Starting phenix.real_space_refine on Thu Jul 2 01:40:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7f6v_31482/07_2026/7f6v_31482.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f6v_31482/07_2026/7f6v_31482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7f6v_31482/07_2026/7f6v_31482.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7f6v_31482/07_2026/7f6v_31482.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f6v_31482/07_2026/7f6v_31482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f6v_31482/07_2026/7f6v_31482.map" model { file = "/net/cci-nas-00/data/ceres_data/7f6v_31482/07_2026/7f6v_31482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f6v_31482/07_2026/7f6v_31482.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.048 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 30 5.16 5 C 3526 2.51 5 N 866 2.21 5 O 892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5314 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2629 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2629 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.26, per 1000 atoms: 0.24 Number of scatterers: 5314 At special positions: 0 Unit cell: (94.302, 116.61, 92.274, 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 30 16.00 O 892 8.00 N 866 7.00 C 3526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 177.8 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 87.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 9 through 69 removed outlier: 3.562A pdb=" N ARG A 34 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU A 35 " --> pdb=" O ARG A 31 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 99 Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 122 through 154 Processing helix chain 'A' and resid 159 through 186 Processing helix chain 'A' and resid 192 through 210 removed outlier: 3.758A pdb=" N TYR A 198 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 248 removed outlier: 4.307A pdb=" N LYS A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 299 Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 303 through 334 Proline residue: A 313 - end of helix Processing helix chain 'B' and resid 9 through 69 removed outlier: 3.562A pdb=" N ARG B 34 " --> pdb=" O HIS B 30 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU B 35 " --> pdb=" O ARG B 31 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 99 Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 122 through 154 Processing helix chain 'B' and resid 159 through 186 Processing helix chain 'B' and resid 192 through 210 removed outlier: 3.758A pdb=" N TYR B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 248 removed outlier: 4.307A pdb=" N LYS B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 299 Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 303 through 334 Proline residue: B 313 - end of helix 452 hydrogen bonds defined for protein. 1356 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: 0.85 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1596 1.34 - 1.46: 1356 1.46 - 1.58: 2474 1.58 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 5470 Sorted by residual: bond pdb=" C10 CLR A 401 " pdb=" C9 CLR A 401 " ideal model delta sigma weight residual 1.551 1.520 0.031 2.00e-02 2.50e+03 2.44e+00 bond pdb=" C10 CLR B 401 " pdb=" C9 CLR B 401 " ideal model delta sigma weight residual 1.551 1.520 0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C5 CLR B 401 " pdb=" C6 CLR B 401 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.37e+00 bond pdb=" C5 CLR A 401 " pdb=" C6 CLR A 401 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C13 CLR A 401 " pdb=" C17 CLR A 401 " ideal model delta sigma weight residual 1.550 1.525 0.025 2.00e-02 2.50e+03 1.57e+00 ... (remaining 5465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 7161 1.86 - 3.72: 191 3.72 - 5.59: 40 5.59 - 7.45: 8 7.45 - 9.31: 4 Bond angle restraints: 7404 Sorted by residual: angle pdb=" C CYS A 68 " pdb=" N LYS A 69 " pdb=" CA LYS A 69 " ideal model delta sigma weight residual 119.78 123.78 -4.00 1.24e+00 6.50e-01 1.04e+01 angle pdb=" C CYS