Starting phenix.real_space_refine on Mon Feb 10 20:12:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jv2_22491/02_2025/7jv2_22491.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jv2_22491/02_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_22491/02_2025/7jv2_22491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jv2_22491/02_2025/7jv2_22491.map" model { file = "/net/cci-nas-00/data/ceres_data/7jv2_22491/02_2025/7jv2_22491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jv2_22491/02_2025/7jv2_22491.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.07, per 1000 atoms: 1.43 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: 0.61 Conformation dependent library (CDL) restraints added in 256.7 milliseconds 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: 0.36 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: 0.51 Time building geometry restraints manager: 0.68 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: 3.630 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.100 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.840 ------------------------------------------------------------------------------- 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 2204 Z= 0.946 Angle : 1.386 6.959 2991 Z= 0.934 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 (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: 0.82 (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 TRP 0.030 0.006 TRP H 33 HIS 0.002 0.001 HIS L 57 PHE 0.018 0.004 PHE L 101 TYR 0.042 0.007 TYR H 32 ARG 0.003 0.001 ARG H 72 *********************** 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 : 0.226 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 65 average time/residue: 0.1628 time to fit residues: 12.1232 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 : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 0.0870 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 21 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 overall best weight: 0.2558 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.159461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.146761 restraints weight = 3124.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.149416 restraints weight = 1770.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.151160 restraints weight = 1163.158| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 2204 Z= 0.247 Angle : 0.662 7.708 2991 Z= 0.354 Chirality : 0.044 0.139 316 Planarity : 0.004 0.023 385 Dihedral : 4.780 16.586 310 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.08 % Allowed : 9.25 % 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 (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: 0.52 (0.48), residues: 274 helix: None (None), residues: 0 sheet: 0.26 (0.46), residues: 112 loop : 0.56 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 33 HIS 0.002 0.001 HIS L 57 PHE 0.008 0.002 PHE L 101 TYR 0.014 0.002 TYR A 453 ARG 0.003 0.001 ARG L 63 *********************** 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 59 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: L 31 SER cc_start: 0.7872 (m) cc_final: 0.7353 (t) REVERT: L 47 ARG cc_start: 0.8578 (ptm160) cc_final: 0.8320 (ptm160) REVERT: L 81 ARG cc_start: 0.6274 (mtp-110) cc_final: 0.6008 (mtt-85) REVERT: L 87 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7875 (mm-30) outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 0.1448 time to fit residues: 9.2314 Evaluate side-chains 52 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 91 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 0.1980 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.150058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.137492 restraints weight = 3132.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.140092 restraints weight = 1820.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.141892 restraints weight = 1222.447| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 2204 Z= 0.432 Angle : 0.746 7.036 2991 Z= 0.400 Chirality : 0.046 0.147 316 Planarity : 0.004 0.026 385 Dihedral : 5.542 17.491 310 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 4.41 % Allowed : 10.57 % Favored : 85.02 % 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: -0.31 (0.48), residues: 274 helix: None (None), residues: 0 sheet: -0.06 (0.46), residues: 115 loop : -0.23 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP H 36 HIS 0.005 0.002 HIS L 57 PHE 0.010 0.002 PHE L 101 TYR 0.025 0.002 TYR H 60 ARG 0.003 0.001 ARG L 63 *********************** 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 59 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.239 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 54 average time/residue: 0.1188 time to fit residues: 7.7837 Evaluate side-chains 55 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 91 THR Chi-restraints excluded: chain L residue 10 LEU 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 494 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 0.0970 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 7 optimal weight: 0.4980 chunk 20 optimal weight: 0.0670 chunk 13 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 16 optimal weight: 0.1980 chunk 6 optimal weight: 0.0970 overall best weight: 0.1714 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.156852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.144574 restraints weight = 3041.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.147013 restraints weight = 1784.