Starting phenix.real_space_refine on Fri Aug 22 12:37:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5m5h_4155/08_2025/5m5h_4155.cif Found real_map, /net/cci-nas-00/data/ceres_data/5m5h_4155/08_2025/5m5h_4155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5m5h_4155/08_2025/5m5h_4155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5m5h_4155/08_2025/5m5h_4155.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5m5h_4155/08_2025/5m5h_4155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5m5h_4155/08_2025/5m5h_4155.map" } resolution = 4.5 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= 0.001 sd= 0.005 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 757 2.51 5 N 157 2.21 5 O 164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 1086 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1086 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 121} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 0.32, per 1000 atoms: 0.29 Number of scatterers: 1086 At special positions: 0 Unit cell: (54.2, 49.864, 54.2, 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 164 8.00 N 157 7.00 C 757 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.18 Conformation dependent library (CDL) restraints added in 27.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 252 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 0 sheets defined 68.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.02 Creating SS restraints... Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 355 through 369 Processing helix chain 'A' and resid 425 through 428 removed outlier: 3.881A pdb=" N ILE A 428 " --> pdb=" O PRO A 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 428' Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 465 through 476 removed outlier: 3.714A pdb=" N ILE A 469 " --> pdb=" O TYR A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 496 removed outlier: 3.501A pdb=" N THR A 496 " --> pdb=" O LYS A 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 493 through 496' Processing helix chain 'A' and resid 497 through 507 removed outlier: 3.510A pdb=" N ILE A 501 " --> pdb=" O PHE A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 527 removed outlier: 3.932A pdb=" N VAL A 514 " --> pdb=" O PRO A 510 " (cutoff:3.500A) 55 hydrogen bonds defined for protein. 165 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: 0.08 Time building geometry restraints manager: 0.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 240 1.34 - 1.46: 290 1.46 - 1.58: 581 1.58 - 1.70: 0 1.70 - 1.82: 15 Bond restraints: 1126 Sorted by residual: bond pdb=" C MET A 498 " pdb=" O MET A 498 " ideal model delta sigma weight residual 1.238 1.222 0.016 9.50e-03 1.11e+04 2.79e+00 bond pdb=" CA VAL A 351 " pdb=" C VAL A 351 " ideal model delta sigma weight residual 1.523 1.544 -0.021 1.31e-02 5.83e+03 2.58e+00 bond pdb=" CA TYR A 465 " pdb=" C TYR A 465 " ideal model delta sigma weight residual 1.525 1.547 -0.021 1.40e-02 5.10e+03 2.30e+00 bond pdb=" C PHE A 502 " pdb=" O PHE A 502 " ideal model delta sigma weight residual 1.236 1.220 0.016 1.15e-02 7.56e+03 2.03e+00 bond pdb=" N PHE A 424 " pdb=" CA PHE A 424 " ideal model delta sigma weight residual 1.465 1.451 0.014 1.05e-02 9.07e+03 1.75e+00 ... (remaining 1121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 1401 2.31 - 4.63: 111 4.63 - 6.94: 16 6.94 - 9.25: 5 9.25 - 11.56: 4 Bond angle restraints: 1537 Sorted by residual: angle pdb=" C TRP A 334 " pdb=" N PHE A 335 " pdb=" CA PHE A 335 " ideal model delta sigma weight residual 122.26 114.49 7.77 1.59e+00 3.96e-01 2.39e+01 angle pdb=" N GLY A 352 " pdb=" CA GLY A 352 " pdb=" C GLY A 352 " ideal model delta sigma weight residual 113.18 124.74 -11.56 2.37e+00 1.78e-01 2.38e+01 angle pdb=" C CYS A 423 " pdb=" N PHE A 424 " pdb=" CA PHE A 424 " ideal model delta sigma weight residual 122.28 117.93 4.35 1.02e+00 9.61e-01 1.82e+01 angle pdb=" CA TYR A 464 " pdb=" CB TYR A 464 " pdb=" CG TYR A 464 " ideal model delta sigma weight residual 113.90 121.19 -7.29 1.80e+00 3.09e-01 1.64e+01 angle pdb=" C PHE A 497 " pdb=" N MET A 498 " pdb=" CA MET A 498 " ideal model delta sigma weight residual 121.62 127.11 -5.49 1.57e+00 4.06e-01 1.22e+01 ... (remaining 1532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.25: 467 8.25 - 16.50: 103 16.50 - 24.75: 40 24.75 - 33.00: 10 33.00 - 41.25: 12 Dihedral angle restraints: 632 sinusoidal: 244 harmonic: 388 Sorted by residual: dihedral pdb=" CA PHE A 424 " pdb=" C PHE A 424 " pdb=" N PRO A 425 " pdb=" CA PRO A 425 " ideal model delta harmonic sigma weight residual 180.00 141.50 38.50 0 5.00e+00 4.00e-02 5.93e+01 dihedral pdb=" CA VAL A 351 " pdb=" C VAL A 351 " pdb=" N GLY A 352 " pdb=" CA GLY A 352 " ideal model delta harmonic sigma weight residual -180.00 -143.11 -36.89 0 5.00e+00 4.00e-02 5.44e+01 