Starting phenix.real_space_refine on Fri Apr 5 12:01:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/04_2024/5m5h_4155.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/04_2024/5m5h_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/04_2024/5m5h_4155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/04_2024/5m5h_4155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/04_2024/5m5h_4155.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/04_2024/5m5h_4155.pdb" } 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 Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 1.12, per 1000 atoms: 1.03 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 - 3.50 Amino acid : False - 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: 0.36 Conformation dependent library (CDL) restraints added in 298.3 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: 0.11 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: 0.24 Time building geometry restraints manager: 0.41 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: 97.96 - 105.20: 36 105.20 - 112.45: 521 112.45 - 119.70: 429 119.70 - 126.94: 527 126.94 - 134.19: 24 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 2.520 nonbonded pdb=" O LEU A 344 " pdb=" ND1 HIS A 348 " model vdw 2.310 2.520 nonbonded pdb=" O PHE A 506 " pdb=" N PHE A 509 " model vdw 2.361 2.520 nonbonded pdb=" O ILE A 364 " pdb=" N GLY A 367 " model vdw 2.381 2.520 nonbonded pdb=" O LEU A 426 " pdb=" N GLN A 429 " model vdw 2.384 2.520 ... (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: 5.190 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: 17.430 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.420 Find NCS groups from input model: 0.030 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.920 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.112 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: 0.0794 time to fit residues: 2.2056 Evaluate side-chains 19 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.093 ------------------------------------------------------------------------------- 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: 6.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 1 optimal weight: 0.0980 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1458 moved from start: 0.3604 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= 0.239 Angle : 0.941 7.975 1537 Z= 0.485 Chirality : 0.054 0.147 174 Planarity : 0.009 0.060 180 Dihedral : 8.568 29.085 138 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 27.51 Ramachandran Plot: Outliers : 0.79 % Allowed : 8.73 % Favored : 90.48 % 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 (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: -4.09 (0.61), residues: 126 helix: -2.08 (0.48), residues: 76 sheet: None (None), residues: 0 loop : -3.68 (0.76), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 354 HIS 0.003 0.002 HIS A 348 PHE 0.031 0.003 PHE A 335 TYR 0.016 0.002 TYR A 464 ARG 0.002 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 20 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 ILE cc_start: 0.3907 (tt) cc_final: 0.3137 (mm) REVERT: A 441 MET cc_start: 0.2471 (mmp) cc_final: 0.1861 (ppp) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0762 time to fit residues: 1.9017 Evaluate side-chains 15 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 5 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1453 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1126 Z= 0.271 Angle : 0.934 6.349 1537 Z= 0.484 Chirality : 0.056 0.203 174 Planarity : 0.009 0.069 180 Dihedral : 8.404 29.488 138 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 25.68 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: -3.66 (0.63), residues: 126 helix: -1.70 (0.48), residues: 78 sheet: None (None), residues: 0 loop : -3.62 (0.79), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 334 HIS 0.003 0.002 HIS A 456 PHE 0.026 0.003 PHE A 350 TYR 0.025 0.003 TYR A 464 ARG 0.004 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 18 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: A 361 ILE cc_start: 0.4074 (tt) cc_final: 0.3697 (tp) REVERT: A 441 MET cc_start: 0.2459 (mmp) cc_final: 0.1804 (ppp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0732 time to fit residues: 1.6767 Evaluate side-chains 16 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 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 11 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 7 optimal weight: 0.0040 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1398 moved from start: 0.5389 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= 0.203 Angle : 0.826 7.251 1537 Z= 0.413 Chirality : 0.049 0.194 174 Planarity : 0.008 0.060 180 Dihedral : 7.011 24.632 138 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 25.22 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.94 % Favored : 91.27 % 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: -2.90 (0.67), residues: 126 helix: -1.11 (0.51), residues: 78 sheet: None (None), residues: 0 loop : -3.29 (0.86), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 354 HIS 0.002 0.001 HIS A 456 PHE 0.022 0.002 PHE A 350 TYR 0.010 0.002 TYR A 438 ARG 0.001 0.000 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 