Starting phenix.real_space_refine on Wed Mar 5 20:17:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xwn_38739/03_2025/8xwn_38739.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xwn_38739/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xwn_38739/03_2025/8xwn_38739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xwn_38739/03_2025/8xwn_38739.map" model { file = "/net/cci-nas-00/data/ceres_data/8xwn_38739/03_2025/8xwn_38739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xwn_38739/03_2025/8xwn_38739.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLU:plan': 1, 'ARG:plan': 2} 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: 3.23, per 1000 atoms: 0.92 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: 0.97 Conformation dependent library (CDL) restraints added in 457.1 milliseconds 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: 0.38 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: 0.97 Time building geometry restraints manager: 1.17 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: 0.600 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.210 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.130 ------------------------------------------------------------------------------- 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 3575 Z= 0.149 Angle : 0.474 4.569 4860 Z= 0.269 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.005 0.001 TRP E 64 HIS 0.002 0.001 HIS R 150 PHE 0.006 0.001 PHE D 72 TYR 0.010 0.001 TYR R 49 ARG 0.002 0.000 ARG D 13 *********************** 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 : 0.451 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: 0.8631 (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: 0.7197 (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: 0.2061 time to fit residues: 35.7897 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 : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.0060 chunk 39 optimal weight: 0.3980 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.122405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.095617 restraints weight = 5989.284| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.27 r_work: 0.3055 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3575 Z= 0.194 Angle : 0.542 4.987 4860 Z= 0.287 Chirality : 0.042 0.173 582 Planarity : 0.004 0.029 596 Dihedral : 3.778 17.481 476 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.39 % Allowed : 12.27 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.40), residues: 435 helix: 2.82 (0.31), residues: 270 sheet: 0.21 (0.86), residues: 34 loop : -0.72 (0.47), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 64 HIS 0.004 0.001 HIS D 25 PHE 0.016 0.001 PHE D 72 TYR 0.013 0.001 TYR D 20 ARG 0.003 0.000 ARG E 54 *********************** 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 129 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 203 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7793 (t0) REVERT: D 27 LYS cc_start: 0.9380 (ptmt) cc_final: 0.9172 (ttpp) REVERT: D 31 GLU cc_start: 0.8119 (tt0) cc_final: 0.7884 (tt0) REVERT: D 43 ASN cc_start: 0.9139 (m-40) cc_final: 0.8548 (p0) REVERT: D 59 ASP cc_start: 0.8189 (t0) cc_final: 0.7948 (t70) REVERT: D 75 ARG cc_start: 0.9081 (ttp-170) cc_final: 0.8855 (ttp-110) REVERT: E 15 GLN cc_start: 0.8010 (mp10) cc_final: 0.7649 (mp10) REVERT: E 36 GLU cc_start: 0.7671 (tt0) cc_final: 0.7241 (tp30) REVERT: E 49 LYS cc_start: 0.8740 (mmmt) cc_final: 0.8090 (mttp) outliers start: 13 outliers final: 11 residues processed: 127 average time/residue: 0.1869 time to fit residues: 27.9136 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 : 0.386 ------------------------------------------------------------------------------- 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 D residue 29 ILE 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 33 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 E 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.120508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.093643 restraints weight = 6033.696| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.26 r_work: 0.3023 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3575 Z= 0.255 Angle : 0.537 5.548 4860 Z= 0.286 Chirality : 0.042 0.164 582 Planarity : 0.004 0.039 596 Dihedral : 3.771 15.847 476 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 5.48 % Allowed : 11.