R 76 " --> pdb=" O VAL R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 111 Proline residue: R 102 - end of helix Processing helix chain 'R' and resid 115 through 149 Processing helix chain 'R' and resid 154 through 160 removed outlier: 3.877A pdb=" N TYR R 160 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 177 Processing helix chain 'R' and resid 177 through 183 removed outlier: 3.542A pdb=" N LEU R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 212 Processing helix chain 'R' and resid 212 through 218 Processing helix chain 'R' and resid 220 through 241 removed outlier: 3.587A pdb=" N LYS R 240 " --> pdb=" O ARG R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 279 Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 285 through 304 Processing helix chain 'R' and resid 305 through 315 Proline residue: R 311 - end of helix Processing helix chain 'R' and resid 318 through 329 Processing helix chain 'D' and resid 25 through 27 No H-bonds generated for 'chain 'D' and resid 25 through 27' Processing helix chain 'D' and resid 62 through 78 removed outlier: 3.815A pdb=" N GLN D 66 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 27 No H-bonds generated for 'chain 'E' and resid 25 through 27' Processing helix chain 'E' and resid 62 through 77 Processing sheet with id=AA1, first strand: chain 'R' and resid 184 through 187 Processing sheet with id=AA2, first strand: chain 'D' and resid 55 through 58 removed outlier: 4.364A pdb=" N ILE D 46 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU D 31 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE E 46 " --> pdb=" O LEU E 58 " (cutoff:3.500A) 230 hydrogen bonds defined for protein. 672 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: 0.57 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1091 1.35 - 1.47: 830 1.47 - 1.58: 1623 1.58 - 1.70: 0 1.70 - 1.82: 31 Bond restraints: 3575 Sorted by residual: bond pdb=" CA LEU R 99 " pdb=" C LEU R 99 " ideal model delta sigma weight residual 1.522 1.506 0.017 1.36e-02 5.41e+03 1.48e+00 bond pdb=" CA GLU R 45 " pdb=" CB GLU R 45 " ideal model delta sigma weight residual 1.534 1.521 0.013 1.45e-02 4.76e+03 8.09e-01 bond pdb=" CB ASP R 35 " pdb=" CG ASP R 35 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 6.03e-01 bond pdb=" CA LEU R 101 " pdb=" C LEU R 101 " ideal model delta sigma weight residual 1.521 1.530 -0.009 1.17e-02 7.31e+03 5.65e-01 bond pdb=" CA LYS E 18 " pdb=" CB LYS E 18 " ideal model delta sigma weight residual 1.536 1.521 0.014 2.08e-02 2.31e+03 4.68e-01 ... (remaining 3570 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 4626 0.91 - 1.83: 190 1.83 - 2.74: 24 2.74 - 3.66: 15 3.66 - 4.57: 5 Bond angle restraints: 4860 Sorted by residual: angle pdb=" N HIS D 40 " pdb=" CA HIS D 40 " pdb=" C HIS D 40 " ideal model delta sigma weight residual 111.14 113.08 -1.94 1.08e+00 8.57e-01 3.22e+00 angle pdb=" N ILE R 113 " pdb=" CA ILE R 113 " pdb=" C ILE R 113 " ideal model delta sigma weight residual 112.90 111.37 1.53 9.60e-01 1.09e+00 2.54e+00 angle pdb=" N ASN R 110 " pdb=" CA ASN R 110 " pdb=" C ASN R 110 " ideal model delta sigma weight residual 111.56 113.68 -2.12 1.38e+00 5.25e-01 2.35e+00 angle pdb=" N GLY R 244 " pdb=" CA GLY R 244 " pdb=" C GLY R 244 " ideal model delta sigma weight residual 115.66 113.27 2.39 1.56e+00 4.11e-01 2.34e+00 angle pdb=" C ALA R 98 " pdb=" N LEU R 99 " pdb=" CA LEU R 99 " ideal model delta sigma weight residual 120.28 122.41 -2.13 1.44e+00 4.82e-01 2.19e+00 ... (remaining 4855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 1950 17.77 - 35.54: 167 35.54 - 53.31: 26 53.31 - 71.08: 13 71.08 - 88.85: 3 Dihedral angle restraints: 2159 sinusoidal: 859 harmonic: 1300 Sorted by residual: dihedral pdb=" CB CYS E 14 " pdb=" SG CYS E 14 " pdb=" SG CYS E 41 " pdb=" CB CYS E 41 " ideal model delta sinusoidal sigma weight residual -86.00 -141.87 55.87 1 1.00e+01 1.00e-02 