dihedral pdb=" CA GLN A 527 " pdb=" C GLN A 527 " pdb=" N GLN A 528 " pdb=" CA GLN A 528 " ideal model delta harmonic sigma weight residual -180.00 -150.38 -29.62 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 90 0.047 - 0.094: 53 0.094 - 0.141: 17 0.141 - 0.188: 10 0.188 - 0.235: 4 Chirality restraints: 174 Sorted by residual: chirality pdb=" CG LEU A 446 " pdb=" CB LEU A 446 " pdb=" CD1 LEU A 446 " pdb=" CD2 LEU A 446 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE A 336 " pdb=" CA ILE A 336 " pdb=" CG1 ILE A 336 " pdb=" CG2 ILE A 336 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA LEU A 446 " pdb=" N LEU A 446 " pdb=" C LEU A 446 " pdb=" CB LEU A 446 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 171 not shown) Planarity restraints: 180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 517 " -0.032 2.00e-02 2.50e+03 2.14e-02 9.15e+00 pdb=" CG TYR A 517 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR A 517 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 517 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 517 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 517 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 517 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 517 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 467 " -0.045 5.00e-02 4.00e+02 6.75e-02 7.28e+00 pdb=" N PRO A 468 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 468 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 468 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 424 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO A 425 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 425 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 425 " -0.036 5.00e-02 4.00e+02 ... (remaining 177 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 107 2.73 - 3.27: 1132 3.27 - 3.81: 1718 3.81 - 4.36: 2184 4.36 - 4.90: 3185 Nonbonded interactions: 8326 Sorted by model distance: nonbonded pdb=" O MET A 498 " pdb=" N ILE A 501 " model vdw 2.186 3.120 nonbonded pdb=" O LEU A 344 " pdb=" ND1 HIS A 348 " model vdw 2.310 3.120 nonbonded pdb=" O PHE A 506 " pdb=" N PHE A 509 " model vdw 2.361 3.120 nonbonded pdb=" O ILE A 364 " pdb=" N GLY A 367 " model vdw 2.381 3.120 nonbonded pdb=" O LEU A 426 " pdb=" N GLN A 429 " model vdw 2.384 3.120 ... (remaining 8321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 4.700 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.260 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1505 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 : 0.007 0.044 1126 Z= 0.350 Angle : 1.498 11.564 1537 Z= 0.831 Chirality : 0.075 0.235 174 Planarity : 0.011 0.067 180 Dihedral : 12.373 41.255 380 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 39.89 Ramachandran Plot: Outliers : 2.38 % Allowed : 8.73 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % Twisted Proline : 11.11 % Twisted General : 0.83 % 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: -5.94 (0.48), residues: 126 helix: -3.97 (0.37), residues: 70 sheet: None (None), residues: 0 loop : -3.84 (0.60), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.003 ARG A 447 TYR 0.050 0.005 TYR A 517 PHE 0.038 0.006 PHE A 424 TRP 0.022 0.005 TRP A 346 HIS 0.005 0.002 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00715 ( 1126) covalent geometry : angle 1.49808 ( 1537) hydrogen bonds : bond 0.13539 ( 55) hydrogen bonds : angle 14.05668 ( 165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 477 PHE cc_start: 0.3905 (m-10) cc_final: 0.2995 (m-80) REVERT: A 506 PHE cc_start: 0.1223 (m-80) cc_final: 0.0718 (m-80) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0190 time to fit residues: 0.5474 Evaluate side-chains 19 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 6 optimal weight: 0.2980 chunk 12 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 0.3980 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- 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 = 0.4936 r_free = 0.4936 target = 0.195216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.190641 restraints weight = 4505.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.191508 restraints weight = 3472.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.192306 restraints weight = 2739.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.192857 restraints weight = 2154.