Starting phenix.real_space_refine on Fri Aug 22 12:39:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jv2_22491/08_2025/7jv2_22491.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jv2_22491/08_2025/7jv2_22491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jv2_22491/08_2025/7jv2_22491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jv2_22491/08_2025/7jv2_22491.map" model { file = "/net/cci-nas-00/data/ceres_data/7jv2_22491/08_2025/7jv2_22491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jv2_22491/08_2025/7jv2_22491.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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 8 5.16 5 C 1361 2.51 5 N 363 2.21 5 O 419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2151 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 915 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 812 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "A" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain breaks: 1 Time building chain proxies: 0.82, per 1000 atoms: 0.38 Number of scatterers: 2151 At special positions: 0 Unit cell: (68.25, 55.65, 66.15, 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 8 16.00 O 419 8.00 N 363 7.00 C 1361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.01 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.15 Conformation dependent library (CDL) restraints added in 85.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 494 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 5.0% alpha, 40.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'L' and resid 30 through 34 Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.839A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.513A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 90 hydrogen bonds defined for protein. 195 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: 0.34 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 459 1.32 - 1.45: 593 1.45 - 1.57: 1134 1.57 - 1.69: 8 1.69 - 1.82: 10 Bond restraints: 2204 Sorted by residual: bond pdb=" CB ILE A 468 " pdb=" CG1 ILE A 468 " ideal model delta sigma weight residual 1.530 1.623 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" CB LEU A 461 " pdb=" CG LEU A 461 " ideal model delta sigma weight residual 1.530 1.610 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" CB LEU L 110 " pdb=" CG LEU L 110 " ideal model delta sigma weight residual 1.530 1.597 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" CB ILE H 70 " pdb=" CG1 ILE H 70 " ideal model delta sigma weight residual 1.530 1.468 0.062 2.00e-02 2.50e+03 9.52e+00 bond pdb=" CG GLN L 1 " pdb=" CD GLN L 1 " ideal model delta sigma weight residual 1.516 1.587 -0.071 2.50e-02 1.60e+03 8.01e+00 ... (remaining 2199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 2245 1.39 - 2.78: 582 2.78 - 4.18: 117 4.18 - 5.57: 37 5.57 - 6.96: 10 Bond angle restraints: 2991 Sorted by residual: angle pdb=" C GLN A 498 " pdb=" N PRO A 499 " pdb=" CA PRO A 499 " ideal model delta sigma weight residual 119.82 126.78 -6.96 9.80e-01 1.04e+00 5.04e+01 angle pdb=" C PHE A 490 " pdb=" N PRO A 491 " pdb=" CA PRO A 491 " ideal model delta sigma weight residual 119.56 125.42 -5.86 1.01e+00 9.80e-01 3.36e+01 angle pdb=" C GLU L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta sigma weight residual 119.32 125.73 -6.41 1.14e+00 7.69e-01 3.16e+01 angle pdb=" C ALA L 45 " pdb=" N PRO L 46 " pdb=" CA PRO L 46 " ideal model delta sigma weight residual 119.76 125.21 -5.45 1.00e+00 1.00e+00 2.97e+01 angle pdb=" C ARG L 81 " pdb=" N PRO L 82 " pdb=" CA PRO L 82 " ideal model delta sigma weight residual 119.47 125.67 -6.20 1.16e+00 7.43e-01 2.86e+01 ... (remaining 2986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 1219 17.29 - 34.57: 35 34.57 - 51.85: 10 51.85 - 69.14: 3 69.14 - 86.42: 5 Dihedral angle restraints: 1272 sinusoidal: 479 harmonic: 793 Sorted by residual: dihedral pdb=" CB GLU H 46 " pdb=" CG GLU H 46 " pdb=" CD GLU H 46 " pdb=" OE1 GLU H 46 " ideal model delta sinusoidal sigma weight residual 0.00 -86.42 86.42 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" N TYR H 59 " pdb=" CA TYR H 59 " pdb=" CB TYR H 59 " pdb=" CG TYR H 59 " ideal model delta sinusoidal sigma weight residual -180.00 -123.33 -56.67 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CB GLU H 6 " pdb=" CG GLU H 6 " pdb=" CD GLU H 6 " pdb=" OE1 GLU H 6 " ideal model delta sinusoidal sigma weight residual 0.00 -82.50 82.50 1 3.00e+01 1.11e-03 9.27e+00 ... (remaining 1269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 216 0.069 - 0.139: 85 0.139 - 0.208: 11 0.208 - 0.277: 2 0.277 - 0.347: 2 Chirality restraints: 316 Sorted by residual: chirality pdb=" CG LEU L 110 " pdb=" CB LEU L 110 " pdb=" CD1 LEU L 110 " pdb=" CD2 LEU L 110 " both_signs ideal model delta sigma weight residual False -2.59 -2.94 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CG LEU A 461 " pdb=" CB LEU A 461 " pdb=" CD1 LEU A 461 " pdb=" CD2 LEU A 461 " both_signs ideal model delta sigma weight residual False -2.59 -2.93 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CB ILE A 468 " pdb=" CA ILE A 468 " pdb=" CG1 ILE A 468 " pdb=" CG2 ILE A 468 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 313 not shown) Planarity