B 68 " pdb=" N LYS B 69 " pdb=" CA LYS B 69 " ideal model delta sigma weight residual 119.78 123.78 -4.00 1.24e+00 6.50e-01 1.04e+01 angle pdb=" C13 CLR A 401 " pdb=" C17 CLR A 401 " pdb=" C20 CLR A 401 " ideal model delta sigma weight residual 119.60 110.29 9.31 3.00e+00 1.11e-01 9.64e+00 angle pdb=" C13 CLR B 401 " pdb=" C17 CLR B 401 " pdb=" C20 CLR B 401 " ideal model delta sigma weight residual 119.60 110.33 9.27 3.00e+00 1.11e-01 9.54e+00 angle pdb=" C LYS B 69 " pdb=" CA LYS B 69 " pdb=" CB LYS B 69 " ideal model delta sigma weight residual 113.04 108.81 4.23 1.63e+00 3.76e-01 6.74e+00 ... (remaining 7399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 2844 17.67 - 35.34: 260 35.34 - 53.00: 42 53.00 - 70.67: 8 70.67 - 88.34: 4 Dihedral angle restraints: 3158 sinusoidal: 1310 harmonic: 1848 Sorted by residual: dihedral pdb=" CA LEU B 32 " pdb=" C LEU B 32 " pdb=" N TYR B 33 " pdb=" CA TYR B 33 " ideal model delta harmonic sigma weight residual -180.00 -163.61 -16.39 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA LEU A 32 " pdb=" C LEU A 32 " pdb=" N TYR A 33 " pdb=" CA TYR A 33 " ideal model delta harmonic sigma weight residual -180.00 -163.61 -16.39 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB GLU B 304 " pdb=" CG GLU B 304 " pdb=" CD GLU B 304 " pdb=" OE1 GLU B 304 " ideal model delta sinusoidal sigma weight residual 0.00 88.34 -88.34 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 3155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 772 0.105 - 0.210: 18 0.210 - 0.315: 2 0.315 - 0.420: 2 0.420 - 0.525: 2 Chirality restraints: 796 Sorted by residual: chirality pdb=" C14 CLR A 401 " pdb=" C13 CLR A 401 " pdb=" C15 CLR A 401 " pdb=" C8 CLR A 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.52 2.00e-01 2.50e+01 6.88e+00 chirality pdb=" C14 CLR B 401 " pdb=" C13 CLR B 401 " pdb=" C15 CLR B 401 " pdb=" C8 CLR B 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.52 2.00e-01 2.50e+01 6.77e+00 chirality pdb=" C10 CLR A 401 " pdb=" C1 CLR A 401 " pdb=" C5 CLR A 401 " pdb=" C9 CLR A 401 " both_signs ideal model delta sigma weight residual False -2.85 -2.49 -0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 793 not shown) Planarity restraints: 904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 313 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.10e+00 pdb=" C PRO B 313 " 0.025 2.00e-02 2.50e+03 pdb=" O PRO B 313 " -0.009 2.00e-02 2.50e+03 pdb=" N PHE B 314 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 313 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.10e+00 pdb=" C PRO A 313 " -0.025 2.00e-02 2.50e+03 pdb=" O PRO A 313 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE A 314 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 307 " 0.007 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" C VAL A 307 " -0.022 2.00e-02 2.50e+03 pdb=" O VAL A 307 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU A 308 " 0.008 2.00e-02 2.50e+03 ... (remaining 901 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 1925 2.86 - 3.37: 5619 3.37 - 3.88: 8442 3.88 - 4.39: 8547 4.39 - 4.90: 14431 Nonbonded interactions: 38964 Sorted by model distance: nonbonded pdb=" O LYS B 332 " pdb=" OG SER B 335 " model vdw 2.356 3.040 nonbonded pdb=" O LYS A 332 " pdb=" OG SER A 335 " model vdw 2.356 3.040 nonbonded pdb=" OG SER B 157 " pdb=" NH1 ARG B 220 " model vdw 2.436 3.120 nonbonded pdb=" OG SER A 157 " pdb=" NH1 ARG A 220 " model vdw 2.436 3.120 nonbonded pdb=" O VAL B 159 " pdb=" N ALA B 162 " model vdw 2.443 3.120 ... (remaining 38959 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: 0.01 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 group one per residue 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: 0.750 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.540 Find NCS groups from input model: 0.050 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 : 0.011 0.681 5471 Z= 0.953 Angle : 0.774 9.312 7404 Z= 0.392 Chirality : 0.054 0.525 796 Planarity : 0.003 0.024 904 Dihedral : 14.140 88.339 1962 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.32), residues: 