Starting phenix.real_space_refine on Sun Apr 27 11:13:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t05_40935/04_2025/8t05_40935.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t05_40935/04_2025/8t05_40935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t05_40935/04_2025/8t05_40935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t05_40935/04_2025/8t05_40935.map" model { file = "/net/cci-nas-00/data/ceres_data/8t05_40935/04_2025/8t05_40935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t05_40935/04_2025/8t05_40935.cif" } resolution = 3.22 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= 0.004 sd= 0.066 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 22 5.16 5 C 3387 2.51 5 N 798 2.21 5 O 893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 5104 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain: "B" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain: "C" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 3.84, per 1000 atoms: 0.75 Number of scatterers: 5104 At special positions: 0 Unit cell: (81.34, 88.81, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 22 16.00 P 2 15.00 O 893 8.00 N 798 7.00 C 3387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 60 " distance=2.04 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 60 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.05 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: 1.18 Conformation dependent library (CDL) restraints added in 549.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 182 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 186 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 48 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 48 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 186 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 182 " 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1158 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 4 sheets defined 55.6% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 3.844A pdb=" N VAL A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) Proline residue: A 11 - end of helix Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 18 through 28 removed outlier: 3.546A pdb=" N GLY A 22 " --> pdb=" O PHE A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 51 removed outlier: 4.083A pdb=" N LEU A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.692A pdb=" N MET A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 86 removed outlier: 3.738A pdb=" N THR A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 112 removed outlier: 3.555A pdb=" N GLU A 112 " --> pdb=" O ARG A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 142 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 154 through 171 Processing helix chain 'A' and resid 177 through 198 removed outlier: 3.787A pdb=" N SER A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 14 Proline residue: B 11 - end of helix Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 18 through 28 removed outlier: 3.721A pdb=" N GLY B 22 " --> pdb=" O PHE B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 52 Processing helix chain 'B' and resid 63 through 86 removed outlier: 3.628A pdb=" N PHE B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 112 Processing helix chain 'B' and resid 119 through 141 Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 154 through 171 Processing helix chain 'B' and resid 177 through 197 removed outlier: 3.965A pdb=" N SER B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.885A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 11 removed outlier: 5.688A pdb=" N GLU C 10 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA C 92 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.072A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 19 through 24 removed outlier: 3.533A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) 298 hydrogen bonds defined for protein. 