restraints: 385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 32 " -0.042 2.00e-02 2.50e+03 2.24e-02 1.00e+01 pdb=" CG TYR H 32 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR H 32 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR H 32 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR H 32 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR H 32 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR H 32 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 32 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 105 " 0.036 2.00e-02 2.50e+03 1.86e-02 6.94e+00 pdb=" CG TYR H 105 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR H 105 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR H 105 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR H 105 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR H 105 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR H 105 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 105 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 33 " 0.030 2.00e-02 2.50e+03 1.50e-02 5.63e+00 pdb=" CG TRP H 33 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP H 33 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP H 33 " -0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP H 33 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP H 33 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP H 33 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 33 " 0.016 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 33 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 33 " 0.015 2.00e-02 2.50e+03 ... (remaining 382 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 1312 3.05 - 3.51: 1905 3.51 - 3.97: 3466 3.97 - 4.44: 3915 4.44 - 4.90: 6436 Nonbonded interactions: 17034 Sorted by model distance: nonbonded pdb=" N HIS L 33 " pdb=" N TYR L 34 " model vdw 2.587 2.560 nonbonded pdb=" N LYS H 76 " pdb=" N ASN H 77 " model vdw 2.587 2.560 nonbonded pdb=" N SER H 71 " pdb=" O SER H 71 " model vdw 2.589 2.496 nonbonded pdb=" N ASP H 62 " pdb=" OD1 ASP H 62 " model vdw 2.594 3.120 nonbonded pdb=" O TYR L 34 " pdb=" CB TYR L 34 " model vdw 2.596 2.752 ... (remaining 17029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.900 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.093 2207 Z= 0.781 Angle : 1.392 6.959 2997 Z= 0.936 Chirality : 0.075 0.347 316 Planarity : 0.006 0.022 385 Dihedral : 11.432 86.421 769 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.32 % Allowed : 0.88 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.50), residues: 274 helix: None (None), residues: 0 sheet: 0.23 (0.50), residues: 102 loop : 0.93 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 72 TYR 0.042 0.007 TYR H 32 PHE 0.018 0.004 PHE L 101 TRP 0.030 0.006 TRP H 33 HIS 0.002 0.001 HIS L 57 Details of bonding type rmsd covalent geometry : bond 0.01471 ( 2204) covalent geometry : angle 1.38584 ( 2991) SS BOND : bond 0.01109 ( 3) SS BOND : angle 3.28913 ( 6) hydrogen bonds : bond 0.18284 ( 78) hydrogen bonds : angle 8.01654 ( 195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.094 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 65 average time/residue: 0.0783 time to fit residues: 5.8338 Evaluate side-chains 45 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.4980 chunk 24 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.0970 chunk 16 optimal weight: 0.0980 chunk 15 optimal weight: 0.0980 chunk 25 optimal weight: 0.3980 chunk 26 optimal weight: 0.0970 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 overall best weight: 0.1576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.163402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.150624 restraints weight = 3107.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.153485 restraints weight = 1756.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.155326 restraints weight = 1134.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.156598 restraints weight = 804.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.157444 restraints weight = 616.692| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 2207 Z= 0.136 Angle : 0.629 7.810 2997 Z= 0.333 Chirality : 0.043 0.145 316 Planarity : 0.003 0.022 385 Dihedral : 4.614 16.016 310 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.20 % Allowed : 10.13 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.48), residues: 274 helix: None (None), residues: 0 sheet: 0.29 (0.47), residues: 112 loop : 0.61 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 63 TYR 0.011 0.001 TYR A 453 PHE 0.010 0.001 PHE L 101 TRP 0.007 0.001 TRP H 33 HIS 0.001 0.000 HIS L 57 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 2204) covalent geometry : angle 0.62867 ( 2991) SS BOND : bond 0.00343 ( 3) SS BOND : angle 0.77649 ( 6) hydrogen bonds : bond 0.04111 ( 78) hydrogen bonds : angle 5.92272 ( 195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: L 31 SER cc_start: 0.7790 (m) cc_final: 0.7275 (t) REVERT: L 47 ARG cc_start: 0.8562 (ptm160) cc_final: 0.8299 (ptm160) REVERT: L 87 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7796 (mm-30) outliers start: 5 outliers final: 4 residues processed: 57 average time/residue: 0.0627 time to fit residues: 4.2183 Evaluate side-chains 52 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 10 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 11 optimal weight: 0.0670 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 26 optimal weight: 0.4980 chunk 4 optimal weight: 0.2980 chunk 14 optimal weight: 0.0370 chunk 2 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 0.0570 chunk 18 optimal weight: 0.5980 overall best weight: 0.1314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.162342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.149497 restraints weight = 3167.