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.193438 restraints weight = 1757.298| |-----------------------------------------------------------------------------| r_work (final): 0.4918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1467 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1126 Z= 0.188 Angle : 0.935 7.641 1537 Z= 0.482 Chirality : 0.053 0.157 174 Planarity : 0.009 0.062 180 Dihedral : 8.400 28.988 138 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 24.30 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.94 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -3.85 (0.63), residues: 126 helix: -1.99 (0.48), residues: 76 sheet: None (None), residues: 0 loop : -3.38 (0.81), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 447 TYR 0.015 0.002 TYR A 464 PHE 0.030 0.003 PHE A 335 TRP 0.007 0.001 TRP A 354 HIS 0.003 0.002 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 1126) covalent geometry : angle 0.93491 ( 1537) hydrogen bonds : bond 0.05907 ( 55) hydrogen bonds : angle 7.31126 ( 165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 ILE cc_start: 0.3956 (tt) cc_final: 0.3088 (mm) REVERT: A 441 MET cc_start: 0.2417 (mmp) cc_final: 0.1813 (ppp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0289 time to fit residues: 0.6625 Evaluate side-chains 15 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 9 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 11 optimal weight: 0.0270 overall best weight: 5.0046 ------------------------------------------------------------------------------- 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 = 0.4992 r_free = 0.4992 target = 0.201267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.193429 restraints weight = 4540.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.194197 restraints weight = 3712.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.195073 restraints weight = 3223.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.195569 restraints weight = 2758.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.196187 restraints weight = 2466.900| |-----------------------------------------------------------------------------| r_work (final): 0.4914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1503 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 1126 Z= 0.180 Angle : 0.888 6.396 1537 Z= 0.455 Chirality : 0.053 0.197 174 Planarity : 0.009 0.069 180 Dihedral : 7.890 28.745 138 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 1.59 % Allowed : 8.73 % Favored : 89.68 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -3.23 (0.66), residues: 126 helix: -1.49 (0.50), residues: 78 sheet: None (None), residues: 0 loop : -3.18 (0.87), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 447 TYR 0.019 0.002 TYR A 464 PHE 0.026 0.003 PHE A 350 TRP 0.013 0.002 TRP A 334 HIS 0.003 0.001 HIS A 456 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 1126) covalent geometry : angle 0.88759 ( 1537) hydrogen bonds : bond 0.05385 ( 55) hydrogen bonds : angle 6.43482 ( 165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.040 Fit side-chains REVERT: A 361 ILE cc_start: 0.4176 (tt) cc_final: 0.3322 (mm) REVERT: A 441 MET cc_start: 0.2598 (mmp) cc_final: 0.1829 (ppp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0283 time to fit residues: 0.6539 Evaluate side-chains 16 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 3 optimal weight: 0.0070 chunk 0 optimal weight: 30.0000 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 0.0060 chunk 9 optimal weight: 20.0000 chunk 6 optimal weight: 40.0000 chunk 11 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 overall best weight: 3.0020 ------------------------------------------------------------------------------- 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 = 0.4979 r_free = 0.4979 target = 0.200799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.194168 restraints weight = 4503.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.195682 restraints weight = 3227.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.196759 restraints weight = 2421.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.197491 restraints weight = 1851.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.197872 restraints weight = 1454.635| |-----------------------------------------------------------------------------| r_work (final): 0.4939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1462 moved from start: 0.5476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1126 Z= 0.157 Angle : 0.814 6.990 1537 Z= 0.409 Chirality : 0.049 0.191 174 Planarity : 0.008 0.057 180 Dihedral : 6.888 23.010 138 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 22.93 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.14 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -2.87 (0.64), residues: 126 helix: -1.05 (0.49), residues: 79 sheet: None (None), residues: 0 loop : -3.39 (0.80), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 447 TYR 0.011 0.002 TYR A 464 PHE 0.020 0.002 PHE A 350 TRP 0.007 0.001 TRP A 334 HIS 0.008 0.004 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 1126) covalent geometry : angle 0.81450 ( 1537) hydrogen bonds : bond 0.04534 ( 55) hydrogen bonds : angle 5.85804 ( 165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.046 Fit side-chains REVERT: A 361 ILE cc_start: 0.4263 (tt) cc_final: 0.3726 (mm) REVERT: A 441 MET cc_start: 0.2572 (mmp) cc_final: 0.1832 (ppp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0300 time to fit residues: 0.6709 Evaluate side-chains 14 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 11 optimal weight: 6.9990 chunk 9 optimal weight: 0.0770 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.5942 ------------------------------------------------------------------------------- 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 = 0.4972 r_free = 0.4972 target = 0.201951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.194706 restraints weight = 4536.