Starting phenix.real_space_refine on Tue Feb 11 11:12:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f6v_31482/02_2025/7f6v_31482.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f6v_31482/02_2025/7f6v_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7f6v_31482/02_2025/7f6v_31482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f6v_31482/02_2025/7f6v_31482.map" model { file = "/net/cci-nas-00/data/ceres_data/7f6v_31482/02_2025/7f6v_31482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f6v_31482/02_2025/7f6v_31482.cif" } resolution = 3.66 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= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.71, per 1000 atoms: 0.70 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: 1.42 Conformation dependent library (CDL) restraints added in 654.7 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: 0.38 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: 1.38 Time building geometry restraints manager: 1.60 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: 2954 17.67 - 35.34: 262 35.34 - 53.00: 42 53.00 - 70.67: 8 70.67 - 88.34: 4 Dihedral angle restraints: 3270 sinusoidal: 1422 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 3267 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: 0.03 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: 0.520 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.000 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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 : 0.005 0.039 5470 Z= 0.345 Angle : 0.774 9.312 7404 Z= 0.392 Chirality : 0.054 0.525 796 Planarity : 0.003 0.024 904 Dihedral : 13.915 88.339 2074 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 (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: 0.27 (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 TRP 0.010 0.001 TRP A 193 HIS 0.002 0.001 HIS A 283 PHE 0.016 0.001 PHE A 219 TYR 0.016 0.002 TYR B 33 ARG 0.004 0.001 ARG A 152 *********************** 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 : 0.615 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: 0.8392 (tt) cc_final: 0.8168 (tt) REVERT: B 154 LEU cc_start: 0.8204 (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: 0.2285 time to fit residues: 44.1571 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 : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4280 r_free = 0.4280 target = 0.158472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.118910 restraints weight = 8929.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.123070 restraints weight = 4275.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.125660 restraints weight = 2883.240| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5470 Z= 0.194 Angle : 0.602 6.077 7404 Z= 0.301 Chirality : 0.034 0.129 796 Planarity : 0.004 0.025 904 Dihedral : 5.165 34.194 810 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.29 % Allowed : 15.49 % 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 (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: 3.15 (0.34), residues: 618 helix: 2.89 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -4.06 (0.65), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 305 HIS 0.009 0.001 HIS A 330 PHE 0.019 0.001 PHE B 235 TYR 0.011 0.001 TYR B 171 ARG 0.008 0.001 ARG A 14 *********************** 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 138 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8728 (mtt) cc_final: 0.8455 (ppp) REVERT: A 238 TYR cc_start: 0.7913 (t80) cc_final: 0.7592 (t80) REVERT: A 319 LEU cc_start: 0.8951 (tt) cc_final: 0.8688 (tp) REVERT: B 31 ARG cc_start: 0.9135 (tmm160) cc_final: 0.8855 (ttp80) REVERT: B 87 MET cc_start: 0.8717 (mtt) cc_final: 0.8447 (ppp) REVERT: B 238 TYR cc_start: 0.7908 (t80) cc_final: 0.7563 (t80) REVERT: B 239 TYR cc_start: 0.7715 (t80) cc_final: 0.7282 (m-80) REVERT: B 319 LEU cc_start: 0.8954 (tt) cc_final: 0.8691 (tp) outliers start: 13 outliers final: 10 residues processed: 129 average time/residue: 0.1824 time to fit residues: 30.2470 Evaluate side-chains 113 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 1 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.158253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.118752 restraints weight = 9115.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.122882 restraints weight = 4275.