Starting phenix.real_space_refine on Wed Mar 5 14:17:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5m5h_4155/03_2025/5m5h_4155.cif Found real_map, /net/cci-nas-00/data/ceres_data/5m5h_4155/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5m5h_4155/03_2025/5m5h_4155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5m5h_4155/03_2025/5m5h_4155.map" model { file = "/net/cci-nas-00/data/ceres_data/5m5h_4155/03_2025/5m5h_4155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5m5h_4155/03_2025/5m5h_4155.cif" } resolution = 4.5 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= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 1.33, per 1000 atoms: 1.22 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: 1.67 Conformation dependent library (CDL) restraints added in 130.1 milliseconds 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: 0.12 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: 0.23 Time building geometry restraints manager: 1.73 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: 3.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 10.180 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.920 ------------------------------------------------------------------------------- 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= 0.465 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 (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: -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 TRP 0.022 0.005 TRP A 346 HIS 0.005 0.002 HIS A 348 PHE 0.038 0.006 PHE A 424 TYR 0.050 0.005 TYR A 517 ARG 0.007 0.003 ARG A 447 *********************** 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 : 0.123 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: 0.0894 time to fit residues: 2.4792 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 : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 10 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 6 optimal weight: 50.0000 chunk 7 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 0.0870 chunk 1 optimal weight: 3.9990 overall best weight: 5.2166 ------------------------------------------------------------------------------- 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 = 0.4994 r_free = 0.4994 target = 0.200932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.193617 restraints weight = 4376.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.195013 restraints weight = 3312.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.195695 restraints weight = 2599.047| |-----------------------------------------------------------------------------| r_work (final): 0.4916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1553 moved from start: 0.3462 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= 0.249 Angle : 0.965 8.214 1537 Z= 0.496 Chirality : 0.055 0.213 174 Planarity : 0.010 0.062 180 Dihedral : 8.678 29.012 138 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 26.13 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.94 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.62), residues: 126 helix: -2.09 (0.48), residues: 75 sheet: None (None), residues: 0 loop : -3.59 (0.78), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 346 HIS 0.002 0.001 HIS A 348 PHE 0.027 0.003 PHE A 335 TYR 0.018 0.002 TYR A 464 ARG 0.003 0.001 ARG A 447 *********************** 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 : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 ILE cc_start: 0.3803 (tt) cc_final: 0.2980 (mm) REVERT: A 441 MET cc_start: 0.2750 (mmp) cc_final: 0.2047 (ppp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0761 time to fit residues: 1.7372 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 : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 4 optimal weight: 0.0770 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 overall best weight: 3.6144 ------------------------------------------------------------------------------- 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 = 0.4983 r_free = 0.4983 target = 0.201148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.194187 restraints weight = 4409.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4892 r_free = 0.4892 target = 0.195095 restraints weight = 3564.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.195828 restraints weight = 2981.329| |-----------------------------------------------------------------------------| r_work (final): 0.4904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1474 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1126 Z= 0.220 Angle : 0.861 6.538 1537 Z= 0.437 Chirality : 0.052 0.193 174 Planarity : 0.009 0.067 180 Dihedral : 7.683 28.785 138 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 1.59 % Allowed : 9.52 % Favored : 88.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.67), residues: 126 helix: -1.36 (0.51), residues: 78 sheet: None (None), residues: 0 loop : -3.05 (0.88), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 334 HIS 0.003 0.001 HIS A 456 PHE 0.026 0.003 PHE A 350 TYR 0.014 0.002 TYR A 464 ARG 0.003 0.001 ARG A 447 *********************** 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 19 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.105 Fit side-chains REVERT: A 361 ILE cc_start: 0.4203 (tt) cc_final: 0.3388 (mm) REVERT: A 433 PHE cc_start: -0.0304 (t80) cc_final: -0.0667 (t80) REVERT: A 441 MET cc_start: 0.2566 (mmp) cc_final: 0.1755 (ppp) REVERT: A 458 LEU cc_start: 0.2996 (mp) cc_final: 0.2723 (mt) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0773 time to fit residues: 1.8393 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 : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 4 optimal weight: 0.0010 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 0.0270 chunk 11 optimal weight: 0.0970 chunk 8 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 overall best weight: 0.3844 ------------------------------------------------------------------------------- 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 = 0.4975 r_free = 0.4975 target = 0.201392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.195297 restraints weight = 4456.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.196705 restraints weight = 3158.