Starting phenix.real_space_refine on Mon Sep 23 11:32:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/09_2024/5m5h_4155.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/09_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_4155/09_2024/5m5h_4155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/09_2024/5m5h_4155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/09_2024/5m5h_4155.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m5h_4155/09_2024/5m5h_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-5461/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: 1.25, per 1000 atoms: 1.15 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: 1.30 Conformation dependent library (CDL) restraints added in 160.9 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: 1.34 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: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 10.090 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.470 ------------------------------------------------------------------------------- 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 : 0.109 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: 0.0866 time to fit residues: 2.3945 Evaluate side-chains 19 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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: 8.9990 chunk 1 optimal weight: 3.9990 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: 0.1494 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1126 Z= 0.271 Angle : 0.999 9.090 1537 Z= 0.516 Chirality : 0.055 0.148 174 Planarity : 0.010 0.062 180 Dihedral : 9.092 29.086 138 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 29.80 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.94 % Favored : 91.27 % Rotamer: Outliers : 0.86 % Allowed : 10.34 % Favored : 88.79 % 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: -4.31 (0.59), residues: 126 helix: -2.28 (0.47), residues: 75 sheet: None (None), residues: 0 loop : -3.70 (0.73), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 346 HIS 0.004 0.002 HIS A 348 PHE 0.029 0.003 PHE A 335 TYR 0.023 0.002 TYR A 464 ARG 0.004 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 19 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: A 361 ILE cc_start: 0.3731 (tt) cc_final: 0.3435 (tp) REVERT: A 441 MET cc_start: 0.2189 (mmp) cc_final: 0.1546 (ppp) REVERT: A 445 GLU cc_start: 0.1380 (OUTLIER) cc_final: -0.1756 (mm-30) outliers start: 1 outliers final: 0 residues processed: 19 average time/residue: 0.0882 time to fit residues: 2.0673 Evaluate side-chains 15 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.119 ------------------------------------------------------------------------------- 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: 8.9990 chunk 7 optimal weight: 0.1980 chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 overall best weight: 5.0388 ------------------------------------------------------------------------------- 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: 0.1426 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1126 Z= 0.235 Angle : 0.894 6.511 1537 Z= 0.455 Chirality : 0.054 0.201 174 Planarity : 0.009 0.068 180 Dihedral : 8.072 29.597 138 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 23.38 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: -3.41 (0.66), residues: 126 helix: -1.57 (0.50), residues: 78 sheet: None (None), residues: 0 loop : -3.37 (0.84), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 334 HIS 0.003 0.001 HIS A 456 PHE 0.026 0.003 PHE A 350 TYR 0.017 0.002 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 19 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 361 ILE cc_start: 0.4097 (tt) cc_final: 0.3255 (mm) REVERT: A 441 MET cc_start: 0.2109 (mmp) cc_final: 0.1634 (ppp) REVERT: A 458 LEU cc_start: 0.2697 (mp) cc_final: 0.2434 (mt) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1297 time to fit residues: 3.0002 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.0370 overall best weight: 1.9862 ------------------------------------------------------------------------------- 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: 0.1360 moved from start: 0.5524 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= 0.192 Angle : 0.823 7.478 1537 Z= 0.405 Chirality : 0.048 0.188 174 Planarity : 0.008 0.059 180 Dihedral : 6.728 22.316 138 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.79 % Allowed : 6.35 % Favored : 92.86 % 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: -2.67 (0.66), residues: 126 helix: -0.85 (0.51), residues: 79 sheet: None (None), residues: 0 loop : -3.38 (0.80), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 454 HIS 0.008 0.003 HIS A 348 PHE 0.021 0.002 PHE A 350 TYR 0.009 0.002 TYR A 516 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 20 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.117 Fit side-chains REVERT: A 361 ILE cc_start: 0.4293 (tt) cc_final: 0.3807 (mm) REVERT: A 430 MET cc_start: 0.0672 (mmp) cc_final: 0.0416 (mtp) REVERT: A 433 PHE cc_start: 0.0219 (t80) cc_final: -0.0216 (t80) REVERT: A 441 MET cc_start: 0.1960 (mmp) cc_final: 0.1604 (ppp) REVERT: A 498 MET cc_start: -0.1059 (mmm) cc_final: -0.1303 (mmm) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0758 time to fit residues: 1.9069 Evaluate side-chains 16 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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: 7.