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.125449 restraints weight = 2868.714| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5470 Z= 0.236 Angle : 0.600 6.705 7404 Z= 0.304 Chirality : 0.036 0.122 796 Planarity : 0.004 0.038 904 Dihedral : 4.521 28.262 810 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.17 % Allowed : 19.72 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.87 (0.35), residues: 618 helix: 3.39 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -3.91 (0.67), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 305 HIS 0.012 0.002 HIS A 330 PHE 0.017 0.002 PHE B 219 TYR 0.012 0.001 TYR A 171 ARG 0.007 0.001 ARG B 14 *********************** 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 127 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8750 (mtt) cc_final: 0.8301 (tmm) REVERT: A 237 GLN cc_start: 0.7329 (tm-30) cc_final: 0.7076 (tm-30) REVERT: A 238 TYR cc_start: 0.8029 (t80) cc_final: 0.7755 (t80) REVERT: A 319 LEU cc_start: 0.8978 (tt) cc_final: 0.8702 (tp) REVERT: B 87 MET cc_start: 0.8747 (mtt) cc_final: 0.8301 (tmm) REVERT: B 237 GLN cc_start: 0.7347 (tm-30) cc_final: 0.7082 (tm-30) REVERT: B 238 TYR cc_start: 0.7962 (t80) cc_final: 0.7750 (t80) REVERT: B 319 LEU cc_start: 0.9008 (tt) cc_final: 0.8747 (tp) outliers start: 18 outliers final: 14 residues processed: 116 average time/residue: 0.1504 time to fit residues: 23.1547 Evaluate side-chains 118 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 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 272 LEU Chi-restraints excluded: chain B residue 323 PHE 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 34 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 0.0870 chunk 20 optimal weight: 0.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.159191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.119920 restraints weight = 9240.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.124025 restraints weight = 4345.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.126576 restraints weight = 2932.391| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5470 Z= 0.192 Angle : 0.559 7.816 7404 Z= 0.282 Chirality : 0.034 0.124 796 Planarity : 0.004 0.033 904 Dihedral : 4.194 25.653 810 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.52 % Allowed : 22.18 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.22 (0.35), residues: 618 helix: 3.60 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -3.61 (0.69), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 305 HIS 0.001 0.000 HIS A 30 PHE 0.017 0.001 PHE B 219 TYR 0.012 0.001 TYR B 100 ARG 0.008 0.001 ARG B 14 *********************** 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 129 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8776 (mtt) cc_final: 0.8328 (tmm) REVERT: A 238 TYR cc_start: 0.7845 (t80) cc_final: 0.7620 (t80) REVERT: A 319 LEU cc_start: 0.9001 (tt) cc_final: 0.8735 (tp) REVERT: B 87 MET cc_start: 0.8776 (mtt) cc_final: 0.8322 (tmm) REVERT: B 238 TYR cc_start: 0.7812 (t80) cc_final: 0.7602 (t80) REVERT: B 319 LEU cc_start: 0.8982 (tt) cc_final: 0.8714 (tp) outliers start: 20 outliers final: 16 residues processed: 117 average time/residue: 0.1440 time to fit residues: 22.6253 Evaluate side-chains 120 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 244 CYS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 PHE 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.157708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.118781 restraints weight = 8552.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.122628 restraints weight = 4160.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.125058 restraints weight = 2841.531| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5470 Z= 0.207 Angle : 0.587 8.593 7404 Z= 0.290 Chirality : 0.034 0.128 796 Planarity : 0.004 0.044 904 Dihedral : 4.050 20.031 810 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.58 % Allowed : 22.54 % 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 (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: 4.54 (0.35), residues: 618 helix: 3.76 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -2.61 (0.75), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 305 HIS 0.001 0.000 HIS A 30 PHE 0.019 0.001 PHE A 235 TYR 0.011 0.001 TYR B 171 ARG 0.009 0.001 ARG B 14 *********************** 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 134 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8740 (mtt) cc_final: 0.8324 (tmm) REVERT: A 197 HIS cc_start: 0.8439 (OUTLIER) cc_final: 0.8195 (m170) REVERT: A 238 TYR cc_start: 0.7890 (t80) cc_final: 0.7676 (t80) REVERT: A 319 LEU cc_start: 0.9048 (tt) cc_final: 0.8782 (tp) REVERT: B 56 LYS cc_start: 0.9428 (tmtt) cc_final: 0.9218 (tmtt) REVERT: B 87 MET cc_start: 0.8738 (mtt) cc_final: 0.8311 (tmm) REVERT: B 197 HIS cc_start: 0.8408 (OUTLIER) cc_final: 0.8163 (m170) REVERT: B 319 LEU cc_start: 0.9017 (tt) cc_final: 0.8746 (tp) outliers start: 26 outliers final: 21 residues processed: 124 average time/residue: 0.1573 time to fit residues: 25.6049 Evaluate side-chains 127 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 181 ILE Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 209 THR 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 181 ILE Chi-restraints excluded: chain B residue 197 HIS 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 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.4289 r_free = 0.4289 target = 0.159470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.120138 restraints weight = 9099.