864 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: 1.26 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 746 1.31 - 1.44: 1499 1.44 - 1.56: 2946 1.56 - 1.69: 14 1.69 - 1.82: 32 Bond restraints: 5237 Sorted by residual: bond pdb=" C GLY C 8 " pdb=" N ALA C 9 " ideal model delta sigma weight residual 1.331 1.409 -0.077 1.30e-02 5.92e+03 3.53e+01 bond pdb=" C25 LBN A 303 " pdb=" O5 LBN A 303 " ideal model delta sigma weight residual 1.326 1.433 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C25 LBN B 303 " pdb=" O5 LBN B 303 " ideal model delta sigma weight residual 1.326 1.429 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C34 LBN A 303 " pdb=" O7 LBN A 303 " ideal model delta sigma weight residual 1.331 1.427 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C34 LBN B 303 " pdb=" O7 LBN B 303 " ideal model delta sigma weight residual 1.331 1.424 -0.093 2.00e-02 2.50e+03 2.16e+01 ... (remaining 5232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 6281 2.92 - 5.84: 805 5.84 - 8.76: 12 8.76 - 11.68: 5 11.68 - 14.60: 2 Bond angle restraints: 7105 Sorted by residual: angle pdb=" N PHE C 109 " pdb=" CA PHE C 109 " pdb=" C PHE C 109 " ideal model delta sigma weight residual 111.24 118.85 -7.61 1.38e+00 5.25e-01 3.04e+01 angle pdb=" C GLY A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta sigma weight residual 120.03 125.59 -5.56 1.12e+00 7.97e-01 2.47e+01 angle pdb=" N THR D 94 " pdb=" CA THR D 94 " pdb=" C THR D 94 " ideal model delta sigma weight residual 108.82 117.00 -8.18 1.65e+00 3.67e-01 2.46e+01 angle pdb=" O1 LBN B 303 " pdb=" P1 LBN B 303 " pdb=" O2 LBN B 303 " ideal model delta sigma weight residual 93.45 108.05 -14.60 3.00e+00 1.11e-01 2.37e+01 angle pdb=" O1 LBN A 303 " pdb=" P1 LBN A 303 " pdb=" O2 LBN A 303 " ideal model delta sigma weight residual 93.45 107.88 -14.43 3.00e+00 1.11e-01 2.31e+01 ... (remaining 7100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.48: 3038 30.48 - 60.96: 92 60.96 - 91.44: 11 91.44 - 121.92: 7 121.92 - 152.40: 4 Dihedral angle restraints: 3152 sinusoidal: 1337 harmonic: 1815 Sorted by residual: dihedral pdb=" CA THR D 94 " pdb=" C THR D 94 " pdb=" N PRO D 95 " pdb=" CA PRO D 95 " ideal model delta harmonic sigma weight residual 180.00 70.79 109.21 0 5.00e+00 4.00e-02 4.77e+02 dihedral pdb=" CA ALA D 50 " pdb=" C ALA D 50 " pdb=" N ALA D 51 " pdb=" CA ALA D 51 " ideal model delta harmonic sigma weight residual -180.00 -151.52 -28.48 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA SER B 56 " pdb=" C SER B 56 " pdb=" N LEU B 57 " pdb=" CA LEU B 57 " ideal model delta harmonic sigma weight residual -180.00 -155.12 -24.88 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 3149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.985: 803 0.985 - 1.969: 0 1.969 - 2.954: 0 2.954 - 3.938: 0 3.938 - 4.923: 2 Chirality restraints: 805 Sorted by residual: chirality pdb=" C2 LBN B 303 " pdb=" C1 LBN B 303 " pdb=" C3 LBN B 303 " pdb=" O7 LBN B 303 " both_signs ideal model delta sigma weight residual False -2.36 2.56 -4.92 2.00e-01 2.50e+01 6.06e+02 chirality pdb=" C2 LBN A 303 " pdb=" C1 LBN A 303 " pdb=" C3 LBN A 303 " pdb=" O7 LBN A 303 " both_signs ideal model delta sigma weight residual False -2.36 2.55 -4.92 2.00e-01 2.50e+01 6.04e+02 chirality pdb=" C14 CLR A 302 " pdb=" C13 CLR A 302 " pdb=" C15 CLR A 302 " pdb=" C8 CLR A 302 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.40 2.00e-01 2.50e+01 3.97e+00 ... (remaining 802 not shown) Planarity restraints: 848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 145 " -0.060 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO B 146 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 13 " -0.054 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO C 14 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 94 " -0.042 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO D 95 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 95 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 