17 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.106 Fit side-chains REVERT: A 361 ILE cc_start: 0.4262 (tt) cc_final: 0.3757 (mm) REVERT: A 441 MET cc_start: 0.2025 (mmp) cc_final: 0.1686 (ppp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0768 time to fit residues: 1.6870 Evaluate side-chains 15 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 6 optimal weight: 30.0000 chunk 1 optimal weight: 0.3980 chunk 9 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1357 moved from start: 0.6265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1126 Z= 0.176 Angle : 0.793 7.710 1537 Z= 0.386 Chirality : 0.049 0.205 174 Planarity : 0.008 0.061 180 Dihedral : 6.334 21.883 138 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.52 % 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 (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: -2.05 (0.68), residues: 126 helix: -0.22 (0.53), residues: 79 sheet: None (None), residues: 0 loop : -3.43 (0.76), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 354 HIS 0.003 0.001 HIS A 456 PHE 0.019 0.002 PHE A 335 TYR 0.017 0.002 TYR A 438 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 19 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.119 Fit side-chains REVERT: A 361 ILE cc_start: 0.4120 (tt) cc_final: 0.3594 (mm) REVERT: A 433 PHE cc_start: 0.0226 (t80) cc_final: -0.0116 (t80) REVERT: A 441 MET cc_start: 0.1890 (mmp) cc_final: 0.1539 (ppp) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0752 time to fit residues: 1.8075 Evaluate side-chains 17 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 12 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1386 moved from start: 0.6561 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= 0.199 Angle : 0.815 7.640 1537 Z= 0.403 Chirality : 0.050 0.193 174 Planarity : 0.008 0.045 180 Dihedral : 6.197 20.533 138 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.94 % Favored : 91.27 % 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 (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: -1.80 (0.70), residues: 126 helix: 0.04 (0.55), residues: 82 sheet: None (None), residues: 0 loop : -3.66 (0.74), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 454 HIS 0.004 0.002 HIS A 456 PHE 0.023 0.002 PHE A 335 TYR 0.020 0.002 TYR A 438 ARG 0.000 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 19 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.110 Fit side-chains REVERT: A 361 ILE cc_start: 0.4143 (tt) cc_final: 0.3588 (mm) REVERT: A 433 PHE cc_start: 0.0461 (t80) cc_final: 0.0082 (t80) REVERT: A 441 MET cc_start: 0.1897 (mmp) cc_final: 0.1489 (ppp) REVERT: A 458 LEU cc_start: 0.2447 (mp) cc_final: 0.2231 (mp) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0757 time to fit residues: 1.8302 Evaluate side-chains 19 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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: 5.9990 chunk 4 optimal weight: 0.0870 chunk 1 optimal weight: 10.0000 chunk 9 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 6 optimal weight: 0.0980 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 overall best weight: 2.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1353 moved from start: 0.7069 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= 0.193 Angle : 0.784 8.852 1537 Z= 0.385 Chirality : 0.050 0.236 174 Planarity : 0.008 0.049 180 Dihedral : 5.961 20.174 138 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.79 % Allowed : 8.73 % Favored : 90.48 % 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 (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: -1.19 (0.72), residues: 126 helix: 0.49 (0.56), residues: 83 sheet: None (None), residues: 0 loop : -3.48 (0.76), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 454 HIS 0.004 0.001 HIS A 456 PHE 0.018 0.002 PHE A 335 TYR 0.018 0.002 TYR A 438 ARG 0.000 0.000 ARG A 447 *********************** 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 fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.114 Fit side-chains REVERT: A 361 ILE cc_start: 0.3983 (tt) cc_final: 0.3483 (mm) REVERT: A 433 PHE cc_start: 0.0590 (t80) cc_final: 0.0178 (t80) REVERT: A 441 MET cc_start: 0.1621 (mmp) cc_final: 0.1272 (ppp) REVERT: A 458 LEU cc_start: 0.2225 (mp) cc_final: 0.2005 (mp) REVERT: A 498 MET cc_start: 0.0974 (mmm) cc_final: 0.0180 (mmp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0759 time to fit residues: 1.7435 Evaluate side-chains 16 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 0 optimal weight: 40.0000 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 6 optimal weight: 0.1980 chunk 9 optimal weight: 3.