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.152350 restraints weight = 1779.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.154246 restraints weight = 1153.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.155404 restraints weight = 822.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.156374 restraints weight = 649.606| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2207 Z= 0.119 Angle : 0.588 7.073 2997 Z= 0.307 Chirality : 0.041 0.138 316 Planarity : 0.003 0.022 385 Dihedral : 4.535 17.445 310 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.52 % Allowed : 11.01 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.49), residues: 274 helix: None (None), residues: 0 sheet: 0.91 (0.52), residues: 102 loop : 0.34 (0.44), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 63 TYR 0.020 0.001 TYR H 32 PHE 0.013 0.001 PHE L 101 TRP 0.006 0.001 TRP H 33 HIS 0.001 0.001 HIS L 57 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 2204) covalent geometry : angle 0.58532 ( 2991) SS BOND : bond 0.00469 ( 3) SS BOND : angle 1.37798 ( 6) hydrogen bonds : bond 0.03815 ( 78) hydrogen bonds : angle 5.74231 ( 195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: H 59 TYR cc_start: 0.6360 (m-80) cc_final: 0.6146 (m-80) REVERT: L 31 SER cc_start: 0.7700 (m) cc_final: 0.7275 (t) REVERT: L 47 ARG cc_start: 0.8550 (ptm160) cc_final: 0.8332 (ptm-80) REVERT: L 87 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7777 (mm-30) outliers start: 8 outliers final: 5 residues processed: 60 average time/residue: 0.0614 time to fit residues: 4.3559 Evaluate side-chains 56 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 chunk 17 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.0870 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.150258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.138187 restraints weight = 3148.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.140688 restraints weight = 1878.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142379 restraints weight = 1272.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.143498 restraints weight = 939.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.144233 restraints weight = 748.431| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 2207 Z= 0.289 Angle : 0.754 7.197 2997 Z= 0.400 Chirality : 0.047 0.143 316 Planarity : 0.004 0.024 385 Dihedral : 5.306 17.822 310 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 5.73 % Allowed : 11.89 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.49), residues: 274 helix: None (None), residues: 0 sheet: 0.31 (0.48), residues: 115 loop : -0.18 (0.48), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 81 TYR 0.023 0.002 TYR H 60 PHE 0.016 0.002 PHE L 101 TRP 0.007 0.002 TRP H 33 HIS 0.003 0.002 HIS L 57 Details of bonding type rmsd covalent geometry : bond 0.00658 ( 2204) covalent geometry : angle 0.75140 ( 2991) SS BOND : bond 0.00678 ( 3) SS BOND : angle 1.50031 ( 6) hydrogen bonds : bond 0.04651 ( 78) hydrogen bonds : angle 6.42480 ( 195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: L 31 SER cc_start: 0.7900 (m) cc_final: 0.7343 (t) outliers start: 13 outliers final: 12 residues processed: 57 average time/residue: 0.0471 time to fit residues: 3.3322 Evaluate side-chains 61 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 495 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.0980 chunk 5 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 16 optimal weight: 0.0970 chunk 11 optimal weight: 0.4980 overall best weight: 0.2578 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.154220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142036 restraints weight = 3187.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.144711 restraints weight = 1804.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146561 restraints weight = 1189.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147798 restraints weight = 860.