618 helix: 0.94 (0.20), residues: 530 sheet: None (None), residues: 0 loop : -4.45 (0.59), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 152 TYR 0.016 0.002 TYR B 33 PHE 0.016 0.001 PHE A 219 TRP 0.010 0.001 TRP A 193 HIS 0.002 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.25 ( 5470) covalent geometry : angle 0.77396 / 0.39 ( 7404) hydrogen bonds : bond 0.11008 / 7.88 ( 452) hydrogen bonds : angle 5.17977 / 3.60 ( 1356) Misc. bond : bond 0.68126 / 45.42 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.8727 (mtt) cc_final: 0.8420 (ppp) REVERT: A 145 ILE cc_start: 0.8404 (tt) cc_final: 0.8183 (tt) REVERT: A 154 LEU cc_start: 0.8208 (mm) cc_final: 0.7425 (tt) REVERT: A 228 MET cc_start: 0.8435 (ttt) cc_final: 0.7824 (ttm) REVERT: A 239 TYR cc_start: 0.8022 (t80) cc_final: 0.7550 (m-80) REVERT: B 87 MET cc_start: 0.8724 (mtt) cc_final: 0.8420 (ppp) REVERT: B 145 ILE cc_start: 0.8393 (tt) cc_final: 0.8169 (tt) REVERT: B 154 LEU cc_start: 0.8205 (mm) cc_final: 0.7428 (tt) REVERT: B 228 MET cc_start: 0.8434 (ttt) cc_final: 0.7817 (ttm) REVERT: B 239 TYR cc_start: 0.8015 (t80) cc_final: 0.7542 (m-80) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.0778 time to fit residues: 15.2584 Evaluate side-chains 119 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN A 241 GLN A 330 HIS B 165 ASN B 241 GLN B 330 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.157521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.117859 restraints weight = 9042.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.122005 restraints weight = 4297.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.124604 restraints weight = 2894.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.125765 restraints weight = 2337.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.126348 restraints weight = 2106.275| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5471 Z= 0.151 Angle : 0.606 5.968 7404 Z= 0.302 Chirality : 0.034 0.125 796 Planarity : 0.004 0.029 904 Dihedral : 4.379 33.479 698 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.46 % Allowed : 15.32 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.12 (0.34), residues: 618 helix: 2.87 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -4.06 (0.65), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 14 TYR 0.011 0.001 TYR B 171 PHE 0.018 0.001 PHE B 235 TRP 0.012 0.001 TRP B 305 HIS 0.009 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 ( 5470) covalent geometry : angle 0.60615 / 0.30 ( 7404) hydrogen bonds : bond 0.05600 / 3.71 ( 452) hydrogen bonds : angle 3.92002 / 2.78 ( 1356) Misc. bond : bond 0.00322 / 0.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8695 (mtt) cc_final: 0.8452 (ppp) REVERT: A 238 TYR cc_start: 0.7961 (t80) cc_final: 0.7624 (t80) REVERT: A 319 LEU cc_start: 0.8961 (tt) cc_final: 0.8689 (tp) REVERT: B 31 ARG cc_start: 0.9139 (tmm160) cc_final: 0.8858 (ttp80) REVERT: B 87 MET cc_start: 0.8680 (mtt) cc_final: 0.8439 (ppp) REVERT: B 238 TYR cc_start: 0.7955 (t80) cc_final: 0.7619 (t80) REVERT: B 319 LEU cc_start: 0.8959 (tt) cc_final: 0.8690 (tp) outliers start: 14 outliers final: 10 residues processed: 131 average time/residue: 0.0695 time to fit residues: 11.8393 Evaluate side-chains 117 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 330 HIS Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 330 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 HIS B 30 HIS B 330 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.161240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.122080 restraints weight = 9075.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.126280 restraints weight = 4285.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.128918 restraints weight = 2879.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.130094 restraints weight = 2325.