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.124269 restraints weight = 4328.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.126767 restraints weight = 2921.685| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5470 Z= 0.197 Angle : 0.597 8.472 7404 Z= 0.292 Chirality : 0.034 0.134 796 Planarity : 0.004 0.044 904 Dihedral : 3.951 19.484 810 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.40 % Allowed : 23.42 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.63 (0.35), residues: 618 helix: 3.82 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -2.49 (0.76), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 305 HIS 0.001 0.000 HIS A 30 PHE 0.022 0.001 PHE B 235 TYR 0.022 0.001 TYR B 238 ARG 0.009 0.001 ARG B 14 *********************** 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 132 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8784 (mtt) cc_final: 0.8330 (tmm) REVERT: A 319 LEU cc_start: 0.8954 (tt) cc_final: 0.8691 (tp) REVERT: B 87 MET cc_start: 0.8781 (mtt) cc_final: 0.8315 (tmm) REVERT: B 319 LEU cc_start: 0.9015 (tt) cc_final: 0.8755 (tp) outliers start: 25 outliers final: 17 residues processed: 122 average time/residue: 0.1481 time to fit residues: 24.0365 Evaluate side-chains 115 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 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 32 LEU 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 209 THR 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 60 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4311 r_free = 0.4311 target = 0.161416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.122376 restraints weight = 9070.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.126605 restraints weight = 4292.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.129132 restraints weight = 2890.386| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5470 Z= 0.172 Angle : 0.617 12.176 7404 Z= 0.289 Chirality : 0.034 0.145 796 Planarity : 0.003 0.036 904 Dihedral : 3.876 20.563 810 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.35 % Allowed : 23.59 % 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 (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: 4.69 (0.35), residues: 618 helix: 3.85 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -2.42 (0.77), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 305 HIS 0.003 0.000 HIS B 283 PHE 0.023 0.001 PHE A 235 TYR 0.020 0.001 TYR A 238 ARG 0.009 0.001 ARG B 14 *********************** 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: 19 poor density : 103 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8772 (mtt) cc_final: 0.8319 (tmm) REVERT: A 237 GLN cc_start: 0.7268 (tm-30) cc_final: 0.7042 (tm-30) REVERT: A 319 LEU cc_start: 0.8929 (tt) cc_final: 0.8671 (tp) REVERT: B 87 MET cc_start: 0.8771 (mtt) cc_final: 0.8307 (tmm) REVERT: B 237 GLN cc_start: 0.7250 (tm-30) cc_final: 0.6968 (tm-30) REVERT: B 319 LEU cc_start: 0.9037 (tt) cc_final: 0.8757 (tp) outliers start: 19 outliers final: 16 residues processed: 113 average time/residue: 0.1365 time to fit residues: 20.9609 Evaluate side-chains 115 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 323 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 32 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.4980 chunk 36 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4295 r_free = 0.4295 target = 0.159904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.120653 restraints weight = 9104.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.124739 restraints weight = 4368.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.127258 restraints weight = 2970.860| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5470 Z= 0.193 Angle : 0.631 11.079 7404 Z= 0.297 Chirality : 0.038 0.308 796 Planarity : 0.004 0.048 904 Dihedral : 3.916 18.427 810 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.35 % Allowed : 23.24 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.56 (0.35), residues: 618 helix: 3.75 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -2.35 (0.78), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 305 HIS 0.003 0.000 HIS A 283 PHE 0.023 0.001 PHE B 235 TYR 0.023 0.002 TYR A 238 ARG 0.012 0.001 ARG B 31 *********************** 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 116 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8784 (mtt) cc_final: 0.8315 (tmm) REVERT: A 237 GLN cc_start: 0.7252 (tm-30) cc_final: 0.6967 (tm-30) REVERT: B 87 MET cc_start: 0.8795 (mtt) cc_final: 0.8321 (tmm) REVERT: B 237 GLN cc_start: 0.7238 (tm-30) cc_final: 0.6950 (tm-30) REVERT: B 319 LEU cc_start: 0.9045 (tt) cc_final: 0.8780 (tp) REVERT: B 334 HIS cc_start: 0.8029 (OUTLIER) cc_final: 0.7419 (t-170) outliers start: 19 outliers final: 17 residues processed: 107 average time/residue: 0.1319 time to fit residues: 19.7299 Evaluate side-chains 116 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 183 ILE Chi-restraints excluded: chain A residue 209 THR 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 32 LEU 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 183 ILE Chi-restraints excluded: chain B residue 209 THR 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 58 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.4318 r_free = 0.4318 target = 0.161336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.122450 restraints weight = 9021.