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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: 0.1393 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1126 Z= 0.228 Angle : 0.873 7.499 1537 Z= 0.438 Chirality : 0.052 0.217 174 Planarity : 0.009 0.063 180 Dihedral : 7.017 20.697 138 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.79 % Allowed : 8.73 % Favored : 90.48 % Rotamer: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % 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: -2.78 (0.65), residues: 126 helix: -0.94 (0.48), residues: 77 sheet: None (None), residues: 0 loop : -3.34 (0.86), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 334 HIS 0.008 0.004 HIS A 348 PHE 0.021 0.002 PHE A 350 TYR 0.017 0.002 TYR A 464 ARG 0.003 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 18 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.117 Fit side-chains REVERT: A 361 ILE cc_start: 0.4061 (tt) cc_final: 0.3566 (mm) REVERT: A 433 PHE cc_start: 0.0431 (t80) cc_final: 0.0050 (t80) REVERT: A 441 MET cc_start: 0.1853 (mmp) cc_final: 0.1464 (ppp) REVERT: A 458 LEU cc_start: 0.2715 (mp) cc_final: 0.2493 (mp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0764 time to fit residues: 1.7414 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 12 optimal weight: 10.0000 chunk 10 optimal weight: 0.2980 chunk 11 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 8 optimal weight: 0.2980 chunk 1 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 2 optimal weight: 6.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- 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: 0.1377 moved from start: 0.6189 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= 0.201 Angle : 0.820 7.932 1537 Z= 0.410 Chirality : 0.051 0.207 174 Planarity : 0.008 0.048 180 Dihedral : 6.527 20.465 138 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 22.47 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: -2.27 (0.66), residues: 126 helix: -0.42 (0.51), residues: 82 sheet: None (None), residues: 0 loop : -3.64 (0.75), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 454 HIS 0.009 0.004 HIS A 348 PHE 0.023 0.002 PHE A 335 TYR 0.018 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 19 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.125 Fit side-chains REVERT: A 361 ILE cc_start: 0.4161 (tt) cc_final: 0.3625 (mm) REVERT: A 433 PHE cc_start: 0.0308 (t80) cc_final: -0.0007 (t80) REVERT: A 441 MET cc_start: 0.1616 (mmp) cc_final: 0.1336 (ppp) REVERT: A 458 LEU cc_start: 0.2410 (mp) cc_final: 0.2169 (mp) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0802 time to fit residues: 1.9080 Evaluate side-chains 18 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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: 0.0980 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1360 moved from start: 0.7001 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= 0.168 Angle : 0.790 8.616 1537 Z= 0.387 Chirality : 0.049 0.223 174 Planarity : 0.008 0.049 180 Dihedral : 5.890 19.553 138 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 19.26 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: -1.35 (0.70), residues: 126 helix: 0.28 (0.54), residues: 82 sheet: None (None), residues: 0 loop : -3.24 (0.80), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 454 HIS 0.008 0.004 HIS A 348 PHE 0.017 0.002 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 18 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.119 Fit side-chains REVERT: A 433 PHE cc_start: 0.0330 (t80) cc_final: 0.0032 (t80) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0747 time to fit residues: 1.7196 Evaluate side-chains 15 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.117 ------------------------------------------------------------------------------- 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: 6.9990 chunk 1 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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: 0.1418 moved from start: 0.6928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 1126 Z= 0.232 Angle : 0.884 8.911 1537 Z= 0.444 Chirality : 0.055 0.234 174 Planarity : 0.008 0.049 180 Dihedral : 6.572 20.610 138 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.79 % Allowed : 8.73 % Favored : 90.48 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.83 (0.71), residues: 126 helix: -0.04 (0.55), residues: 82 sheet: None (None), residues: 0 loop : -3.55 (0.77), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 334 HIS 0.011 0.005 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 