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.131142 restraints weight = 2093.171| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5471 Z= 0.140 Angle : 0.567 7.133 7404 Z= 0.287 Chirality : 0.034 0.121 796 Planarity : 0.004 0.035 904 Dihedral : 4.128 34.897 698 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.52 % Allowed : 19.54 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.01 (0.35), residues: 618 helix: 3.48 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -3.88 (0.68), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 14 TYR 0.012 0.001 TYR A 171 PHE 0.016 0.001 PHE B 219 TRP 0.011 0.001 TRP A 305 HIS 0.010 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 5470) covalent geometry : angle 0.56738 / 0.29 ( 7404) hydrogen bonds : bond 0.05376 / 3.57 ( 452) hydrogen bonds : angle 3.71928 / 2.62 ( 1356) Misc. bond : bond 0.00168 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8715 (mtt) cc_final: 0.8461 (ppp) REVERT: A 237 GLN cc_start: 0.7365 (tm-30) cc_final: 0.7084 (tm-30) REVERT: A 238 TYR cc_start: 0.7919 (t80) cc_final: 0.7704 (t80) REVERT: A 319 LEU cc_start: 0.8954 (tt) cc_final: 0.8677 (tp) REVERT: B 87 MET cc_start: 0.8709 (mtt) cc_final: 0.8461 (ppp) REVERT: B 237 GLN cc_start: 0.7378 (tm-30) cc_final: 0.7090 (tm-30) REVERT: B 238 TYR cc_start: 0.7908 (t80) cc_final: 0.7694 (t80) REVERT: B 319 LEU cc_start: 0.8984 (tt) cc_final: 0.8718 (tp) outliers start: 20 outliers final: 16 residues processed: 119 average time/residue: 0.0535 time to fit residues: 8.4314 Evaluate side-chains 121 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 330 HIS Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 330 HIS Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 45 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.158644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.119635 restraints weight = 9128.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.123733 restraints weight = 4351.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.126332 restraints weight = 2939.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.127650 restraints weight = 2373.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.128607 restraints weight = 2121.688| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5471 Z= 0.136 Angle : 0.548 7.187 7404 Z= 0.276 Chirality : 0.033 0.135 796 Planarity : 0.004 0.036 904 Dihedral : 4.018 35.261 698 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.35 % Allowed : 20.60 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.37 (0.35), residues: 618 helix: 3.66 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -2.70 (0.74), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 14 TYR 0.011 0.001 TYR B 171 PHE 0.016 0.001 PHE B 219 TRP 0.010 0.001 TRP A 305 HIS 0.009 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 ( 5470) covalent geometry : angle 0.54760 / 0.28 ( 7404) hydrogen bonds : bond 0.05197 / 3.44 ( 452) hydrogen bonds : angle 3.65153 / 2.57 ( 1356) Misc. bond : bond 0.00163 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8745 (mtt) cc_final: 0.8310 (tmm) REVERT: A 319 LEU cc_start: 0.8970 (tt) cc_final: 0.8683 (tp) REVERT: B 87 MET cc_start: 0.8752 (mtt) cc_final: 0.8310 (tmm) REVERT: B 319 LEU cc_start: 0.8998 (tt) cc_final: 0.8734 (tp) outliers start: 19 outliers final: 16 residues processed: 118 average time/residue: 0.0467 time to fit residues: 7.7455 Evaluate side-chains 116 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.168052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.127434 restraints weight = 8808.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.131504 restraints weight = 4232.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.134146 restraints weight = 2824.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.135476 restraints weight = 2237.