95 " -0.036 5.00e-02 4.00e+02 ... (remaining 845 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 71 2.68 - 3.23: 4609 3.23 - 3.79: 7701 3.79 - 4.34: 10686 4.34 - 4.90: 18018 Nonbonded interactions: 41085 Sorted by model distance: nonbonded pdb=" OE1 GLN A 44 " pdb="ZN ZN A 301 " model vdw 2.120 2.230 nonbonded pdb=" OE1 GLN B 44 " pdb="ZN ZN B 301 " model vdw 2.172 2.230 nonbonded pdb=" NH2 ARG D 61 " pdb=" OE2 GLU D 81 " model vdw 2.356 3.120 nonbonded pdb=" NH2 ARG A 108 " pdb=" O PRO A 116 " model vdw 2.413 3.120 nonbonded pdb=" O HIS D 90 " pdb=" ND1 HIS D 90 " model vdw 2.433 3.120 ... (remaining 41080 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 'A' selection = chain 'B' } 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 16.510 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 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 : 0.015 0.181 5247 Z= 1.079 Angle : 1.851 14.605 7113 Z= 1.349 Chirality : 0.259 4.923 805 Planarity : 0.006 0.091 848 Dihedral : 16.958 152.400 1982 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.94 % Favored : 93.90 % Rotamer: Outliers : 0.93 % Allowed : 6.16 % Favored : 92.91 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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 (0.31), residues: 623 helix: -1.21 (0.25), residues: 313 sheet: -1.44 (0.49), residues: 86 loop : -1.32 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 151 HIS 0.007 0.002 HIS D 90 PHE 0.019 0.002 PHE B 43 TYR 0.043 0.003 TYR D 49 ARG 0.003 0.000 ARG B 108 Details of bonding type rmsd hydrogen bonds : bond 0.19464 ( 298) hydrogen bonds : angle 9.16980 ( 864) metal coordination : bond 0.11605 ( 6) SS BOND : bond 0.01077 ( 4) SS BOND : angle 1.19535 ( 8) covalent geometry : bond 0.01446 ( 5237) covalent geometry : angle 1.85126 ( 7105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.537 Fit side-chains REVERT: A 137 GLU cc_start: 0.6864 (tp30) cc_final: 0.6262 (mm-30) REVERT: A 198 ARG cc_start: 0.6886 (ttm170) cc_final: 0.6588 (ttp80) REVERT: B 62 MET cc_start: 0.6309 (mtt) cc_final: 0.6034 (mtm) REVERT: B 184 ILE cc_start: 0.7178 (mm) cc_final: 0.6907 (mt) REVERT: C 10 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7500 (mp0) REVERT: C 28 THR cc_start: 0.8525 (m) cc_final: 0.8298 (t) REVERT: C 32 TYR cc_start: 0.8080 (m-80) cc_final: 0.7604 (m-80) REVERT: C 34 MET cc_start: 0.8066 (mmm) cc_final: 0.7480 (tpt) REVERT: D 30 TYR cc_start: 0.8035 (m-80) cc_final: 0.7673 (m-80) REVERT: D 71 TYR cc_start: 0.7538 (m-80) cc_final: 0.7100 (m-80) REVERT: D 100 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7906 (tp30) outliers start: 5 outliers final: 4 residues processed: 92 average time/residue: 0.2304 time to fit residues: 25.9734 Evaluate side-chains 79 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 PRO Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain D residue 90 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.0170 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 95 HIS B 113 ASN B 186 HIS D 6 GLN D 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.172765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.140867 restraints weight = 5946.780| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.19 r_work: 0.3621 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.232 5247 Z= 0.180 Angle : 0.636 7.865 7113 Z= 0.328 Chirality : 0.042 0.185 805 Planarity : 0.005 0.076 848 Dihedral : 16.629 146.199 890 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.31 % Allowed : 11.38 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.34), residues: 623 helix: 1.34 (0.28), residues: 314 sheet: -0.95 (0.47), residues: 117 loop : -0.74 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 47 HIS 0.005 0.001 HIS C 35 PHE 0.016 0.002 PHE B 70 TYR 0.012 0.001 TYR B 37 ARG 0.002 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.04427 ( 298) hydrogen bonds : angle 4.94698 ( 864) metal coordination : bond 0.09477 ( 6) SS