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.40), residues: 435 helix: 2.66 (0.31), residues: 270 sheet: -0.97 (1.17), residues: 20 loop : -0.57 (0.45), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 264 HIS 0.003 0.001 HIS R 247 PHE 0.019 0.001 PHE D 72 TYR 0.009 0.001 TYR D 20 ARG 0.002 0.000 ARG D 54 *********************** 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 135 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 327 LYS cc_start: 0.9112 (ttmm) cc_final: 0.8688 (tptt) REVERT: D 25 HIS cc_start: 0.8745 (t-90) cc_final: 0.8069 (t-90) REVERT: D 27 LYS cc_start: 0.9341 (ptmt) cc_final: 0.9122 (ttpp) REVERT: D 28 PHE cc_start: 0.8405 (m-80) cc_final: 0.7890 (m-80) REVERT: D 43 ASN cc_start: 0.9143 (m-40) cc_final: 0.8500 (p0) REVERT: D 54 ARG cc_start: 0.8371 (ptp90) cc_final: 0.7961 (ptp90) REVERT: D 59 ASP cc_start: 0.8120 (t0) cc_final: 0.7848 (t70) REVERT: D 75 ARG cc_start: 0.9108 (ttp-170) cc_final: 0.8899 (ttp-110) REVERT: E 36 GLU cc_start: 0.7578 (tt0) cc_final: 0.7271 (tp30) REVERT: E 49 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8082 (mttp) REVERT: E 77 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7438 (mm-30) outliers start: 21 outliers final: 17 residues processed: 126 average time/residue: 0.1980 time to fit residues: 29.3040 Evaluate side-chains 126 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 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 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 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 7 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 0.0570 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.122371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.095252 restraints weight = 6018.806| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.26 r_work: 0.3048 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: 0.8473 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3575 Z= 0.181 Angle : 0.540 5.347 4860 Z= 0.287 Chirality : 0.041 0.201 582 Planarity : 0.004 0.037 596 Dihedral : 3.773 15.632 476 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 4.18 % Allowed : 14.62 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.40), residues: 435 helix: 2.69 (0.31), residues: 268 sheet: -0.10 (0.78), residues: 42 loop : -0.54 (0.51), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 264 HIS 0.004 0.001 HIS R 323 PHE 0.017 0.001 PHE D 72 TYR 0.011 0.001 TYR E 20 ARG 0.005 0.000 ARG R 185 *********************** 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: 16 poor density : 111 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 327 LYS cc_start: 0.9069 (ttmm) cc_final: 0.8707 (mptt) REVERT: D 43 ASN cc_start: 0.9141 (m-40) cc_final: 0.8605 (p0) REVERT: D 54 ARG cc_start: 0.8385 (ptp90) cc_final: 0.8010 (ptp90) REVERT: D 59 ASP cc_start: 0.8122 (t0) cc_final: 0.7841 (t70) REVERT: D 75 ARG cc_start: 0.9116 (ttp-170) cc_final: 0.8873 (ttp-110) REVERT: E 49 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8136 (mttp) outliers start: 16 outliers final: 13 residues processed: 119 average time/residue: 0.1887 time to fit residues: 26.5488 Evaluate side-chains 118 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 221 ILE 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 50 LEU 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 8 optimal weight: 0.9980 chunk 5 optimal weight: 0.0270 chunk 24 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.121341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.094049 restraints weight = 6076.018| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.28 r_work: 0.3033 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3575 Z= 0.225 Angle : 0.575 13.080 4860 Z= 0.296 Chirality : 0.041 0.202 582 Planarity : 0.004 0.037 596 Dihedral : 3.963 17.257 476 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 5.22 % Allowed : 14.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.40), residues: 435 helix: 2.72 (0.31), residues: 268 sheet: -0.30 (0.79), residues: 42 loop : -0.66 (0.51), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 264 HIS 0.003 0.001 HIS R 323 PHE 0.016 0.001 PHE D 72 TYR 0.007 0.001 TYR D 20 ARG 0.003 0.000 ARG R 185 *********************** 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 128 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 327 LYS cc_start: 0.9088 (ttmm) cc_final: 0.8682 (tptt) REVERT: D 43 ASN cc_start: 0.9145 (m-40) cc_final: 0.8587 (p0) REVERT: D 54 ARG cc_start: 0.8440 (ptp90) cc_final: 0.8091 (ptp90) REVERT: D 59 ASP cc_start: 0.8086 (t0) cc_final: 0.7806 (t70) REVERT: E 15 GLN cc_start: 0.8088 (mp10) cc_final: 0.7753 (mp10) REVERT: E 49 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8162 (mttp) outliers start: 20 outliers final: 16 residues processed: 120 average time/residue: 0.1787 time to fit residues: 25.5403 Evaluate side-chains 118 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 R residue 323 HIS 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 Chi-restraints excluded: chain E residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 33 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.0980 chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.122096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.094975 restraints weight = 6160.562| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.23 r_work: 0.3044 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3575 Z= 0.194 Angle : 0.560 10.347 4860 Z= 0.296 Chirality : 0.041 0.208 582 Planarity : 0.004 0.048 596 Dihedral : 3.991 17.632 476 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 5.22 % Allowed : 15.