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.136583 restraints weight = 1988.534| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5471 Z= 0.136 Angle : 0.564 8.846 7404 Z= 0.277 Chirality : 0.033 0.126 796 Planarity : 0.003 0.026 904 Dihedral : 3.863 32.074 698 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.70 % Allowed : 22.18 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.51 (0.34), residues: 618 helix: 3.73 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -2.51 (0.77), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 14 TYR 0.021 0.001 TYR B 238 PHE 0.020 0.001 PHE A 235 TRP 0.009 0.001 TRP B 305 HIS 0.002 0.000 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 ( 5470) covalent geometry : angle 0.56405 / 0.28 ( 7404) hydrogen bonds : bond 0.05090 / 3.37 ( 452) hydrogen bonds : angle 3.61368 / 2.54 ( 1356) Misc. bond : bond 0.00172 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9457 (tmtt) cc_final: 0.9239 (tmtt) REVERT: A 87 MET cc_start: 0.8730 (mtt) cc_final: 0.8312 (tmm) REVERT: A 319 LEU cc_start: 0.9021 (tt) cc_final: 0.8747 (tp) REVERT: B 56 LYS cc_start: 0.9427 (tmtt) cc_final: 0.9193 (tmtt) REVERT: B 87 MET cc_start: 0.8736 (mtt) cc_final: 0.8302 (tmm) REVERT: B 319 LEU cc_start: 0.9006 (tt) cc_final: 0.8735 (tp) outliers start: 21 outliers final: 16 residues processed: 118 average time/residue: 0.0413 time to fit residues: 6.8591 Evaluate side-chains 122 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.157637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.118494 restraints weight = 8624.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.122439 restraints weight = 4221.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.124877 restraints weight = 2865.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.126211 restraints weight = 2331.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.126832 restraints weight = 2091.494| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5471 Z= 0.159 Angle : 0.643 11.958 7404 Z= 0.302 Chirality : 0.035 0.134 796 Planarity : 0.004 0.030 904 Dihedral : 3.835 26.619 698 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.58 % Allowed : 22.89 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.59 (0.35), residues: 618 helix: 3.79 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -2.51 (0.76), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 14 TYR 0.016 0.002 TYR B 238 PHE 0.017 0.001 PHE A 219 TRP 0.009 0.001 TRP A 305 HIS 0.002 0.000 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 5470) covalent geometry : angle 0.64294 / 0.30 ( 7404) hydrogen bonds : bond 0.05343 / 3.53 ( 452) hydrogen bonds : angle 3.67869 / 2.59 ( 1356) Misc. bond : bond 0.00192 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8695 (mtt) cc_final: 0.8298 (tmm) REVERT: A 319 LEU cc_start: 0.9057 (tt) cc_final: 0.8777 (tp) REVERT: B 87 MET cc_start: 0.8699 (mtt) cc_final: 0.8289 (tmm) REVERT: B 197 HIS cc_start: 0.8445 (OUTLIER) cc_final: 0.8229 (m170) REVERT: B 319 LEU cc_start: 0.9046 (tt) cc_final: 0.8762 (tp) outliers start: 26 outliers final: 19 residues processed: 123 average time/residue: 0.0473 time to fit residues: 8.0567 Evaluate side-chains 121 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 239 TYR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain B residue 239 TYR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.160597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.121800 restraints weight = 9113.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.125921 restraints weight = 4346.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.128406 restraints weight = 2936.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.129642 restraints weight = 2387.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.129642 restraints weight = 2151.244| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5471 Z= 0.135 Angle : 0.619 10.250 7404 Z= 0.293 Chirality : 0.036 0.266 796 Planarity : 0.003 0.024 904 Dihedral : 3.746 27.791 698 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.82 % Allowed : 24.12 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.64 (0.35), residues: 618 helix: 3.82 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -2.43 (0.77), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 14 TYR 0.018 0.001 TYR B 238 PHE 0.024 0.001 PHE B 235 TRP 0.010 0.001 TRP A 305 HIS 0.002 0.000 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 5470) covalent geometry : angle 0.61938 / 0.29 ( 7404) hydrogen bonds : bond 0.04976 / 3.29 ( 452) hydrogen bonds : angle 3.57892 / 2.52 ( 1356) Misc. bond : bond 