BOND : bond 0.00211 ( 4) SS BOND : angle 0.99572 ( 8) covalent geometry : bond 0.00324 ( 5237) covalent geometry : angle 0.63588 ( 7105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.556 Fit side-chains REVERT: A 112 GLU cc_start: 0.7406 (tt0) cc_final: 0.7197 (tt0) REVERT: A 137 GLU cc_start: 0.7873 (tp30) cc_final: 0.7271 (mm-30) REVERT: B 184 ILE cc_start: 0.8294 (mm) cc_final: 0.7966 (mt) REVERT: B 198 ARG cc_start: 0.8706 (ttm170) cc_final: 0.8398 (mtp85) REVERT: D 30 TYR cc_start: 0.8910 (m-80) cc_final: 0.8565 (m-80) outliers start: 7 outliers final: 4 residues processed: 90 average time/residue: 0.2121 time to fit residues: 23.7711 Evaluate side-chains 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 88 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 0.0370 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.170222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.138091 restraints weight = 5883.941| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.18 r_work: 0.3590 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5247 Z= 0.158 Angle : 0.605 6.551 7113 Z= 0.307 Chirality : 0.042 0.209 805 Planarity : 0.005 0.080 848 Dihedral : 14.848 148.420 881 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.24 % Allowed : 12.50 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.36), residues: 623 helix: 2.02 (0.29), residues: 306 sheet: -0.80 (0.49), residues: 110 loop : -0.75 (0.49), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 47 HIS 0.005 0.001 HIS C 35 PHE 0.017 0.002 PHE D 91 TYR 0.014 0.001 TYR D 49 ARG 0.003 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.04251 ( 298) hydrogen bonds : angle 4.47002 ( 864) metal coordination : bond 0.00566 ( 6) SS BOND : bond 0.00238 ( 4) SS BOND : angle 0.96733 ( 8) covalent geometry : bond 0.00366 ( 5237) covalent geometry : angle 0.60428 ( 7105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8616 (tmmt) cc_final: 0.8120 (tptt) REVERT: A 88 ARG cc_start: 0.8040 (mtp-110) cc_final: 0.7750 (mmm-85) REVERT: A 137 GLU cc_start: 0.7877 (tp30) cc_final: 0.7131 (mm-30) REVERT: B 27 LYS cc_start: 0.8347 (mmmt) cc_final: 0.7984 (ttpt) REVERT: C 5 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7932 (tt0) REVERT: C 90 ASP cc_start: 0.8793 (m-30) cc_final: 0.8513 (m-30) outliers start: 12 outliers final: 7 residues processed: 86 average time/residue: 0.2056 time to fit residues: 22.1149 Evaluate side-chains 86 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 chunk 46 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS C 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.191704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.149495 restraints weight = 6367.501| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.22 r_work: 0.3653 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.815 5247 Z= 0.396 Angle : 0.557 6.693 7113 Z= 0.281 Chirality : 0.039 0.193 805 Planarity : 0.005 0.076 848 Dihedral : 12.907 142.594 881 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.87 % Allowed : 14.55 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 1.25 (0.36), residues: 623 helix: 2.33 (0.29), residues: 312 sheet: -0.83 (0.47), residues: 122 loop : -0.51 (0.53), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 47 HIS 0.003 0.001 HIS C 35 PHE 0.015 0.001 PHE B 70 TYR 0.012 0.001 TYR D 49 ARG 0.002 0.000 ARG B 198 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 298) hydrogen bonds : angle 4.25094 ( 864) metal coordination : bond 0.33271 ( 6) SS BOND : bond 0.00198 ( 4) SS BOND : angle 1.59210 ( 8) covalent geometry : bond 0.00290 ( 5237) covalent geometry : angle 0.55513 ( 7105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8668 (tmmt) cc_final: 0.8152 (tptt) REVERT: A 88 ARG cc_start: 0.8065 (mtp-110) cc_final: 0.7837 (mmm-85) REVERT: A 137 GLU cc_start: 0.7842 (tp30) cc_final: 0.7196 (mm-30) REVERT: B 27 LYS cc_start: 0.8338 (mmmt) cc_final: 0.8007 (ttpt) REVERT: B 62 