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.148578 restraints weight = 664.546| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 2207 Z= 0.166 Angle : 0.621 6.711 2997 Z= 0.328 Chirality : 0.041 0.128 316 Planarity : 0.003 0.026 385 Dihedral : 4.844 19.510 310 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 6.17 % Allowed : 13.22 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.49), residues: 274 helix: None (None), residues: 0 sheet: 0.15 (0.49), residues: 112 loop : -0.26 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 63 TYR 0.013 0.002 TYR H 60 PHE 0.017 0.002 PHE L 101 TRP 0.007 0.001 TRP H 33 HIS 0.001 0.001 HIS L 57 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 2204) covalent geometry : angle 0.62033 ( 2991) SS BOND : bond 0.00367 ( 3) SS BOND : angle 0.93689 ( 6) hydrogen bonds : bond 0.03840 ( 78) hydrogen bonds : angle 5.91716 ( 195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: L 31 SER cc_start: 0.7908 (m) cc_final: 0.7330 (t) outliers start: 14 outliers final: 10 residues processed: 59 average time/residue: 0.0565 time to fit residues: 3.9972 Evaluate side-chains 61 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 72 LYS Chi-restraints excluded: chain A residue 495 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 9 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 15 optimal weight: 0.0010 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 0.0870 chunk 6 optimal weight: 0.0980 chunk 21 optimal weight: 0.2980 overall best weight: 0.1564 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.157156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.145529 restraints weight = 3097.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.148083 restraints weight = 1764.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.149854 restraints weight = 1163.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.151061 restraints weight = 841.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.151654 restraints weight = 649.797| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2207 Z= 0.125 Angle : 0.580 6.046 2997 Z= 0.303 Chirality : 0.041 0.123 316 Planarity : 0.003 0.029 385 Dihedral : 4.537 17.511 310 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.73 % Allowed : 15.42 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.49), residues: 274 helix: None (None), residues: 0 sheet: 0.05 (0.50), residues: 112 loop : -0.28 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 47 TYR 0.019 0.001 TYR H 32 PHE 0.016 0.002 PHE L 101 TRP 0.005 0.001 TRP H 36 HIS 0.001 0.000 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 2204) covalent geometry : angle 0.57967 ( 2991) SS BOND : bond 0.00262 ( 3) SS BOND : angle 0.68884 ( 6) hydrogen bonds : bond 0.03430 ( 78) hydrogen bonds : angle 5.84987 ( 195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.082 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 56 average time/residue: 0.0451 time to fit residues: 3.1235 Evaluate side-chains 59 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 0.2980 chunk 14 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.149932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.138111 restraints weight = 3170.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140589 restraints weight = 1847.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.142316 restraints weight = 1247.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.143389 restraints weight = 908.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144226 restraints weight = 725.533| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 2207 Z= 0.250 Angle : 0.700 6.114 2997 Z= 0.367 Chirality : 0.045 0.182 316 Planarity : 0.004 0.030 385 Dihedral : 5.077 19.679 310 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 10.13 % Allowed : 11.89 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.49), residues: 274 helix: None (None), residues: 0 sheet: -0.20 (0.49), residues: 112 loop : -0.44 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 457 TYR 0.019 0.002 TYR H 60 PHE 0.018 0.002 PHE L 101 TRP 0.007 0.002 TRP H 33 HIS 0.002 0.001 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00573 ( 2204) covalent geometry : angle 0.69866 ( 2991) SS BOND : bond 0.00558 ( 3) SS BOND : angle 1.08769 ( 6) hydrogen bonds : bond 0.04053 ( 78) hydrogen bonds : angle 6.35252 ( 195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.099 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 20 residues processed: 64 average time/residue: 0.0479 time to fit residues: 3.7641 Evaluate side-chains 72 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 3 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 13 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 overall best weight: 0.3378 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.151223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139303 restraints weight = 3161.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.141895 restraints weight = 1853.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.143613 restraints weight = 1239.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.144708 restraints weight = 908.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145571 restraints weight = 719.516| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 2207 Z= 0.201 Angle : 0.661 6.571 2997 Z= 0.345 Chirality : 0.043 0.143 316 Planarity : 0.004 0.030 385 Dihedral : 4.943 18.989 310 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 8.81 % Allowed : 14.10 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.49), residues: 274 helix: None (None), residues: 0 sheet: -0.46 (0.48), residues: 112 loop : -0.52 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 47 TYR 0.015 0.002 TYR H 60 PHE 0.024 0.002 PHE L 101 TRP 0.007 0.002 TRP H 33 HIS 0.001 0.001 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 2204) covalent geometry : angle 0.66028 ( 2991) SS BOND : bond 0.00438 ( 3) SS BOND : angle 0.92632 ( 6) hydrogen bonds : bond 0.03764 ( 78) hydrogen bonds : angle 6.24517 ( 195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.097 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 19 residues processed: 59 average time/residue: 0.0443 time to fit residues: 3.2697 Evaluate side-chains 67 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.0870 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 25 optimal weight: 0.2980 chunk 24 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 overall best weight: 0.3158 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.151206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.139251 restraints weight = 3193.