4.21e+01 dihedral pdb=" CA LEU R 182 " pdb=" C LEU R 182 " pdb=" N PHE R 183 " pdb=" CA PHE R 183 " ideal model delta harmonic sigma weight residual -180.00 -164.46 -15.54 0 5.00e+00 4.00e-02 9.65e+00 dihedral pdb=" CA LYS D 71 " pdb=" CB LYS D 71 " pdb=" CG LYS D 71 " pdb=" CD LYS D 71 " ideal model delta sinusoidal sigma weight residual -180.00 -121.25 -58.75 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 2156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 350 0.024 - 0.048: 127 0.048 - 0.071: 59 0.071 - 0.095: 27 0.095 - 0.119: 19 Chirality restraints: 582 Sorted by residual: chirality pdb=" CA ILE D 35 " pdb=" N ILE D 35 " pdb=" C ILE D 35 " pdb=" CB ILE D 35 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.53e-01 chirality pdb=" CA ILE E 47 " pdb=" N ILE E 47 " pdb=" C ILE E 47 " pdb=" CB ILE E 47 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 chirality pdb=" CA ILE E 35 " pdb=" N ILE E 35 " pdb=" C ILE E 35 " pdb=" CB ILE E 35 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.37e-01 ... (remaining 579 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 25 " 0.018 5.00e-02 4.00e+02 2.65e-02 1.12e+00 pdb=" N PRO D 26 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO D 26 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 26 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 38 " -0.014 5.00e-02 4.00e+02 2.04e-02 6.69e-01 pdb=" N PRO E 39 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO E 39 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO E 39 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 119 " 0.004 2.00e-02 2.50e+03 8.15e-03 6.64e-01 pdb=" C CYS R 119 " -0.014 2.00e-02 2.50e+03 pdb=" O CYS R 119 " 0.005 2.00e-02 2.50e+03 pdb=" N LYS R 120 " 0.005 2.00e-02 2.50e+03 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 550 2.76 - 3.30: 3369 3.30 - 3.83: 5666 3.83 - 4.37: 6074 4.37 - 4.90: 11181 Nonbonded interactions: 26840 Sorted by model distance: nonbonded pdb=" O GLY R 201 " pdb=" OG1 THR R 204 " model vdw 2.229 3.040 nonbonded pdb=" OD1 ASP R 143 " pdb=" NH1 ARG R 159 " model vdw 2.415 3.120 nonbonded pdb=" O LEU R 125 " pdb=" ND2 ASN R 129 " model vdw 2.449 3.120 nonbonded pdb=" OE2 GLU D 31 " pdb=" NE ARG E 33 " model vdw 2.460 3.120 nonbonded pdb=" O LEU R 34 " pdb=" OD1 ASP R 35 " model vdw 2.469 3.040 ... (remaining 26835 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 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 14 through 17 or (resid 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 through 26 or (resid 27 and (name N or nam \ e CA or name C or name O or name CB )) or resid 28 through 60 or (resid 61 throu \ gh 62 and (name N or name CA or name C or name O or name CB )) or resid 63 throu \ gh 70 or (resid 71 and (name N or name CA or name C or name O or name CB )) or r \ esid 72 through 77 or (resid 78 and (name N or name CA or name C or name O or na \ me CB )))) selection = (chain 'E' and (resid 14 through 61 or (resid 62 and (name N or name CA or name \ C or name O or name CB )) or resid 63 through 78)) } 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.420 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.002 0.021 3581 Z= 0.123 Angle : 0.476 4.569 4872 Z= 0.270 Chirality : 0.037 0.119 582 Planarity : 0.003 0.026 596 Dihedral : 14.065 88.855 1293 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % 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 aren not related in a simple way. whole: 2.53 (0.40), residues: 435 helix: 2.86 (0.31), residues: 264 sheet: 0.35 (0.82), residues: 41 loop : -0.45 (0.49), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 13 TYR 0.010 0.001 TYR R 49 PHE 0.006 0.001 PHE D 72 TRP 0.005 0.001 TRP E 64 HIS 0.002 0.001 HIS R 150 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 3575) covalent geometry : angle 0.47363 ( 4860) SS BOND : bond 0.00158 ( 6) SS BOND : angle 1.04269 ( 12) hydrogen