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6948 (ttm) REVERT: B 138 MET cc_start: 0.7813 (mtp) cc_final: 0.7586 (mtp) REVERT: C 5 GLN cc_start: 0.8139 (tt0) cc_final: 0.7915 (tt0) REVERT: C 90 ASP cc_start: 0.8757 (m-30) cc_final: 0.8523 (m-30) outliers start: 10 outliers final: 7 residues processed: 79 average time/residue: 0.2093 time to fit residues: 20.7782 Evaluate side-chains 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.173856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.141908 restraints weight = 5938.498| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.22 r_work: 0.3630 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.903 5247 Z= 0.444 Angle : 0.578 6.452 7113 Z= 0.293 Chirality : 0.041 0.197 805 Planarity : 0.005 0.079 848 Dihedral : 12.184 148.883 881 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.05 % Allowed : 15.11 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 1.13 (0.36), residues: 623 helix: 2.29 (0.29), residues: 306 sheet: -0.86 (0.47), residues: 122 loop : -0.61 (0.52), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 47 HIS 0.004 0.001 HIS C 35 PHE 0.017 0.001 PHE D 91 TYR 0.015 0.001 TYR D 49 ARG 0.005 0.000 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 298) hydrogen bonds : angle 4.30342 ( 864) metal coordination : bond 0.36870 ( 6) SS BOND : bond 0.00306 ( 4) SS BOND : angle 1.41785 ( 8) covalent geometry : bond 0.00367 ( 5237) covalent geometry : angle 0.57663 ( 7105) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8663 (tmmt) cc_final: 0.8116 (tptt) REVERT: A 88 ARG cc_start: 0.8082 (mtp-110) cc_final: 0.7862 (mmm-85) REVERT: A 137 GLU cc_start: 0.7830 (tp30) cc_final: 0.7187 (mm-30) REVERT: B 27 LYS cc_start: 0.8366 (mmmt) cc_final: 0.8022 (ttpt) REVERT: B 62 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6918 (ttm) REVERT: B 138 MET cc_start: 0.7893 (mtp) cc_final: 0.7668 (mtp) REVERT: C 5 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: D 71 TYR cc_start: 0.8618 (m-80) cc_final: 0.8197 (m-80) outliers start: 11 outliers final: 8 residues processed: 75 average time/residue: 0.2107 time to fit residues: 19.9672 Evaluate side-chains 80 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.173817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.142831 restraints weight = 6062.029| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.13 r_work: 0.3511 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 0.032 5247 Z= 0.146 Angle : 0.555 6.083 7113 Z= 0.281 Chirality : 0.040 0.197 805 Planarity : 0.005 0.078 848 Dihedral : 11.737 150.975 881 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.17 % Allowed : 14.74 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 1.11 (0.36), residues: 623 helix: 2.31 (0.29), residues: 308 sheet: -0.85 (0.47), residues: 122 loop : -0.74 (0.51), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 47 HIS 0.005 0.001 HIS B 48 PHE 0.014 0.001 PHE B 70 TYR 0.014 0.001 TYR D 49 ARG 0.004 0.000 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 298) hydrogen bonds : angle 4.23498 ( 864) metal coordination : bond 0.00388 ( 6) SS BOND : bond 0.00233 ( 4) SS BOND : angle 1.26179 ( 8) covalent geometry : bond 0.00340 ( 5237) covalent geometry : angle 0.55350 ( 7105) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8645 (tmmt) cc_final: 0.8083 (tptt) REVERT: A 137 GLU cc_start: 0.7841 (tp30) cc_final: 0.7141 (mm-30) REVERT: B 27 LYS cc_start: 0.8314 (mmmt) cc_final: 0.7940 (ttpt) REVERT: B 62 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6881 (ttm) REVERT: B 138 MET cc_start: 0.7928 (mtp) cc_final: 0.7708 (mtp) REVERT: C 5 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7857 (tt0) REVERT: D 74 LYS cc_start: 0.8527 (ptmm) cc_final: 0.8123 (ptmm) outliers start: 17 outliers final: 13 residues processed: 81 average time/residue: 0.2007 time to fit residues: 20.4144 Evaluate side-chains 87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.171337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.139308 