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.197680 restraints weight = 2322.072| |-----------------------------------------------------------------------------| r_work (final): 0.4922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1419 moved from start: 0.5918 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= 0.188 Angle : 0.805 7.967 1537 Z= 0.391 Chirality : 0.048 0.182 174 Planarity : 0.008 0.056 180 Dihedral : 6.314 20.558 138 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.79 % Allowed : 8.73 % Favored : 90.48 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % 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: -2.11 (0.67), residues: 126 helix: -0.53 (0.51), residues: 79 sheet: None (None), residues: 0 loop : -2.91 (0.83), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 454 HIS 0.007 0.003 HIS A 348 PHE 0.017 0.002 PHE A 350 TYR 0.007 0.001 TYR A 516 ARG 0.001 0.001 ARG A 447 *********************** 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 18 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: A 361 ILE cc_start: 0.4331 (tt) cc_final: 0.3750 (mm) REVERT: A 441 MET cc_start: 0.2318 (mmp) cc_final: 0.1657 (ppp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0736 time to fit residues: 1.6846 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 : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 0 optimal weight: 30.0000 chunk 11 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 1 optimal weight: 0.0770 chunk 4 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 overall best weight: 5.0146 ------------------------------------------------------------------------------- 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 = 0.4956 r_free = 0.4956 target = 0.199830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.193583 restraints weight = 4311.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4892 r_free = 0.4892 target = 0.194851 restraints weight = 3183.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.195829 restraints weight = 2423.417| |-----------------------------------------------------------------------------| r_work (final): 0.4907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1450 moved from start: 0.5793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1126 Z= 0.213 Angle : 0.838 7.369 1537 Z= 0.418 Chirality : 0.050 0.210 174 Planarity : 0.008 0.060 180 Dihedral : 6.544 18.991 138 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 22.01 Ramachandran Plot: Outliers : 0.79 % Allowed : 8.73 % Favored : 90.48 % 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 (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: -2.38 (0.65), residues: 126 helix: -0.61 (0.50), residues: 79 sheet: None (None), residues: 0 loop : -3.27 (0.80), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 334 HIS 0.009 0.004 HIS A 348 PHE 0.020 0.002 PHE A 350 TYR 0.017 0.003 TYR A 464 ARG 0.002 0.001 ARG A 447 *********************** 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 20 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 361 ILE cc_start: 0.4223 (tt) cc_final: 0.3699 (mm) REVERT: A 441 MET cc_start: 0.1879 (mmp) cc_final: 0.1359 (ppp) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0762 time to fit residues: 1.9471 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 : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 5 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.195329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.190279 restraints weight = 4645.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.191389 restraints weight = 3408.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4892 r_free = 0.4892 target = 0.192303 restraints weight = 2552.132| |-----------------------------------------------------------------------------| r_work (final): 0.4897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1397 moved from start: 0.6360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1126 Z= 0.178 Angle : 0.825 8.081 1537 Z= 0.403 Chirality : 0.051 0.212 174 Planarity : 0.008 0.047 180 Dihedral : 6.055 16.520 138 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.14 % Favored : 92.06 % 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 (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: -1.84 (0.68), residues: 126 helix: -0.20 (0.52), residues: 82 sheet: None (None), residues: 0 loop : -3.20 (0.82), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 454 HIS 0.008 0.003 HIS A 348 PHE 0.018 0.002 PHE A 335 TYR 0.017 0.002 TYR A 438 ARG 0.001 0.000 ARG A 447 *********************** 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 20 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.104 Fit side-chains REVERT: A 361 ILE cc_start: 0.3467 (tt) cc_final: 0.2963 (mm) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0681 time to fit residues: 1.7086 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 : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 0 optimal weight: 30.0000 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 0.0870 chunk 7 optimal weight: 0.2980 overall best weight: 1.0562 ------------------------------------------------------------------------------- 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 = 0.4941 r_free = 0.4941 target = 0.197855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.191126 restraints weight = 5290.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.191642 restraints weight = 4546.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.192071 restraints weight = 3924.258| |-----------------------------------------------------------------------------| r_work (final): 0.4868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1353 moved from start: 0.6985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1126 Z= 0.183 Angle : 0.780 8.162 1537 Z= 0.377 Chirality : 0.048 0.204 174 Planarity : 0.008 0.048 180 Dihedral : 5.750 19.454 138 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.14 % 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 (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: -1.23 (0.71), residues: 126 helix: 0.15 (0.54), residues: 82 sheet: None (None), residues: 0 loop : -2.68 (0.88), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 334 HIS 0.009 0.004 HIS A 348 PHE 0.020 0.001 PHE A 335 TYR 0.017 0.002 TYR A 438 ARG 0.001 0.000 ARG A 366 *********************** 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 20 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.124 Fit side-chains REVERT: A 361 ILE cc_start: 0.4337 (tt) cc_final: 0.3870 (mm) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0741 time to fit residues: 1.8754 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 : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 10 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 6 optimal weight: 0.0050 chunk 7 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 9 optimal weight: 5.9990 overall best weight: 4.1400 ------------------------------------------------------------------------------- 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 = 0.4980 r_free = 0.4980 target = 0.204086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.198382 restraints weight = 4696.