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 18 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.106 Fit side-chains REVERT: A 361 ILE cc_start: 0.4335 (tt) cc_final: 0.3743 (mm) REVERT: A 433 PHE cc_start: 0.0791 (t80) cc_final: 0.0411 (t80) REVERT: A 475 MET cc_start: 0.0878 (mmt) cc_final: 0.0404 (mmt) REVERT: A 498 MET cc_start: 0.1257 (mmm) cc_final: 0.0691 (mmm) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0721 time to fit residues: 1.6656 Evaluate side-chains 16 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.119 ------------------------------------------------------------------------------- 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: 2.9990 chunk 11 optimal weight: 0.0870 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- 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: 0.1358 moved from start: 0.7561 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= 0.193 Angle : 0.855 10.083 1537 Z= 0.409 Chirality : 0.055 0.245 174 Planarity : 0.008 0.050 180 Dihedral : 6.053 22.369 138 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.94 % Favored : 91.27 % 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 (0.73), residues: 126 helix: 0.40 (0.56), residues: 82 sheet: None (None), residues: 0 loop : -3.27 (0.81), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 334 HIS 0.011 0.004 HIS A 348 PHE 0.017 0.002 PHE A 335 TYR 0.021 0.002 TYR A 438 ARG 0.001 0.000 ARG A 366 *********************** 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 : 0.129 Fit side-chains REVERT: A 336 ILE cc_start: 0.1743 (mt) cc_final: 0.1182 (mm) REVERT: A 433 PHE cc_start: 0.0718 (t80) cc_final: 0.0347 (t80) REVERT: A 475 MET cc_start: 0.0995 (mmt) cc_final: 0.0629 (mmt) REVERT: A 498 MET cc_start: 0.1285 (mmm) cc_final: 0.0506 (mmp) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0708 time to fit residues: 1.7241 Evaluate side-chains 16 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.117 ------------------------------------------------------------------------------- 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: 7.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 9 optimal weight: 0.0270 chunk 12 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 overall best weight: 4.4046 ------------------------------------------------------------------------------- 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: 0.1384 moved from start: 0.7585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1126 Z= 0.224 Angle : 0.897 10.025 1537 Z= 0.436 Chirality : 0.057 0.249 174 Planarity : 0.007 0.048 180 Dihedral : 6.159 22.026 138 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.79 % Allowed : 8.73 % Favored : 90.48 % 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: -1.35 (0.74), residues: 126 helix: 0.24 (0.56), residues: 82 sheet: None (None), residues: 0 loop : -3.15 (0.87), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.011 0.005 HIS A 348 PHE 0.022 0.002 PHE A 335 TYR 0.026 0.003 TYR A 438 ARG 0.001 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 19 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.114 Fit side-chains REVERT: A 359 ILE cc_start: 0.1290 (mp) cc_final: 0.0914 (tp) REVERT: A 433 PHE cc_start: 0.1144 (t80) cc_final: 0.0641 (t80) REVERT: A 475 MET cc_start: 0.1054 (mmt) cc_final: 0.0689 (mmt) REVERT: A 498 MET cc_start: 0.0480 (mmm) cc_final: -0.0267 (mmp) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0691 time to fit residues: 1.6795 Evaluate side-chains 16 residues out of total 122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.114 ------------------------------------------------------------------------------- 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: 9.9990 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.4890 r_free = 0.4890 target = 0.197084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.192315 restraints weight = 4500.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.193490 restraints weight = 3104.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.194343 restraints weight = 2224.510| |-----------------------------------------------------------------------------| r_work (final): 0.4849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1501 moved from start: 0.7641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 1126 Z= 0.251 Angle : 0.931 7.314 1537 Z= 0.476 Chirality : 0.056 0.177 174 Planarity : 0.008 0.049 180 Dihedral : 6.705 23.590 138 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 23.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % 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: -1.32 (0.76), residues: 126 helix: 0.16 (0.58), residues: 81 sheet: None (None), residues: 0 loop : -2.83 (0.93), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 334 HIS 0.012 0.004 HIS A 348 PHE 0.024 0.003 PHE A 335 TYR 0.022 0.003 TYR A 438 ARG 0.002 0.001 ARG A 366 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 802.22 seconds wall clock time: 14 minutes 54.40 seconds (894.40 seconds total)