0.00167 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8758 (mtt) cc_final: 0.8319 (tmm) REVERT: A 319 LEU cc_start: 0.9028 (tt) cc_final: 0.8758 (tp) REVERT: A 334 HIS cc_start: 0.7933 (OUTLIER) cc_final: 0.7361 (t-170) REVERT: B 87 MET cc_start: 0.8764 (mtt) cc_final: 0.8307 (tmm) REVERT: B 319 LEU cc_start: 0.9026 (tt) cc_final: 0.8750 (tp) REVERT: B 334 HIS cc_start: 0.7914 (OUTLIER) cc_final: 0.7338 (t-170) outliers start: 16 outliers final: 13 residues processed: 114 average time/residue: 0.0467 time to fit residues: 7.4021 Evaluate side-chains 117 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.161401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.122648 restraints weight = 9020.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.126704 restraints weight = 4373.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.128949 restraints weight = 2985.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.130505 restraints weight = 2464.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.130523 restraints weight = 2189.128| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5471 Z= 0.133 Angle : 0.612 9.654 7404 Z= 0.289 Chirality : 0.035 0.213 796 Planarity : 0.004 0.047 904 Dihedral : 3.721 25.162 698 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.17 % Allowed : 23.94 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.58 (0.34), residues: 618 helix: 3.76 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -2.36 (0.77), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 31 TYR 0.016 0.001 TYR A 238 PHE 0.015 0.001 PHE A 219 TRP 0.009 0.001 TRP B 305 HIS 0.002 0.000 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 5470) covalent geometry : angle 0.61180 / 0.29 ( 7404) hydrogen bonds : bond 0.04833 / 3.21 ( 452) hydrogen bonds : angle 3.56426 / 2.50 ( 1356) Misc. bond : bond 0.00165 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8764 (mtt) cc_final: 0.8321 (tmm) REVERT: A 319 LEU cc_start: 0.9043 (tt) cc_final: 0.8787 (tp) REVERT: A 334 HIS cc_start: 0.7938 (OUTLIER) cc_final: 0.7302 (t-170) REVERT: B 87 MET cc_start: 0.8772 (mtt) cc_final: 0.8306 (tmm) REVERT: B 319 LEU cc_start: 0.9044 (tt) cc_final: 0.8774 (tp) REVERT: B 334 HIS cc_start: 0.7912 (OUTLIER) cc_final: 0.7273 (t-170) outliers start: 18 outliers final: 15 residues processed: 112 average time/residue: 0.0404 time to fit residues: 6.2911 Evaluate side-chains 117 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.9990 chunk 19 optimal weight: 0.0050 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.162656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.123618 restraints weight = 9107.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.127770 restraints weight = 4415.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.130270 restraints weight = 3017.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.131431 restraints weight = 2460.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.131495 restraints weight = 2225.623| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5471 Z= 0.128 Angle : 0.607 9.134 7404 Z= 0.287 Chirality : 0.035 0.188 796 Planarity : 0.003 0.036 904 Dihedral : 3.642 22.809 698 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.11 % Allowed : 24.82 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.67 (0.35), residues: 618 helix: 3.78 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -2.36 (0.80), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 31 TYR 0.015 0.001 TYR B 238 PHE 0.022 0.001 PHE B 235 TRP 0.009 0.001 TRP B 193 HIS 0.002 0.000 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 ( 5470) covalent geometry : angle 0.60716 / 0.29 ( 7404) hydrogen bonds : bond 0.04652 / 3.10 ( 452) hydrogen bonds : angle 3.49684 / 2.45 ( 1356) Misc. bond : bond 0.00159 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8772 (mtt) cc_final: 0.8315 (tmm) REVERT: A 237 GLN cc_start: 0.7317 (tm-30) cc_final: 0.6942 (tm-30) REVERT: A 319 LEU cc_start: 0.8977 (tt) cc_final: 0.8727 (tp) REVERT: A 334 HIS cc_start: 0.7954 (OUTLIER) cc_final: 0.7334 (t-170) REVERT: B 87 MET cc_start: 0.8780 (mtt) cc_final: 0.8302 (tmm) REVERT: B 237 GLN cc_start: 0.7308 (tm-30) cc_final: 0.6935 (tm-30) REVERT: B 319 LEU cc_start: 0.9038 (tt) cc_final: 0.8778 (tp) REVERT: B 334 HIS cc_start: 0.7944 (OUTLIER) cc_final: 0.7324 (t-170) outliers start: 12 outliers final: 9 residues processed: 113 average time/residue: 0.0451 time to fit residues: 7.1827 Evaluate side-chains 114 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.160000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.121172 restraints weight = 9091.