restraints weight = 6033.837| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.21 r_work: 0.3599 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5247 Z= 0.173 Angle : 0.585 6.992 7113 Z= 0.296 Chirality : 0.041 0.199 805 Planarity : 0.005 0.082 848 Dihedral : 11.276 160.053 881 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.99 % Allowed : 14.55 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 1.07 (0.36), residues: 623 helix: 2.24 (0.29), residues: 306 sheet: -0.81 (0.47), residues: 122 loop : -0.69 (0.51), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 47 HIS 0.003 0.001 HIS C 35 PHE 0.017 0.002 PHE D 91 TYR 0.016 0.001 TYR D 49 ARG 0.005 0.001 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 298) hydrogen bonds : angle 4.34712 ( 864) metal coordination : bond 0.00187 ( 6) SS BOND : bond 0.00263 ( 4) SS BOND : angle 1.33364 ( 8) covalent geometry : bond 0.00412 ( 5237) covalent geometry : angle 0.58393 ( 7105) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8693 (tmmt) cc_final: 0.8129 (tptt) REVERT: A 137 GLU cc_start: 0.7782 (tp30) cc_final: 0.7166 (mm-30) REVERT: B 27 LYS cc_start: 0.8350 (mmmt) cc_final: 0.7992 (ttpt) REVERT: B 62 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.7012 (ttm) REVERT: B 138 MET cc_start: 0.7960 (mtp) cc_final: 0.7750 (mtp) REVERT: C 5 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7930 (tt0) outliers start: 16 outliers final: 13 residues processed: 76 average time/residue: 0.1977 time to fit residues: 19.1276 Evaluate side-chains 82 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 28 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.174090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.143015 restraints weight = 6030.384| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.14 r_work: 0.3640 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.845 5247 Z= 0.413 Angle : 0.545 6.112 7113 Z= 0.275 Chirality : 0.040 0.195 805 Planarity : 0.005 0.080 848 Dihedral : 10.794 162.069 881 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.43 % Allowed : 15.30 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 1.22 (0.36), residues: 623 helix: 2.33 (0.29), residues: 314 sheet: -0.74 (0.48), residues: 122 loop : -0.70 (0.52), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 47 HIS 0.003 0.001 HIS C 35 PHE 0.014 0.001 PHE A 39 TYR 0.013 0.001 TYR D 49 ARG 0.006 0.001 ARG A 88 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 298) hydrogen bonds : angle 4.22851 ( 864) metal coordination : bond 0.34500 ( 6) SS BOND : bond 0.00267 ( 4) SS BOND : angle 1.16999 ( 8) covalent geometry : bond 0.00320 ( 5237) covalent geometry : angle 0.54396 ( 7105) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8694 (tmmt) cc_final: 0.8133 (tptt) REVERT: A 88 ARG cc_start: 0.8135 (mmm-85) cc_final: 0.7849 (mtp-110) REVERT: A 137 GLU cc_start: 0.7760 (tp30) cc_final: 0.7200 (mm-30) REVERT: B 27 LYS cc_start: 0.8333 (mmmt) cc_final: 0.7988 (ttpt) REVERT: B 138 MET cc_start: 0.7935 (mtp) cc_final: 0.7705 (mtt) REVERT: C 32 TYR cc_start: 0.8096 (m-80) cc_final: 0.7865 (m-10) REVERT: D 30 TYR cc_start: 0.8936 (m-80) cc_final: 0.8641 (m-10) outliers start: 13 outliers final: 11 residues processed: 74 average time/residue: 0.2552 time to fit residues: 23.8244 Evaluate side-chains 77 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 49 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.174414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.143255 restraints weight = 5959.071| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.21 r_work: 0.3515 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.901 5247 Z= 0.439 Angle : 0.556 6.427 7113 Z= 0.280 Chirality : 0.040 0.195 805 Planarity : 0.005 0.079 848 Dihedral : 10.750 168.014 881 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.05 % Allowed : 15.67 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 1.22 (0.36), residues: 