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.148844 restraints weight = 1215.113| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 2204 Z= 0.185 Angle : 0.592 6.480 2991 Z= 0.313 Chirality : 0.042 0.124 316 Planarity : 0.003 0.024 385 Dihedral : 4.825 20.254 310 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.41 % Allowed : 12.78 % Favored : 82.82 % 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: -0.24 (0.48), residues: 274 helix: None (None), residues: 0 sheet: -0.01 (0.47), residues: 112 loop : -0.18 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 37 HIS 0.002 0.001 HIS L 57 PHE 0.016 0.002 PHE L 101 TYR 0.015 0.001 TYR H 32 ARG 0.002 0.000 ARG L 63 *********************** 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 60 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.219 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 53 average time/residue: 0.1207 time to fit residues: 7.7009 Evaluate side-chains 55 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 91 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.146628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.134674 restraints weight = 3233.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.137106 restraints weight = 1953.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.138716 restraints weight = 1327.972| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 2204 Z= 0.509 Angle : 0.809 6.259 2991 Z= 0.429 Chirality : 0.048 0.151 316 Planarity : 0.005 0.029 385 Dihedral : 5.693 20.743 310 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 6.17 % Allowed : 12.33 % Favored : 81.50 % 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: -0.77 (0.47), residues: 274 helix: None (None), residues: 0 sheet: -0.31 (0.48), residues: 107 loop : -0.60 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP H 33 HIS 0.005 0.002 HIS L 57 PHE 0.018 0.002 PHE L 101 TYR 0.024 0.003 TYR H 60 ARG 0.003 0.001 ARG A 454 *********************** 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 65 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.239 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 59 average time/residue: 0.1193 time to fit residues: 8.5786 Evaluate side-chains 60 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 72 LYS Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 484 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 9 optimal weight: 0.1980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.0980 chunk 13 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 = 0.151195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.139032 restraints weight = 3136.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.141547 restraints weight = 1814.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143278 restraints weight = 1212.596| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 2204 Z= 0.290 Angle : 0.672 7.290 2991 Z= 0.351 Chirality : 0.043 0.130 316 Planarity : 0.004 0.032 385 Dihedral : 5.163 20.809 310 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 5.73 % Allowed : 14.98 % Favored : 79.30 % 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: -0.96 (0.48), residues: 274 helix: None (None), residues: 0 sheet: -0.56 (0.47), residues: 112 loop : -0.62 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP H 33 HIS 0.002 0.001 HIS L 57 PHE 0.017 0.002 PHE L 101 TYR 0.015 0.002 TYR H 60 ARG 0.002 0.000 ARG L 47 *********************** 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 62 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.202 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 55 average time/residue: 0.1099 time to fit residues: 7.3823 Evaluate side-chains 59 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 484 GLU 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 17 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 0.2980 chunk 10 optimal weight: 0.0870 chunk 0 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 16 optimal weight: 0.0010 chunk 24 optimal weight: 0.8980 overall best weight: 0.1964 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.144382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.131177 restraints weight = 3192.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.133721 restraints weight = 1916.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.135407 restraints weight = 1306.929| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2204 Z= 0.198 Angle : 0.611 7.042 2991 Z= 0.315 Chirality : 0.042 0.119 316 Planarity : 0.004 0.035 385 Dihedral : 4.787 21.646 310 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 4.41 % Allowed : 16.74 % 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 (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: -0.94 (0.48), residues: 274 helix: None (None), residues: 0 sheet: -0.65 (0.47), residues: 112 loop : -0.52 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 47 HIS 0.001 0.001 HIS L 57 PHE 0.020 0.002 PHE L 101 TYR 0.013 0.001 TYR H 32 ARG 0.002 0.000 ARG L 47 *********************** 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 54 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.224 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 49 average time/residue: 0.1087 time to fit residues: 6.5648 Evaluate side-chains 50 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 83 MET Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 495 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 17 optimal weight: 0.0070 chunk 18 optimal weight: 0.4980 chunk 16 optimal weight: 0.1980 chunk 4 optimal weight: 0.0370 overall best weight: 0.2276 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.151820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.139426 restraints weight = 3138.