bonds : bond 0.12909 ( 230) hydrogen bonds : angle 4.54908 ( 672) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 84 ASP cc_start: 0.8606 (m-30) cc_final: 0.8282 (m-30) REVERT: R 141 SER cc_start: 0.9031 (t) cc_final: 0.8807 (p) REVERT: R 300 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7935 (mt-10) REVERT: R 325 LEU cc_start: 0.9105 (tp) cc_final: 0.8870 (tp) REVERT: R 327 LYS cc_start: 0.9147 (ttmm) cc_final: 0.8633 (tptt) REVERT: D 27 LYS cc_start: 0.9247 (ptmt) cc_final: 0.8782 (ttpp) REVERT: D 31 GLU cc_start: 0.7413 (tt0) cc_final: 0.7198 (tt0) REVERT: D 43 ASN cc_start: 0.8826 (m-40) cc_final: 0.8236 (p0) REVERT: D 59 ASP cc_start: 0.7987 (t0) cc_final: 0.7638 (t70) REVERT: D 66 GLN cc_start: 0.8567 (mt0) cc_final: 0.7990 (mm-40) REVERT: D 75 ARG cc_start: 0.8997 (ttp-170) cc_final: 0.8744 (ttp-110) REVERT: E 49 LYS cc_start: 0.8036 (mmmt) cc_final: 0.7454 (mttp) REVERT: E 57 CYS cc_start: 0.6149 (m) cc_final: 0.5922 (m) REVERT: E 59 ASP cc_start: 0.9117 (t0) cc_final: 0.8507 (t0) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.0896 time to fit residues: 15.4410 Evaluate side-chains 118 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 47 ASN R 203 ASN R 216 GLN R 323 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.121305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.094141 restraints weight = 6094.807| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.30 r_work: 0.3029 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3581 Z= 0.161 Angle : 0.566 5.098 4872 Z= 0.298 Chirality : 0.042 0.177 582 Planarity : 0.004 0.024 596 Dihedral : 3.791 17.442 476 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 4.44 % Allowed : 12.27 % Favored : 83.29 % 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 aren not related in a simple way. whole: 2.35 (0.39), residues: 435 helix: 2.77 (0.31), residues: 270 sheet: 0.17 (0.86), residues: 34 loop : -0.73 (0.47), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 13 TYR 0.012 0.001 TYR D 20 PHE 0.015 0.001 PHE D 72 TRP 0.007 0.001 TRP R 264 HIS 0.002 0.001 HIS R 323 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 3575) covalent geometry : angle 0.56105 ( 4860) SS BOND : bond 0.00330 ( 6) SS BOND : angle 1.53403 ( 12) hydrogen bonds : bond 0.05184 ( 230) hydrogen bonds : angle 4.11747 ( 672) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 203 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.7834 (t0) REVERT: R 280 GLN cc_start: 0.8747 (mm110) cc_final: 0.8532 (mt0) REVERT: D 25 HIS cc_start: 0.8735 (t-90) cc_final: 0.8067 (t-90) REVERT: D 28 PHE cc_start: 0.8345 (m-80) cc_final: 0.7836 (m-80) REVERT: D 31 GLU cc_start: 0.8166 (tt0) cc_final: 0.7891 (tt0) REVERT: D 43 ASN cc_start: 0.9142 (m-40) cc_final: 0.8507 (p0) REVERT: D 49 LYS cc_start: 0.8622 (mmmt) cc_final: 0.8401 (mtpp) REVERT: D 59 ASP cc_start: 0.8215 (t0) cc_final: 0.7975 (t70) REVERT: D 66 GLN cc_start: 0.8635 (mt0) cc_final: 0.8087 (mm-40) REVERT: E 49 LYS cc_start: 0.8754 (mmmt) cc_final: 0.8101 (mttp) outliers start: 17 outliers final: 14 residues processed: 123 average time/residue: 0.0831 time to fit residues: 11.9885 Evaluate side-chains 119 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain R residue 323 HIS Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 63 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 245 GLN R 323 HIS E 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.121888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.094999 restraints weight = 6095.617| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.30 r_work: 0.3043 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3581 Z= 0.140 Angle : 0.525 5.277 4872 Z= 0.282 Chirality : 0.041 0.162 582 Planarity : 0.004 0.029 596 Dihedral : 3.725 16.193 476 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 4.18 % Allowed : 12.79 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.40), residues: 