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.40), residues: 435 helix: 2.65 (0.31), residues: 270 sheet: -0.35 (0.79), residues: 42 loop : -0.56 (0.52), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 264 HIS 0.006 0.001 HIS D 25 PHE 0.017 0.001 PHE D 72 TYR 0.013 0.001 TYR E 20 ARG 0.002 0.000 ARG R 185 *********************** 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 125 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 ASN cc_start: 0.9134 (m-40) cc_final: 0.8596 (p0) REVERT: D 54 ARG cc_start: 0.8387 (ptp90) cc_final: 0.7963 (ptp90) REVERT: D 59 ASP cc_start: 0.8022 (t0) cc_final: 0.7745 (t70) REVERT: E 49 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8145 (mttp) REVERT: E 77 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7436 (mm-30) outliers start: 20 outliers final: 14 residues processed: 119 average time/residue: 0.1777 time to fit residues: 25.2925 Evaluate side-chains 115 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 R residue 323 HIS 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 49 LYS Chi-restraints excluded: chain E residue 63 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.0030 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- 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 323 HIS E 25 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 = 0.3536 r_free = 0.3536 target = 0.120010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.092350 restraints weight = 6088.811| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.29 r_work: 0.3003 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3575 Z= 0.293 Angle : 0.601 10.107 4860 Z= 0.314 Chirality : 0.043 0.211 582 Planarity : 0.005 0.047 596 Dihedral : 4.155 19.099 476 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 4.96 % Allowed : 15.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.40), residues: 435 helix: 2.61 (0.31), residues: 268 sheet: -0.52 (0.77), residues: 42 loop : -0.68 (0.52), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 264 HIS 0.006 0.002 HIS D 25 PHE 0.016 0.002 PHE D 72 TYR 0.006 0.001 TYR D 20 ARG 0.002 0.000 ARG R 185 *********************** 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 122 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 327 LYS cc_start: 0.9083 (ttmm) cc_final: 0.8740 (mptt) REVERT: D 28 PHE cc_start: 0.8134 (m-80) cc_final: 0.7663 (m-80) REVERT: D 54 ARG cc_start: 0.8434 (ptp90) cc_final: 0.8111 (ptp90) REVERT: D 59 ASP cc_start: 0.8129 (t0) cc_final: 0.7821 (t70) REVERT: E 15 GLN cc_start: 0.8108 (mp10) cc_final: 0.7804 (mp10) REVERT: E 49 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8348 (mttp) REVERT: E 57 CYS cc_start: 0.6837 (m) cc_final: 0.6384 (m) outliers start: 19 outliers final: 14 residues processed: 117 average time/residue: 0.1832 time to fit residues: 25.6978 Evaluate side-chains 115 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 R residue 325 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 D 43 ASN E 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.120999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.093541 restraints weight = 6028.842| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.31 r_work: 0.3002 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3575 Z= 0.249 Angle : 0.584 7.275 4860 Z= 0.311 Chirality : 0.042 0.205 582 Planarity : 0.004 0.048 596 Dihedral : 4.136 19.052 476 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 4.44 % Allowed : 16.97 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.40), residues: 435 helix: 2.61 (0.31), residues: 268 sheet: -0.65 (0.75), residues: 42 loop : -0.66 (0.52), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 264 HIS 0.007 0.002 HIS D 25 PHE 0.014 0.001 PHE D 72 TYR 0.015 0.001 TYR E 20 ARG 0.003 0.000 ARG R 322 *********************** 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 116 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: R 327 LYS cc_start: 0.9031 (ttmm) cc_final: 0.8687 (mptt) REVERT: D 28 PHE cc_start: 0.8107 (m-80) cc_final: 0.7645 (m-80) REVERT: D 54 ARG cc_start: 0.8446 (ptp90) cc_final: 0.8036 (ptp90) REVERT: D 59 ASP cc_start: 0.8134 (t0) cc_final: 0.7842 (t70) REVERT: E 57 CYS cc_start: 0.6963 (m) cc_final: 0.6561 (m) outliers start: 17 outliers final: 15 residues processed: 112 average time/residue: 