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.141955 restraints weight = 1849.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.143499 restraints weight = 1251.166| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2204 Z= 0.221 Angle : 0.653 8.079 2991 Z= 0.329 Chirality : 0.043 0.159 316 Planarity : 0.004 0.036 385 Dihedral : 4.794 20.380 310 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.96 % Allowed : 16.30 % Favored : 79.74 % 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: -0.98 (0.48), residues: 274 helix: None (None), residues: 0 sheet: -0.71 (0.48), residues: 107 loop : -0.53 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 33 HIS 0.001 0.001 HIS L 57 PHE 0.020 0.002 PHE L 101 TYR 0.011 0.001 TYR H 60 ARG 0.002 0.000 ARG L 47 *********************** 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 52 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.221 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 48 average time/residue: 0.1005 time to fit residues: 6.0374 Evaluate side-chains 51 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 83 MET Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 495 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 25 optimal weight: 0.0980 chunk 26 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 0.1980 chunk 4 optimal weight: 0.0980 chunk 22 optimal weight: 0.3980 overall best weight: 0.1580 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.159253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.147433 restraints weight = 2979.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.149830 restraints weight = 1767.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.151442 restraints weight = 1199.893| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2204 Z= 0.186 Angle : 0.635 8.769 2991 Z= 0.322 Chirality : 0.042 0.145 316 Planarity : 0.004 0.036 385 Dihedral : 4.630 19.615 310 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.96 % Allowed : 17.62 % Favored : 78.41 % 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: -0.93 (0.48), residues: 274 helix: None (None), residues: 0 sheet: -0.72 (0.49), residues: 107 loop : -0.47 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.001 0.000 HIS L 57 PHE 0.016 0.002 PHE L 101 TYR 0.009 0.001 TYR H 60 ARG 0.001 0.000 ARG L 47 *********************** 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 51 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.255 Fit side-chains REVERT: H 46 GLU cc_start: 0.6304 (tp30) cc_final: 0.6043 (tp30) REVERT: H 105 TYR cc_start: 0.8507 (p90) cc_final: 0.8299 (p90) outliers start: 9 outliers final: 5 residues processed: 48 average time/residue: 0.1038 time to fit residues: 6.2086 Evaluate side-chains 48 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 83 MET Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain A residue 495 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 6 optimal weight: 0.4980 chunk 5 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.148977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.136835 restraints weight = 3138.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139291 restraints weight = 1837.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.141005 restraints weight = 1232.400| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 2204 Z= 0.402 Angle : 0.754 7.950 2991 Z= 0.389 Chirality : 0.047 0.180 316 Planarity : 0.004 0.034 385 Dihedral : 5.292 21.198 310 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 3.52 % Allowed : 18.06 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.48), residues: 274 helix: None (None), residues: 0 sheet: -1.08 (0.48), residues: 107 loop : -0.60 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP H 33 HIS 0.002 0.001 HIS L 33 PHE 0.019 0.002 PHE L 101 TYR 0.019 0.002 TYR H 60 ARG 0.002 0.001 ARG A 454 ********************** 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 53 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.211 Fit side-chains REVERT: H 46 GLU cc_start: 0.6668 (tp30) cc_final: 0.6350 (tp30) outliers start: 8 outliers final: 7 residues processed: 48 average time/residue: 0.1149 time to fit residues: 6.9145 Evaluate side-chains 52 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 83 MET Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 110 LEU 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 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.148145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.136017 restraints weight = 3213.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.138539 restraints weight = 1872.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.140192 restraints weight = 1252.387| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 2204 Z= 0.410 Angle : 0.775 7.964 2991 Z= 0.401 Chirality : 0.048 0.198 316 Planarity : 0.004 0.034 385 Dihedral : 5.518 22.472 310 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.41 % Allowed : 17.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.47), residues: 274 helix: None (None), residues: 0 sheet: -1.34 (0.47), residues: 107 loop : -0.72 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP H 47 HIS 0.003 0.001 HIS L 57 PHE 0.019 0.002 PHE L 101 TYR 0.021 0.002 TYR H 32 ARG 0.002 0.001 ARG H 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1334.29 seconds wall clock time: 24 minutes 36.85 seconds (1476.85 seconds total)