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.126515 restraints weight = 4441.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.129077 restraints weight = 3047.924| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5470 Z= 0.160 Angle : 0.598 10.287 7404 Z= 0.282 Chirality : 0.036 0.276 796 Planarity : 0.004 0.037 904 Dihedral : 3.821 21.480 810 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.76 % Allowed : 25.18 % 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 (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: 4.63 (0.35), residues: 618 helix: 3.76 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -2.38 (0.79), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 305 HIS 0.003 0.000 HIS A 283 PHE 0.024 0.001 PHE A 235 TYR 0.019 0.001 TYR A 238 ARG 0.009 0.001 ARG B 31 *********************** 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 119 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.8743 (mtt) cc_final: 0.8279 (tmm) REVERT: A 237 GLN cc_start: 0.7342 (tm-30) cc_final: 0.7000 (tm-30) REVERT: A 319 LEU cc_start: 0.9027 (tt) cc_final: 0.8773 (tp) REVERT: B 87 MET cc_start: 0.8780 (mtt) cc_final: 0.8297 (tmm) REVERT: B 237 GLN cc_start: 0.7341 (tm-30) cc_final: 0.6972 (tm-30) REVERT: B 319 LEU cc_start: 0.9029 (tt) cc_final: 0.8759 (tp) REVERT: B 334 HIS cc_start: 0.7979 (OUTLIER) cc_final: 0.7362 (t-170) outliers start: 10 outliers final: 7 residues processed: 116 average time/residue: 0.1732 time to fit residues: 26.1412 Evaluate side-chains 112 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 323 PHE 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 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 57 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 0.0770 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- 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 = 0.4273 r_free = 0.4273 target = 0.157565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.118161 restraints weight = 9055.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.122095 restraints weight = 4550.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.124501 restraints weight = 3154.191| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5470 Z= 0.219 Angle : 0.659 10.660 7404 Z= 0.313 Chirality : 0.037 0.252 796 Planarity : 0.004 0.035 904 Dihedral : 3.928 18.386 810 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.11 % Allowed : 25.18 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.55 (0.35), residues: 618 helix: 3.73 (0.21), residues: 532 sheet: None (None), residues: 0 loop : -2.40 (0.78), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 193 HIS 0.002 0.000 HIS B 283 PHE 0.022 0.001 PHE B 235 TYR 0.021 0.002 TYR A 238 ARG 0.009 0.001 ARG B 31 ********************** 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 110 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 87 MET cc_start: 0.8782 (mtt) cc_final: 0.8311 (tmm) REVERT: A 334 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.7393 (t-170) REVERT: B 87 MET cc_start: 0.8788 (mtt) cc_final: 0.8305 (tmm) REVERT: B 334 HIS cc_start: 0.8040 (OUTLIER) cc_final: 0.7381 (t-170) outliers start: 12 outliers final: 9 residues processed: 106 average time/residue: 0.1065 time to fit residues: 16.7519 Evaluate side-chains 106 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 244 CYS 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 12 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4293 r_free = 0.4293 target = 0.159584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.120508 restraints weight = 9060.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.124543 restraints weight = 4473.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.126998 restraints weight = 3065.274| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5470 Z= 0.196 Angle : 0.638 10.130 7404 Z= 0.304 Chirality : 0.036 0.242 796 Planarity : 0.004 0.033 904 Dihedral : 3.894 19.896 810 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.11 % Allowed : 25.18 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.56 (0.35), residues: 618 helix: 3.74 (0.21), residues: 532 sheet: None (None), residues: 0 loop : -2.45 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 305 HIS 0.002 0.000 HIS A 283 PHE 0.023 0.001 PHE B 235 TYR 0.019 0.001 TYR A 238 ARG 0.008 0.001 ARG B 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1745.66 seconds wall clock time: 32 minutes 5.56 seconds (1925.56 seconds total)