0.1835 time to fit residues: 24.3497 Evaluate side-chains 112 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 ASN R 323 HIS D 43 ASN E 66 GLN 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 = 0.121363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.094142 restraints weight = 6007.659| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.31 r_work: 0.3020 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3575 Z= 0.219 Angle : 0.573 6.317 4860 Z= 0.307 Chirality : 0.042 0.200 582 Planarity : 0.004 0.048 596 Dihedral : 4.150 20.115 476 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 4.70 % Allowed : 17.49 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.40), residues: 435 helix: 2.51 (0.31), residues: 270 sheet: -0.67 (0.75), residues: 42 loop : -0.63 (0.52), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 264 HIS 0.007 0.001 HIS D 25 PHE 0.012 0.001 PHE D 72 TYR 0.008 0.001 TYR E 20 ARG 0.002 0.000 ARG R 185 *********************** 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 115 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: R 327 LYS cc_start: 0.9032 (ttmm) cc_final: 0.8692 (mptt) REVERT: D 28 PHE cc_start: 0.8142 (m-80) cc_final: 0.7700 (m-80) REVERT: D 31 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7825 (mm-30) REVERT: D 43 ASN cc_start: 0.9184 (m-40) cc_final: 0.8573 (p0) REVERT: D 54 ARG cc_start: 0.8440 (ptp90) cc_final: 0.8029 (ptp90) REVERT: D 59 ASP cc_start: 0.8048 (t0) cc_final: 0.7780 (t70) REVERT: E 15 GLN cc_start: 0.8039 (mp10) cc_final: 0.7696 (mp10) outliers start: 18 outliers final: 15 residues processed: 112 average time/residue: 0.1823 time to fit residues: 24.3132 Evaluate side-chains 111 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 109 VAL 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 R residue 325 LEU 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 63 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 20 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 319 GLN ** 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 = 0.3561 r_free = 0.3561 target = 0.121545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.094131 restraints weight = 6081.816| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.31 r_work: 0.2997 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3575 Z= 0.215 Angle : 0.577 5.518 4860 Z= 0.309 Chirality : 0.042 0.196 582 Planarity : 0.004 0.049 596 Dihedral : 4.149 20.351 476 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 4.44 % Allowed : 17.49 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.40), residues: 435 helix: 2.51 (0.31), residues: 270 sheet: -0.56 (0.76), residues: 42 loop : -0.67 (0.51), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 264 HIS 0.007 0.001 HIS D 25 PHE 0.013 0.001 PHE D 72 TYR 0.007 0.001 TYR D 20 ARG 0.003 0.000 ARG R 322 ********************** 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 114 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: R 319 GLN cc_start: 0.8429 (tp40) cc_final: 0.8080 (tp-100) REVERT: R 327 LYS cc_start: 0.9011 (ttmm) cc_final: 0.8698 (mptt) REVERT: D 28 PHE cc_start: 0.8150 (m-80) cc_final: 0.7666 (m-80) REVERT: D 43 ASN cc_start: 0.9167 (m-40) cc_final: 0.8566 (p0) REVERT: D 54 ARG cc_start: 0.8442 (ptp90) cc_final: 0.8035 (ptp90) REVERT: D 59 ASP cc_start: 0.8035 (t0) cc_final: 0.7768 (t70) REVERT: E 15 GLN cc_start: 0.7945 (mp10) cc_final: 0.7724 (mp10) outliers start: 17 outliers final: 14 residues processed: 111 average time/residue: 0.1811 time to fit residues: 23.8458 Evaluate side-chains 109 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 R residue 325 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 0.0870 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 ASN R 216 GLN ** R 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 323 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 = 0.3564 r_free = 0.3564 target = 0.121751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.094283 restraints weight = 6060.251| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.29 r_work: 0.3014 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3575 Z= 0.219 Angle : 0.583 5.680 4860 Z= 0.313 Chirality : 0.042 0.196 582 Planarity : 0.004 0.049 596 Dihedral : 4.177 20.112 476 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.92 % Allowed : 17.75 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.40), residues: 435 helix: 2.50 (0.31), residues: 270 sheet: -0.41 (0.80), residues: 42 loop : -0.83 (0.50), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 264 HIS 0.012 0.002 HIS R 323 PHE 0.012 0.001 PHE D 72 TYR 0.024 0.001 TYR E 20 ARG 0.003 0.000 ARG R 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2503.14 seconds wall clock time: 43 minutes 24.48 seconds (2604.48 seconds total)