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.199715 restraints weight = 3266.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4933 r_free = 0.4933 target = 0.200639 restraints weight = 2353.797| |-----------------------------------------------------------------------------| r_work (final): 0.4933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1491 moved from start: 0.7158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1126 Z= 0.228 Angle : 0.825 8.953 1537 Z= 0.405 Chirality : 0.051 0.217 174 Planarity : 0.007 0.049 180 Dihedral : 5.844 17.322 138 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.52 % Favored : 89.68 % 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 (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: -1.53 (0.70), residues: 126 helix: 0.09 (0.54), residues: 82 sheet: None (None), residues: 0 loop : -3.21 (0.83), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.009 0.004 HIS A 348 PHE 0.020 0.002 PHE A 335 TYR 0.016 0.003 TYR A 438 ARG 0.002 0.001 ARG A 447 *********************** 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 19 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.117 Fit side-chains REVERT: A 361 ILE cc_start: 0.4560 (tt) cc_final: 0.3936 (mm) REVERT: A 475 MET cc_start: 0.1528 (mmt) cc_final: 0.1207 (mmt) REVERT: A 498 MET cc_start: 0.0619 (mmm) cc_final: 0.0000 (mmt) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0728 time to fit residues: 1.7528 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 : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 0.0870 chunk 1 optimal weight: 0.0770 chunk 4 optimal weight: 0.0370 chunk 11 optimal weight: 0.0040 chunk 10 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 30.0000 overall best weight: 0.6408 ------------------------------------------------------------------------------- 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 = 0.4971 r_free = 0.4971 target = 0.205487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.198422 restraints weight = 4581.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.199553 restraints weight = 3557.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.200696 restraints weight = 2917.325| |-----------------------------------------------------------------------------| r_work (final): 0.4919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1428 moved from start: 0.7920 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= 0.190 Angle : 0.792 8.440 1537 Z= 0.380 Chirality : 0.050 0.200 174 Planarity : 0.008 0.050 180 Dihedral : 5.676 20.183 138 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 18.34 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 (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 (0.74), residues: 126 helix: 0.48 (0.55), residues: 83 sheet: None (None), residues: 0 loop : -2.63 (0.93), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 334 HIS 0.010 0.004 HIS A 348 PHE 0.012 0.001 PHE A 335 TYR 0.020 0.002 TYR A 438 ARG 0.001 0.000 ARG A 447 *********************** 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 : 0.117 Fit side-chains REVERT: A 344 LEU cc_start: 0.4025 (tp) cc_final: 0.3811 (tp) REVERT: A 361 ILE cc_start: 0.3866 (tt) cc_final: 0.3462 (mm) REVERT: A 366 ARG cc_start: 0.1898 (mmm160) cc_final: 0.1467 (tmt170) REVERT: A 498 MET cc_start: 0.0073 (mmm) cc_final: -0.0379 (mmt) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1286 time to fit residues: 3.0987 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 : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.199365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.195596 restraints weight = 4543.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.196639 restraints weight = 3069.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.197383 restraints weight = 2097.414| |-----------------------------------------------------------------------------| r_work (final): 0.4908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1452 moved from start: 0.7784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1126 Z= 0.253 Angle : 0.914 7.733 1537 Z= 0.452 Chirality : 0.056 0.186 174 Planarity : 0.008 0.050 180 Dihedral : 6.130 18.537 138 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 23.84 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 (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: -1.74 (0.71), residues: 126 helix: -0.08 (0.55), residues: 83 sheet: None (None), residues: 0 loop : -3.34 (0.81), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 346 HIS 0.009 0.004 HIS A 348 PHE 0.025 0.003 PHE A 335 TYR 0.028 0.004 TYR A 438 ARG 0.003 0.001 ARG A 447 ********************** 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 20 residues out of total 122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.122 Fit side-chains REVERT: A 361 ILE cc_start: 0.3949 (tt) cc_final: 0.3508 (mm) REVERT: A 458 LEU cc_start: 0.2618 (mp) cc_final: 0.2322 (mt) REVERT: A 475 MET cc_start: 0.1555 (mmt) cc_final: 0.1202 (mmt) REVERT: A 498 MET cc_start: 0.0629 (mmm) cc_final: 0.0292 (mmp) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0685 time to fit residues: 1.7503 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 : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 11 optimal weight: 40.0000 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 0.0770 chunk 10 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- 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 = 0.4893 r_free = 0.4893 target = 0.196718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.190792 restraints weight = 4882.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.191713 restraints weight = 3696.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.192726 restraints weight = 2930.494| |-----------------------------------------------------------------------------| r_work (final): 0.4827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1369 moved from start: 0.8049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1126 Z= 0.234 Angle : 0.848 7.747 1537 Z= 0.423 Chirality : 0.052 0.168 174 Planarity : 0.008 0.049 180 Dihedral : 6.081 17.840 138 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % 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 (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: -1.71 (0.72), residues: 126 helix: -0.13 (0.55), residues: 83 sheet: None (None), residues: 0 loop : -3.15 (0.84), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 354 HIS 0.011 0.004 HIS A 348 PHE 0.020 0.002 PHE A 335 TYR 0.022 0.003 TYR A 438 ARG 0.001 0.001 ARG A 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 949.82 seconds wall clock time: 17 minutes 7.92 seconds (1027.92 seconds total)