435 helix: 2.69 (0.31), residues: 270 sheet: 0.17 (0.87), residues: 34 loop : -0.76 (0.48), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 322 TYR 0.009 0.001 TYR D 20 PHE 0.019 0.001 PHE D 72 TRP 0.007 0.001 TRP R 264 HIS 0.003 0.001 HIS R 323 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3575) covalent geometry : angle 0.52349 ( 4860) SS BOND : bond 0.00146 ( 6) SS BOND : angle 1.02038 ( 12) hydrogen bonds : bond 0.04761 ( 230) hydrogen bonds : angle 4.04941 ( 672) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 327 LYS cc_start: 0.9109 (ttmm) cc_final: 0.8750 (mttp) REVERT: D 25 HIS cc_start: 0.8601 (t-90) cc_final: 0.7688 (t70) REVERT: D 28 PHE cc_start: 0.8119 (m-80) cc_final: 0.7589 (m-80) REVERT: D 43 ASN cc_start: 0.9148 (m-40) cc_final: 0.8533 (p0) REVERT: D 54 ARG cc_start: 0.8316 (ptp90) cc_final: 0.7957 (ptp90) REVERT: D 59 ASP cc_start: 0.8197 (t0) cc_final: 0.7908 (t70) REVERT: E 15 GLN cc_start: 0.7989 (mp10) cc_final: 0.7669 (mp10) REVERT: E 49 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8043 (mttp) outliers start: 16 outliers final: 13 residues processed: 117 average time/residue: 0.0846 time to fit residues: 11.5868 Evaluate side-chains 119 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.122074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.095106 restraints weight = 6014.948| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.24 r_work: 0.3049 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3581 Z= 0.137 Angle : 0.537 5.460 4872 Z= 0.285 Chirality : 0.041 0.199 582 Planarity : 0.004 0.041 596 Dihedral : 3.772 15.693 476 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 4.70 % Allowed : 12.53 % Favored : 82.77 % 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 aren not related in a simple way. whole: 2.32 (0.40), residues: 435 helix: 2.71 (0.31), residues: 268 sheet: -0.13 (0.79), residues: 42 loop : -0.51 (0.52), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 185 TYR 0.011 0.001 TYR E 20 PHE 0.017 0.001 PHE D 72 TRP 0.007 0.001 TRP R 264 HIS 0.002 0.001 HIS R 247 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 3575) covalent geometry : angle 0.53458 ( 4860) SS BOND : bond 0.00129 ( 6) SS BOND : angle 1.22923 ( 12) hydrogen bonds : bond 0.04531 ( 230) hydrogen bonds : angle 4.07290 ( 672) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 327 LYS cc_start: 0.9046 (ttmm) cc_final: 0.8694 (mttp) REVERT: D 25 HIS cc_start: 0.8616 (t-90) cc_final: 0.7773 (t70) REVERT: D 28 PHE cc_start: 0.8175 (m-80) cc_final: 0.7639 (m-80) REVERT: D 43 ASN cc_start: 0.9162 (m-40) cc_final: 0.8548 (p0) REVERT: D 54 ARG cc_start: 0.8397 (ptp90) cc_final: 0.8043 (ptp90) REVERT: D 59 ASP cc_start: 0.8155 (t0) cc_final: 0.7853 (t70) REVERT: E 49 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8151 (mttp) outliers start: 18 outliers final: 14 residues processed: 119 average time/residue: 0.0799 time to fit residues: 11.2964 Evaluate side-chains 118 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 73 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.121852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.094841 restraints weight = 6020.993| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.24 r_work: 0.3047 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3581 Z= 0.147 Angle : 0.567 12.451 4872 Z= 0.291 Chirality : 0.041 0.203 582 Planarity : 0.004 0.038 596 Dihedral : 3.903 16.959 476 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 4.96 % Allowed : 14.36 % Favored : 80.68 % 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 aren not related in a simple way. whole: 2.25 (0.41), residues: 435 helix: 2.69 (0.31), residues: 268 sheet: -0.32 (0.79), residues: 42 loop : -0.58 (0.53), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 185 TYR 0.006 0.001 TYR D 20 PHE 0.016 0.001 PHE D 72 TRP 0.007 0.001 TRP R 264 HIS 0.002 0.001 