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1385 moved from start: 0.7068 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= 0.212 Angle : 0.832 8.995 1537 Z= 0.409 Chirality : 0.051 0.232 174 Planarity : 0.008 0.046 180 Dihedral : 6.124 21.240 138 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 21.09 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 (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: -1.14 (0.73), residues: 126 helix: 0.54 (0.57), residues: 82 sheet: None (None), residues: 0 loop : -3.38 (0.77), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 334 HIS 0.003 0.001 HIS A 456 PHE 0.019 0.002 PHE A 335 TYR 0.014 0.002 TYR A 438 ARG 0.001 0.000 ARG A 366 *********************** 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 17 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.102 Fit side-chains REVERT: A 361 ILE cc_start: 0.4235 (tt) cc_final: 0.3861 (mm) REVERT: A 433 PHE cc_start: 0.0230 (t80) cc_final: -0.0175 (t80) REVERT: A 441 MET cc_start: 0.1662 (mmp) cc_final: 0.1262 (ppp) REVERT: A 475 MET cc_start: 0.1450 (mmt) cc_final: 0.1082 (mmt) REVERT: A 498 MET cc_start: 0.0827 (mmm) cc_final: 0.0033 (mmp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0756 time to fit residues: 1.6400 Evaluate side-chains 16 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 10 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 0.0010 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 overall best weight: 4.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1370 moved from start: 0.7293 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= 0.224 Angle : 0.842 10.018 1537 Z= 0.419 Chirality : 0.055 0.239 174 Planarity : 0.008 0.045 180 Dihedral : 6.290 22.467 138 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 23.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % 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 (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: -1.33 (0.73), residues: 126 helix: 0.38 (0.58), residues: 81 sheet: None (None), residues: 0 loop : -3.36 (0.75), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 334 HIS 0.003 0.002 HIS A 456 PHE 0.021 0.002 PHE A 335 TYR 0.022 0.003 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 19 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.119 Fit side-chains REVERT: A 361 ILE cc_start: 0.4476 (tt) cc_final: 0.4085 (mm) REVERT: A 441 MET cc_start: 0.1655 (mmp) cc_final: 0.1338 (ppp) REVERT: A 458 LEU cc_start: 0.2701 (mp) cc_final: 0.2500 (mp) REVERT: A 475 MET cc_start: 0.1391 (mmt) cc_final: 0.1069 (mmt) REVERT: A 498 MET cc_start: 0.1003 (mmm) cc_final: 0.0341 (mmp) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0730 time to fit residues: 1.7738 Evaluate side-chains 18 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 5 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 9 optimal weight: 0.0030 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 overall best weight: 2.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1341 moved from start: 0.7606 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= 0.197 Angle : 0.798 8.394 1537 Z= 0.400 Chirality : 0.049 0.143 174 Planarity : 0.007 0.047 180 Dihedral : 6.072 21.281 138 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.75), residues: 126 helix: 0.54 (0.59), residues: 82 sheet: None (None), residues: 0 loop : -3.04 (0.81), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 508 HIS 0.002 0.001 HIS A 456 PHE 0.031 0.002 PHE A 506 TYR 0.023 0.002 TYR A 438 ARG 0.000 0.000 ARG A 366 ********************** 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 18 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.084 Fit side-chains REVERT: A 361 ILE cc_start: 0.4478 (tt) cc_final: 0.4019 (mm) REVERT: A 441 MET cc_start: 0.1767 (mmp) cc_final: 0.1442 (ppp) REVERT: A 458 LEU cc_start: 0.2537 (mp) cc_final: 0.2332 (mp) REVERT: A 498 MET cc_start: 0.0876 (mmm) cc_final: 0.0218 (mmp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0528 time to fit residues: 1.2284 Evaluate side-chains 15 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.084 ------------------------------------------------------------------------------- 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: 0.0020 chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 0.0070 chunk 0 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 6 optimal weight: 0.0170 chunk 10 optimal weight: 6.9990 overall best weight: 2.6048 ------------------------------------------------------------------------------- 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 = 0.4997 r_free = 0.4997 target = 0.206800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.200400 restraints weight = 4596.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.201548 restraints weight = 3376.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4943 r_free = 0.4943 target = 0.202594 restraints weight = 2624.614| |-----------------------------------------------------------------------------| r_work (final): 0.4945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1433 moved from start: 0.8287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1126 Z= 0.192 Angle : 0.778 8.509 1537 Z= 0.385 Chirality : 0.048 0.131 174 Planarity : 0.007 0.044 180 Dihedral : 6.022 23.396 138 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % 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 (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: -0.80 (0.75), residues: 126 helix: 0.64 (0.59), residues: 82 sheet: None (None), residues: 0 loop : -2.87 (0.83), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 454 HIS 0.001 0.000 HIS A 456 PHE 0.018 0.002 PHE A 335 TYR 0.023 0.002 TYR A 438 ARG 0.000 0.000 ARG A 366 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 838.03 seconds wall clock time: 17 minutes 2.56 seconds (1022.56 seconds total)