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.195935 restraints weight = 3415.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.196965 restraints weight = 2671.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.197479 restraints weight = 2149.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.198219 restraints weight = 1882.594| |-----------------------------------------------------------------------------| r_work (final): 0.4928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1433 moved from start: 0.6412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1126 Z= 0.140 Angle : 0.768 7.751 1537 Z= 0.372 Chirality : 0.047 0.206 174 Planarity : 0.008 0.060 180 Dihedral : 6.142 20.985 138 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.14 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -1.88 (0.68), residues: 126 helix: -0.29 (0.52), residues: 82 sheet: None (None), residues: 0 loop : -3.09 (0.82), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 447 TYR 0.016 0.001 TYR A 438 PHE 0.018 0.002 PHE A 335 TRP 0.006 0.001 TRP A 454 HIS 0.007 0.003 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 1126) covalent geometry : angle 0.76826 ( 1537) hydrogen bonds : bond 0.03974 ( 55) hydrogen bonds : angle 5.32637 ( 165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.044 Fit side-chains REVERT: A 344 LEU cc_start: 0.4051 (tp) cc_final: 0.3732 (tp) REVERT: A 361 ILE cc_start: 0.4287 (tt) cc_final: 0.3661 (mm) REVERT: A 430 MET cc_start: 0.1257 (mmp) cc_final: 0.1011 (mtp) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0328 time to fit residues: 0.8611 Evaluate side-chains 17 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 3 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 6 optimal weight: 0.0370 chunk 8 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.3664 ------------------------------------------------------------------------------- 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 = 0.4973 r_free = 0.4973 target = 0.202666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.197898 restraints weight = 4732.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.199363 restraints weight = 3073.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.200417 restraints weight = 2058.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.201162 restraints weight = 1369.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.201569 restraints weight = 909.038| |-----------------------------------------------------------------------------| r_work (final): 0.4896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1362 moved from start: 0.6686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1126 Z= 0.154 Angle : 0.856 11.618 1537 Z= 0.411 Chirality : 0.051 0.221 174 Planarity : 0.008 0.046 180 Dihedral : 6.001 18.515 138 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 22.01 Ramachandran Plot: Outliers : 0.79 % Allowed : 8.73 % Favored : 90.48 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -1.76 (0.70), residues: 126 helix: -0.23 (0.53), residues: 82 sheet: None (None), residues: 0 loop : -2.96 (0.87), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 447 TYR 0.016 0.002 TYR A 438 PHE 0.018 0.002 PHE A 335 TRP 0.006 0.001 TRP A 454 HIS 0.008 0.004 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 1126) covalent geometry : angle 0.85630 ( 1537) hydrogen bonds : bond 0.04110 ( 55) hydrogen bonds : angle 5.41423 ( 165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.047 Fit side-chains REVERT: A 361 ILE cc_start: 0.4062 (tt) cc_final: 0.3487 (mm) REVERT: A 433 PHE cc_start: -0.0180 (t80) cc_final: -0.0599 (t80) REVERT: A 498 MET cc_start: -0.0401 (mmm) cc_final: -0.0618 (mmm) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0301 time to fit residues: 0.7255 Evaluate side-chains 16 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 10 optimal weight: 6.9990 chunk 11 optimal weight: 0.2980 chunk 4 optimal weight: 0.0670 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 overall best weight: 3.8724 ------------------------------------------------------------------------------- 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 = 0.4937 r_free = 0.4937 target = 0.200533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.194383 restraints weight = 4685.