HIS R 247 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 3575) covalent geometry : angle 0.56334 ( 4860) SS BOND : bond 0.00136 ( 6) SS BOND : angle 1.45436 ( 12) hydrogen bonds : bond 0.04566 ( 230) hydrogen bonds : angle 4.15534 ( 672) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 327 LYS cc_start: 0.9049 (ttmm) cc_final: 0.8662 (mptt) REVERT: D 43 ASN cc_start: 0.9143 (m-40) cc_final: 0.8581 (p0) REVERT: D 49 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8670 (mtmt) REVERT: D 54 ARG cc_start: 0.8454 (ptp90) cc_final: 0.8107 (ptp90) REVERT: D 59 ASP cc_start: 0.8110 (t0) cc_final: 0.7814 (t70) REVERT: E 15 GLN cc_start: 0.8129 (mp10) cc_final: 0.7836 (mp10) REVERT: E 49 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8242 (mttp) outliers start: 19 outliers final: 14 residues processed: 124 average time/residue: 0.0754 time to fit residues: 11.1211 Evaluate side-chains 119 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 63 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 chunk 42 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 319 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.123211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.096112 restraints weight = 6006.970| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.26 r_work: 0.3067 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3581 Z= 0.128 Angle : 0.551 9.283 4872 Z= 0.289 Chirality : 0.041 0.200 582 Planarity : 0.004 0.045 596 Dihedral : 3.981 18.661 476 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 3.13 % Allowed : 16.71 % Favored : 80.16 % 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 aren not related in a simple way. whole: 2.28 (0.41), residues: 435 helix: 2.69 (0.31), residues: 270 sheet: -0.37 (0.78), residues: 42 loop : -0.53 (0.54), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 185 TYR 0.015 0.001 TYR E 20 PHE 0.017 0.001 PHE D 72 TRP 0.006 0.001 TRP R 264 HIS 0.007 0.001 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3575) covalent geometry : angle 0.54854 ( 4860) SS BOND : bond 0.00339 ( 6) SS BOND : angle 1.23792 ( 12) hydrogen bonds : bond 0.04260 ( 230) hydrogen bonds : angle 4.11321 ( 672) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 327 LYS cc_start: 0.9032 (ttmm) cc_final: 0.8660 (mptt) REVERT: D 28 PHE cc_start: 0.8077 (m-80) cc_final: 0.7401 (m-80) REVERT: D 43 ASN cc_start: 0.9147 (m-40) cc_final: 0.8627 (p0) REVERT: D 49 LYS cc_start: 0.8850 (mtpp) cc_final: 0.8645 (mtmt) REVERT: D 54 ARG cc_start: 0.8467 (ptp90) cc_final: 0.8059 (ptp90) REVERT: D 59 ASP cc_start: 0.8035 (t0) cc_final: 0.7733 (t70) REVERT: E 49 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8144 (mttp) outliers start: 12 outliers final: 11 residues processed: 113 average time/residue: 0.0655 time to fit residues: 8.8552 Evaluate side-chains 115 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 49 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 ASN R 319 GLN E 25 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.122818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.095333 restraints weight = 6110.468| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.31 r_work: 0.3053 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3581 Z= 0.141 Angle : 0.557 6.793 4872 Z= 0.294 Chirality : 0.041 0.193 582 Planarity : 0.004 0.041 596 Dihedral : 3.984 17.799 476 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 3.92 % Allowed : 15.93 % Favored : 80.16 % 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 aren not related in a simple way. whole: 2.22 (0.40), residues: 435 helix: 2.67 (0.31), residues: 270 sheet: -0.46 (0.77), residues: 42 loop : -0.60 (0.53), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 185 TYR 0.006 0.001 TYR D 20 PHE 0.012 0.001 PHE D 72 TRP 0.006 0.001 TRP R 264 HIS 0.006 0.001 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 3575) covalent