623 helix: 2.38 (0.29), residues: 308 sheet: -0.71 (0.48), residues: 122 loop : -0.72 (0.51), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 47 HIS 0.003 0.001 HIS B 186 PHE 0.014 0.001 PHE A 39 TYR 0.014 0.001 TYR D 49 ARG 0.005 0.001 ARG A 88 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 298) hydrogen bonds : angle 4.22912 ( 864) metal coordination : bond 0.36774 ( 6) SS BOND : bond 0.00201 ( 4) SS BOND : angle 1.26195 ( 8) covalent geometry : bond 0.00339 ( 5237) covalent geometry : angle 0.55428 ( 7105) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8656 (tmmt) cc_final: 0.8077 (tptt) REVERT: A 88 ARG cc_start: 0.8132 (mmm-85) cc_final: 0.7890 (mtp-110) REVERT: A 137 GLU cc_start: 0.7725 (tp30) cc_final: 0.7121 (mm-30) REVERT: B 27 LYS cc_start: 0.8302 (mmmt) cc_final: 0.7925 (ttpt) REVERT: B 138 MET cc_start: 0.7910 (mtp) cc_final: 0.7673 (mtt) REVERT: C 32 TYR cc_start: 0.8111 (m-80) cc_final: 0.7846 (m-10) outliers start: 11 outliers final: 11 residues processed: 77 average time/residue: 0.2080 time to fit residues: 20.1911 Evaluate side-chains 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.0870 chunk 54 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.174227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.143115 restraints weight = 5989.701| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.16 r_work: 0.3513 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.864 5247 Z= 0.421 Angle : 0.549 6.664 7113 Z= 0.277 Chirality : 0.040 0.193 805 Planarity : 0.005 0.078 848 Dihedral : 10.695 172.431 881 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.05 % Allowed : 16.23 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 1.25 (0.36), residues: 623 helix: 2.41 (0.29), residues: 308 sheet: -0.70 (0.48), residues: 122 loop : -0.71 (0.51), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 47 HIS 0.003 0.001 HIS B 182 PHE 0.014 0.001 PHE A 39 TYR 0.014 0.001 TYR D 49 ARG 0.006 0.001 ARG A 88 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 298) hydrogen bonds : angle 4.20163 ( 864) metal coordination : bond 0.35278 ( 6) SS BOND : bond 0.00209 ( 4) SS BOND : angle 1.28735 ( 8) covalent geometry : bond 0.00323 ( 5237) covalent geometry : angle 0.54783 ( 7105) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8673 (tmmt) cc_final: 0.8098 (tptt) REVERT: A 88 ARG cc_start: 0.8142 (mmm-85) cc_final: 0.7916 (mtp-110) REVERT: A 137 GLU cc_start: 0.7727 (tp30) cc_final: 0.7123 (mm-30) REVERT: B 27 LYS cc_start: 0.8308 (mmmt) cc_final: 0.7938 (ttpt) REVERT: C 32 TYR cc_start: 0.8099 (m-80) cc_final: 0.7843 (m-10) outliers start: 11 outliers final: 11 residues processed: 77 average time/residue: 0.2363 time to fit residues: 22.7559 Evaluate side-chains 80 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.176287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.145133 restraints weight = 5989.227| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.20 r_work: 0.3657 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.915 5247 Z= 0.439 Angle : 0.541 6.646 7113 Z= 0.273 Chirality : 0.039 0.191 805 Planarity : 0.005 0.076 848 Dihedral : 10.526 174.519 881 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.05 % Allowed : 16.23 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 1.37 (0.36), residues: 623 helix: 2.57 (0.29), residues: 308 sheet: -0.38 (0.51), residues: 108 loop : -0.95 (0.48), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 47 HIS 0.003 0.001 HIS B 186 PHE 0.014 0.001 PHE A 39 TYR 0.013 0.001 TYR D 49 ARG 0.006 0.001 ARG A 88 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 298) hydrogen bonds : angle 4.10986 ( 864) metal coordination : bond 0.37373 ( 6) SS BOND : bond 0.00166 ( 4) SS BOND : angle 1.29242 ( 8) covalent geometry : bond 0.00279 ( 5237) covalent geometry : angle 0.54004 ( 7105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2922.77 seconds wall clock time: 51 minutes 48.88 seconds (3108.88 seconds total)