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.141831 restraints weight = 1873.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.143484 restraints weight = 1254.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.144634 restraints weight = 930.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.145556 restraints weight = 730.806| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 2207 Z= 0.193 Angle : 0.653 7.982 2997 Z= 0.340 Chirality : 0.043 0.142 316 Planarity : 0.004 0.031 385 Dihedral : 4.904 18.926 310 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 8.81 % Allowed : 14.10 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.49), residues: 274 helix: None (None), residues: 0 sheet: -0.66 (0.48), residues: 112 loop : -0.53 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 47 TYR 0.014 0.002 TYR H 60 PHE 0.023 0.002 PHE L 101 TRP 0.007 0.002 TRP H 33 HIS 0.001 0.001 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 2204) covalent geometry : angle 0.65234 ( 2991) SS BOND : bond 0.00413 ( 3) SS BOND : angle 0.88524 ( 6) hydrogen bonds : bond 0.03678 ( 78) hydrogen bonds : angle 6.21856 ( 195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.093 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 18 residues processed: 56 average time/residue: 0.0471 time to fit residues: 3.2730 Evaluate side-chains 65 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 20 optimal weight: 0.0670 chunk 5 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 0.0980 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.148216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136601 restraints weight = 3244.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139000 restraints weight = 1927.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.140629 restraints weight = 1302.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.141751 restraints weight = 959.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.142443 restraints weight = 755.475| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 2207 Z= 0.229 Angle : 0.699 7.931 2997 Z= 0.362 Chirality : 0.044 0.168 316 Planarity : 0.004 0.030 385 Dihedral : 5.080 18.968 310 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 9.25 % Allowed : 13.66 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.49), residues: 274 helix: None (None), residues: 0 sheet: -0.92 (0.47), residues: 112 loop : -0.57 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 47 TYR 0.016 0.002 TYR H 60 PHE 0.022 0.002 PHE L 101 TRP 0.007 0.002 TRP H 33 HIS 0.002 0.001 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 2204) covalent geometry : angle 0.69839 ( 2991) SS BOND : bond 0.00479 ( 3) SS BOND : angle 1.02622 ( 6) hydrogen bonds : bond 0.03886 ( 78) hydrogen bonds : angle 6.37309 ( 195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.059 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 20 residues processed: 57 average time/residue: 0.0403 time to fit residues: 2.9187 Evaluate side-chains 67 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 1 optimal weight: 0.0570 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 0 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.147946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.136203 restraints weight = 3229.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.138560 restraints weight = 1887.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.140247 restraints weight = 1282.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.141386 restraints weight = 938.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.142230 restraints weight = 734.352| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 2207 Z= 0.254 Angle : 0.713 8.121 2997 Z= 0.373 Chirality : 0.045 0.170 316 Planarity : 0.004 0.030 385 Dihedral : 5.233 19.806 310 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 10.13 % Allowed : 12.78 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.49), residues: 274 helix: None (None), residues: 0 sheet: -1.09 (0.47), residues: 112 loop : -0.67 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 81 TYR 0.018 0.002 TYR H 60 PHE 0.022 0.002 PHE L 101 TRP 0.007 0.002 TRP H 33 HIS 0.002 0.001 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00587 ( 2204) covalent geometry : angle 0.71248 ( 2991) SS BOND : bond 0.00515 ( 3) SS BOND : angle 0.99096 ( 6) hydrogen bonds : bond 0.03971 ( 78) hydrogen bonds : angle 6.54459 ( 195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 775.39 seconds wall clock time: 14 minutes 35.60 seconds (875.60 seconds total)