geometry : angle 0.55304 ( 4860) SS BOND : bond 0.00139 ( 6) SS BOND : angle 1.40206 ( 12) hydrogen bonds : bond 0.04370 ( 230) hydrogen bonds : angle 4.10303 ( 672) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 327 LYS cc_start: 0.9033 (ttmm) cc_final: 0.8673 (mptt) REVERT: D 28 PHE cc_start: 0.8144 (m-80) cc_final: 0.7426 (m-80) REVERT: D 43 ASN cc_start: 0.9121 (m-40) cc_final: 0.8640 (p0) REVERT: D 49 LYS cc_start: 0.8826 (mtpp) cc_final: 0.8607 (mtmt) REVERT: D 54 ARG cc_start: 0.8429 (ptp90) cc_final: 0.8045 (ptp90) REVERT: D 59 ASP cc_start: 0.8043 (t0) cc_final: 0.7736 (t70) REVERT: E 57 CYS cc_start: 0.7064 (m) cc_final: 0.6656 (m) outliers start: 15 outliers final: 13 residues processed: 117 average time/residue: 0.0764 time to fit residues: 10.5962 Evaluate side-chains 117 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 44 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 ASN R 319 GLN E 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.123132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.095773 restraints weight = 6191.202| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.32 r_work: 0.3052 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3581 Z= 0.136 Angle : 0.556 5.769 4872 Z= 0.297 Chirality : 0.041 0.198 582 Planarity : 0.004 0.040 596 Dihedral : 3.982 18.501 476 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 3.39 % Allowed : 16.97 % Favored : 79.63 % 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 aren not related in a simple way. whole: 2.19 (0.40), residues: 435 helix: 2.64 (0.31), residues: 270 sheet: -0.44 (0.78), residues: 42 loop : -0.58 (0.52), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 185 TYR 0.016 0.001 TYR E 20 PHE 0.011 0.001 PHE D 72 TRP 0.006 0.001 TRP D 64 HIS 0.007 0.001 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3575) covalent geometry : angle 0.55259 ( 4860) SS BOND : bond 0.00132 ( 6) SS BOND : angle 1.40074 ( 12) hydrogen bonds : bond 0.04298 ( 230) hydrogen bonds : angle 4.06643 ( 672) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 327 LYS cc_start: 0.9027 (ttmm) cc_final: 0.8678 (mptt) REVERT: D 28 PHE cc_start: 0.8151 (m-80) cc_final: 0.7481 (m-80) REVERT: D 43 ASN cc_start: 0.9153 (m-40) cc_final: 0.8667 (p0) REVERT: D 54 ARG cc_start: 0.8444 (ptp90) cc_final: 0.8068 (ptp90) REVERT: D 59 ASP cc_start: 0.8021 (t0) cc_final: 0.7717 (t70) REVERT: E 57 CYS cc_start: 0.7001 (m) cc_final: 0.6618 (m) outliers start: 13 outliers final: 12 residues processed: 115 average time/residue: 0.0700 time to fit residues: 9.5570 Evaluate side-chains 116 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 44 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 0 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 GLN E 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.122169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.094884 restraints weight = 5991.069| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.28 r_work: 0.3044 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3581 Z= 0.154 Angle : 0.580 5.733 4872 Z= 0.310 Chirality : 0.042 0.210 582 Planarity : 0.004 0.041 596 Dihedral : 4.078 19.902 476 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.13 % Allowed : 16.97 % Favored : 79.90 % 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 aren not related in a simple way. whole: 2.10 (0.40), residues: 435 helix: 2.57 (0.31), residues: 270 sheet: -0.53 (0.78), residues: 42 loop : -0.59 (0.52), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 75 TYR 0.008 0.001 TYR R 188 PHE 0.013 0.001 PHE D 72 TRP 0.007 0.001 TRP R 264 HIS 0.007 0.001 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 3575) covalent geometry : angle 0.57607 ( 4860) SS BOND : bond 0.00109 ( 6) SS BOND : angle 1.45710 ( 12) hydrogen bonds : bond 0.04513 ( 230) hydrogen bonds : angle 4.07010 ( 672) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 