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.195835 restraints weight = 3245.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.196984 restraints weight = 2349.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.197615 restraints weight = 1716.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.198412 restraints weight = 1365.095| |-----------------------------------------------------------------------------| r_work (final): 0.4833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1420 moved from start: 0.6889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1126 Z= 0.161 Angle : 0.830 8.925 1537 Z= 0.412 Chirality : 0.052 0.239 174 Planarity : 0.008 0.047 180 Dihedral : 6.151 19.531 138 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.14 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -1.82 (0.69), residues: 126 helix: -0.14 (0.53), residues: 82 sheet: None (None), residues: 0 loop : -3.30 (0.82), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 447 TYR 0.019 0.002 TYR A 438 PHE 0.023 0.002 PHE A 341 TRP 0.009 0.001 TRP A 334 HIS 0.008 0.004 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 1126) covalent geometry : angle 0.82964 ( 1537) hydrogen bonds : bond 0.04213 ( 55) hydrogen bonds : angle 5.35141 ( 165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.042 Fit side-chains REVERT: A 361 ILE cc_start: 0.4227 (tt) cc_final: 0.3823 (mm) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0301 time to fit residues: 0.6941 Evaluate side-chains 16 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 5 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 10 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.4868 r_free = 0.4868 target = 0.194761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.190131 restraints weight = 4802.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.191422 restraints weight = 3048.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.192417 restraints weight = 2025.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.192995 restraints weight = 1344.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.193484 restraints weight = 950.777| |-----------------------------------------------------------------------------| r_work (final): 0.4857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1470 moved from start: 0.6957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 1126 Z= 0.189 Angle : 0.896 9.814 1537 Z= 0.451 Chirality : 0.057 0.264 174 Planarity : 0.008 0.048 180 Dihedral : 6.737 20.856 138 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 22.93 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.94 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -1.88 (0.71), residues: 126 helix: -0.14 (0.56), residues: 82 sheet: None (None), residues: 0 loop : -3.43 (0.80), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 447 TYR 0.018 0.003 TYR A 438 PHE 0.020 0.003 PHE A 335 TRP 0.021 0.002 TRP A 334 HIS 0.010 0.004 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 1126) covalent geometry : angle 0.89599 ( 1537) hydrogen bonds : bond 0.05023 ( 55) hydrogen bonds : angle 5.82420 ( 165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.042 Fit side-chains REVERT: A 361 ILE cc_start: 0.4503 (tt) cc_final: 0.4074 (mm) REVERT: A 433 PHE cc_start: 0.0651 (t80) cc_final: 0.0410 (t80) REVERT: A 458 LEU cc_start: 0.2896 (mp) cc_final: 0.2522 (mt) REVERT: A 475 MET cc_start: 0.1303 (mmt) cc_final: 0.0839 (mmt) REVERT: A 498 MET cc_start: 0.0288 (mmm) cc_final: -0.0017 (mmm) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0288 time to fit residues: 0.6711 Evaluate side-chains 15 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 6 optimal weight: 0.0040 chunk 0 optimal weight: 5.9990 overall best weight: 2.7198 ------------------------------------------------------------------------------- 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 = 0.4934 r_free = 0.4934 target = 0.198863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.192558 restraints weight = 5414.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.192975 restraints weight = 4404.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.193506 restraints weight = 3807.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.193731 restraints weight = 3271.