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.125230 restraints weight = 4494.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.127720 restraints weight = 3077.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.129203 restraints weight = 2495.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.129653 restraints weight = 2225.323| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5471 Z= 0.134 Angle : 0.625 9.188 7404 Z= 0.297 Chirality : 0.035 0.184 796 Planarity : 0.004 0.034 904 Dihedral : 3.661 20.926 698 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.64 % Allowed : 25.00 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.64 (0.34), residues: 618 helix: 3.75 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -2.30 (0.80), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 31 TYR 0.015 0.001 TYR B 238 PHE 0.022 0.001 PHE A 235 TRP 0.009 0.001 TRP B 193 HIS 0.002 0.000 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 5470) covalent geometry : angle 0.62528 / 0.30 ( 7404) hydrogen bonds : bond 0.04712 / 3.14 ( 452) hydrogen bonds : angle 3.52248 / 2.46 ( 1356) Misc. bond : bond 0.00163 / 0.11 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.8735 (mtt) cc_final: 0.8283 (tmm) REVERT: A 237 GLN cc_start: 0.7271 (tm-30) cc_final: 0.6875 (tm-30) REVERT: A 238 TYR cc_start: 0.7744 (t80) cc_final: 0.7543 (t80) REVERT: A 319 LEU cc_start: 0.8995 (tt) cc_final: 0.8740 (tp) REVERT: A 334 HIS cc_start: 0.7930 (OUTLIER) cc_final: 0.7235 (t-170) REVERT: B 87 MET cc_start: 0.8746 (mtt) cc_final: 0.8276 (tmm) REVERT: B 237 GLN cc_start: 0.7281 (tm-30) cc_final: 0.6888 (tm-30) REVERT: B 238 TYR cc_start: 0.7739 (t80) cc_final: 0.7537 (t80) REVERT: B 319 LEU cc_start: 0.9055 (tt) cc_final: 0.8792 (tp) REVERT: B 334 HIS cc_start: 0.7925 (OUTLIER) cc_final: 0.7230 (t-170) outliers start: 15 outliers final: 12 residues processed: 111 average time/residue: 0.0489 time to fit residues: 8.0345 Evaluate side-chains 115 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 334 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 6 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 0.0870 chunk 24 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.160731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.121879 restraints weight = 9066.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.125950 restraints weight = 4509.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.128403 restraints weight = 3100.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.129476 restraints weight = 2537.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.130629 restraints weight = 2305.113| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5471 Z= 0.131 Angle : 0.614 9.180 7404 Z= 0.289 Chirality : 0.035 0.180 796 Planarity : 0.003 0.032 904 Dihedral : 3.639 19.141 698 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.29 % Allowed : 25.70 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.66 (0.35), residues: 618 helix: 3.77 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -2.32 (0.80), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 31 TYR 0.014 0.001 TYR B 238 PHE 0.022 0.001 PHE A 235 TRP 0.010 0.001 TRP A 193 HIS 0.002 0.000 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 5470) covalent geometry : angle 0.61374 / 0.29 ( 7404) hydrogen bonds : bond 0.04627 / 3.08 ( 452) hydrogen bonds : angle 3.46478 / 2.42 ( 1356) Misc. bond : bond 0.00160 / 0.11 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 836.70 seconds wall clock time: 15 minutes 9.97 seconds (909.97 seconds total)