327 LYS cc_start: 0.9018 (ttmm) cc_final: 0.8683 (mptt) REVERT: D 28 PHE cc_start: 0.8151 (m-80) cc_final: 0.7493 (m-80) REVERT: D 43 ASN cc_start: 0.9163 (m-40) cc_final: 0.8669 (p0) REVERT: D 54 ARG cc_start: 0.8461 (ptp90) cc_final: 0.8085 (ptp90) REVERT: D 59 ASP cc_start: 0.8038 (t0) cc_final: 0.7733 (t70) REVERT: E 15 GLN cc_start: 0.7993 (mp10) cc_final: 0.7662 (mp10) outliers start: 12 outliers final: 12 residues processed: 110 average time/residue: 0.0884 time to fit residues: 11.4693 Evaluate side-chains 111 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 44 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.0970 chunk 37 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 18 optimal weight: 0.0370 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 ASN R 203 ASN R 319 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.123767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.096406 restraints weight = 6107.053| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.29 r_work: 0.3061 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3581 Z= 0.127 Angle : 0.561 5.582 4872 Z= 0.301 Chirality : 0.041 0.204 582 Planarity : 0.004 0.042 596 Dihedral : 4.052 19.966 476 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 3.13 % Allowed : 18.02 % Favored : 78.85 % 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 aren not related in a simple way. whole: 2.13 (0.40), residues: 435 helix: 2.64 (0.31), residues: 270 sheet: -0.54 (0.79), residues: 42 loop : -0.71 (0.51), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 185 TYR 0.007 0.001 TYR R 188 PHE 0.014 0.001 PHE E 24 TRP 0.006 0.001 TRP R 264 HIS 0.007 0.001 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 3575) covalent geometry : angle 0.55748 ( 4860) SS BOND : bond 0.00140 ( 6) SS BOND : angle 1.37869 ( 12) hydrogen bonds : bond 0.04177 ( 230) hydrogen bonds : angle 4.00162 ( 672) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: R 327 LYS cc_start: 0.9012 (ttmm) cc_final: 0.8679 (mptt) REVERT: D 28 PHE cc_start: 0.8140 (m-80) cc_final: 0.7595 (m-80) REVERT: D 43 ASN cc_start: 0.9166 (m-40) cc_final: 0.8675 (p0) REVERT: D 54 ARG cc_start: 0.8459 (ptp90) cc_final: 0.8092 (ptp90) REVERT: D 59 ASP cc_start: 0.7915 (t0) cc_final: 0.7658 (t70) outliers start: 12 outliers final: 11 residues processed: 103 average time/residue: 0.0879 time to fit residues: 10.6750 Evaluate side-chains 104 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 44 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 41 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 0.0270 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 216 GLN R 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.123212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.096023 restraints weight = 6107.418| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.29 r_work: 0.3027 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3581 Z= 0.130 Angle : 0.559 5.571 4872 Z= 0.299 Chirality : 0.041 0.203 582 Planarity : 0.004 0.042 596 Dihedral : 4.013 19.761 476 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 3.92 % Allowed : 16.97 % Favored : 79.11 % 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 aren not related in a simple way. whole: 2.15 (0.40), residues: 435 helix: 2.65 (0.31), residues: 270 sheet: -0.46 (0.79), residues: 42 loop : -0.75 (0.51), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 185 TYR 0.024 0.001 TYR E 20 PHE 0.012 0.001 PHE E 24 TRP 0.006 0.001 TRP R 264 HIS 0.007 0.002 HIS R 323 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3575) covalent geometry : angle 0.55530 ( 4860) SS BOND : bond 0.00129 ( 6) SS BOND : angle 1.40790 ( 12) hydrogen bonds : bond 0.04160 ( 230) hydrogen bonds : angle 3.99065 ( 672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1195.85 seconds wall clock time: 21 minutes 11.93 seconds (1271.93 seconds total)