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.194282 restraints weight = 2982.799| |-----------------------------------------------------------------------------| r_work (final): 0.4865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1330 moved from start: 0.7584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1126 Z= 0.152 Angle : 0.847 10.305 1537 Z= 0.404 Chirality : 0.055 0.268 174 Planarity : 0.008 0.051 180 Dihedral : 6.053 21.041 138 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 23.38 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.94 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -1.42 (0.72), residues: 126 helix: 0.15 (0.55), residues: 82 sheet: None (None), residues: 0 loop : -3.10 (0.83), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 447 TYR 0.022 0.002 TYR A 438 PHE 0.018 0.002 PHE A 335 TRP 0.005 0.001 TRP A 454 HIS 0.010 0.004 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 1126) covalent geometry : angle 0.84684 ( 1537) hydrogen bonds : bond 0.04106 ( 55) hydrogen bonds : angle 5.38609 ( 165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.042 Fit side-chains REVERT: A 361 ILE cc_start: 0.4275 (tt) cc_final: 0.3859 (mm) REVERT: A 433 PHE cc_start: 0.0230 (t80) cc_final: -0.0081 (t80) REVERT: A 475 MET cc_start: 0.1035 (mmt) cc_final: 0.0821 (mmt) REVERT: A 498 MET cc_start: -0.0138 (mmm) cc_final: -0.0533 (mmp) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0289 time to fit residues: 0.7719 Evaluate side-chains 17 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 12 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 40.0000 chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 = 0.4950 r_free = 0.4950 target = 0.200997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.194917 restraints weight = 4988.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.195408 restraints weight = 4078.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.195639 restraints weight = 3482.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.196072 restraints weight = 3164.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.196200 restraints weight = 2828.833| |-----------------------------------------------------------------------------| r_work (final): 0.4875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1324 moved from start: 0.8200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1126 Z= 0.157 Angle : 0.915 15.359 1537 Z= 0.429 Chirality : 0.055 0.305 174 Planarity : 0.007 0.047 180 Dihedral : 5.735 20.366 138 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.79 % Allowed : 6.35 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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 (0.74), residues: 126 helix: 0.57 (0.57), residues: 82 sheet: None (None), residues: 0 loop : -2.76 (0.86), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 447 TYR 0.024 0.002 TYR A 438 PHE 0.020 0.002 PHE A 335 TRP 0.004 0.001 TRP A 454 HIS 0.011 0.004 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 1126) covalent geometry : angle 0.91495 ( 1537) hydrogen bonds : bond 0.03807 ( 55) hydrogen bonds : angle 5.21964 ( 165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.040 Fit side-chains REVERT: A 361 ILE cc_start: 0.4095 (tt) cc_final: 0.3660 (mm) REVERT: A 433 PHE cc_start: 0.0678 (t80) cc_final: 0.0440 (t80) REVERT: A 458 LEU cc_start: 0.2413 (mp) cc_final: 0.2068 (mt) REVERT: A 475 MET cc_start: 0.1361 (mmt) cc_final: 0.1091 (mmt) REVERT: A 498 MET cc_start: -0.0280 (mmm) cc_final: -0.0510 (mmp) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0286 time to fit residues: 0.7622 Evaluate side-chains 18 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 = 0.4958 r_free = 0.4958 target = 0.202665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.196488 restraints weight = 4913.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.197013 restraints weight = 3963.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.197586 restraints weight = 3357.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.197828 restraints weight = 2840.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.198483 restraints weight = 2552.778| |-----------------------------------------------------------------------------| r_work (final): 0.4896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1382 moved from start: 0.8496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1126 Z= 0.148 Angle : 0.776 8.624 1537 Z= 0.379 Chirality : 0.050 0.234 174 Planarity : 0.007 0.046 180 Dihedral : 5.683 20.781 138 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -0.67 (0.76), residues: 126 helix: 0.58 (0.58), residues: 82 sheet: None (None), residues: 0 loop : -2.45 (0.91), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 447 TYR 0.026 0.002 TYR A 438 PHE 0.021 0.002 PHE A 335 TRP 0.006 0.001 TRP A 334 HIS 0.011 0.004 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 1126) covalent geometry : angle 0.77607 ( 1537) hydrogen bonds : bond 0.03857 ( 55) hydrogen bonds : angle 5.25712 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 553.98 seconds wall clock time: 10 minutes 32.32 seconds (632.32 seconds total)