Starting phenix.real_space_refine on Wed Jan 17 18:10:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rug_24705/01_2024/7rug_24705.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rug_24705/01_2024/7rug_24705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rug_24705/01_2024/7rug_24705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rug_24705/01_2024/7rug_24705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rug_24705/01_2024/7rug_24705.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rug_24705/01_2024/7rug_24705.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 19 5.16 5 C 1815 2.51 5 N 413 2.21 5 O 454 1.98 5 H 2728 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 5429 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5151 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 8, 'TRANS': 306} Chain breaks: 4 Chain: "L" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 278 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Time building chain proxies: 2.96, per 1000 atoms: 0.55 Number of scatterers: 5429 At special positions: 0 Unit cell: (70.35, 82.41, 67.335, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 O 454 8.00 N 413 7.00 C 1815 6.00 H 2728 1.00 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: 4.30 Conformation dependent library (CDL) restraints added in 714.1 milliseconds 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 630 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 1 sheets defined 85.8% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 34 through 57 Processing helix chain 'A' and resid 58 through 67 removed outlier: 3.639A pdb=" N GLU A 62 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR A 63 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 116 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 133 through 150 removed outlier: 3.777A pdb=" N PHE A 149 " --> pdb=" O MET A 145 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 197 Processing helix chain 'A' and resid 198 through 229 removed outlier: 3.685A pdb=" N TRP A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR A 229 " --> pdb=" O TYR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 255 removed outlier: 3.521A pdb=" N SER A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 268 through 289 removed outlier: 3.880A pdb=" N SER A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 404 through 424 Processing helix chain 'A' and resid 440 through 463 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'L' and resid 113 through 117 removed outlier: 3.535A pdb=" N ARG L 117 " --> pdb=" O GLY L 114 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 105 through 106 removed outlier: 3.989A pdb=" N SER L 112 " --> pdb=" O ARG L 105 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 642 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: 1.71 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 2723 1.03 - 1.23: 5 1.23 - 1.42: 1231 1.42 - 1.61: 1518 1.61 - 1.81: 31 Bond restraints: 5508 Sorted by residual: bond pdb=" CA ILE A 151 " pdb=" CB ILE A 151 " ideal model delta sigma weight residual 1.537 1.525 0.012 1.29e-02 6.01e+03 9.35e-01 bond pdb=" C TRP L 108 " pdb=" N TYR L 109 " ideal model delta sigma weight residual 1.335 1.323 0.012 1.35e-02 5.49e+03 7.39e-01 bond pdb=" CB TRP L 108 " pdb=" CG TRP L 108 " ideal model delta sigma weight residual 1.498 1.477 0.021 3.10e-02 1.04e+03 4.63e-01 bond pdb=" CG LEU A 206 " pdb=" CD2 LEU A 206 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 3.86e-01 bond pdb=" CA MET A 105 " pdb=" HA MET A 105 " ideal model delta sigma weight residual 0.970 0.958 0.012 2.00e-02 2.50e+03 3.51e-01 ... (remaining 5503 not shown) Histogram of bond angle deviations from ideal: 100.25 - 107.00: 86 107.00 - 113.75: 6311 113.75 - 120.50: 2060 120.50 - 127.25: 1418 127.25 - 134.00: 37 Bond angle restraints: 9912 Sorted by residual: angle pdb=" C ILE A 107 " pdb=" N PHE A 108 " pdb=" CA PHE A 108 " ideal model delta sigma weight residual 120.29 116.85 3.44 1.42e+00 4.96e-01 5.87e+00 angle pdb=" N TYR L 103 " pdb=" CA TYR L 103 " pdb=" C TYR L 103 " ideal model delta sigma weight residual 108.24 111.62 -3.38 1.81e+00 3.05e-01 3.48e+00 angle pdb=" N VAL A 462 " pdb=" CA VAL A 462 " pdb=" C VAL A 462 " ideal model delta sigma weight residual 111.81 113.20 -1.39 8.60e-01 1.35e+00 2.62e+00 angle pdb=" N PHE A 108 " pdb=" CA PHE A 108 " pdb=" CB PHE A 108 " ideal model delta sigma weight residual 110.16 112.48 -2.32 1.48e+00 4.57e-01 2.46e+00 angle pdb=" CA PHE A 108 " pdb=" CB PHE A 108 " pdb=" CG PHE A 108 " ideal model delta sigma weight residual 113.80 115.34 -1.54 1.00e+00 1.00e+00 2.39e+00 ... (remaining 9907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.36: 2347 15.36 - 30.72: 167 30.72 - 46.08: 41 46.08 - 61.44: 14 61.44 - 76.80: 4 Dihedral angle restraints: 2573 sinusoidal: 1291 harmonic: 1282 Sorted by residual: dihedral pdb=" CB MET A 105 " pdb=" CG MET A 105 " pdb=" SD MET A 105 " pdb=" CE MET A 105 " ideal model delta sinusoidal sigma weight residual 60.00 107.71 -47.71 3 1.50e+01 4.44e-03 8.53e+00 dihedral pdb=" CB MET A 116 " pdb=" CG MET A 116 " pdb=" SD MET A 116 " pdb=" CE MET A 116 " ideal model delta sinusoidal sigma weight residual 60.00 106.93 -46.93 3 1.50e+01 4.44e-03 8.41e+00 dihedral pdb=" CA ASP A 181 " pdb=" CB ASP A 181 " pdb=" CG ASP A 181 " pdb=" OD1 ASP A 181 " ideal model delta sinusoidal sigma weight residual -30.00 -79.34 49.34 1 2.00e+01 2.50e-03 8.36e+00 ... (remaining 2570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 299 0.029 - 0.058: 75 0.058 - 0.087: 37 0.087 - 0.116: 14 0.116 - 0.145: 2 Chirality restraints: 427 Sorted by residual: chirality pdb=" CG LEU A 417 " pdb=" CB LEU A 417 " pdb=" CD1 LEU A 417 " pdb=" CD2 LEU A 417 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA ILE A 151 " pdb=" N ILE A 151 " pdb=" C ILE A 151 " pdb=" CB ILE A 151 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA PRO A 265 " pdb=" N PRO A 265 " pdb=" C PRO A 265 " pdb=" CB PRO A 265 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.23e-01 ... (remaining 424 not shown) Planarity restraints: 757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 105 " -0.138 9.50e-02 1.11e+02 4.61e-02 2.57e+00 pdb=" NE ARG L 105 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG L 105 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG L 105 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG L 105 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG L 105 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG L 105 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG L 105 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG L 105 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 112 " 0.008 2.00e-02 2.50e+03 8.23e-03 2.03e+00 pdb=" CG PHE A 112 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 112 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 112 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 112 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 112 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 112 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 112 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE A 112 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE A 112 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE A 112 " 0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 112 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 108 " 0.014 2.00e-02 2.50e+03 7.67e-03 1.77e+00 pdb=" CG PHE A 108 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 108 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 108 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 108 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 108 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 108 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 108 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 108 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 108 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 108 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 108 " 0.001 2.00e-02 2.50e+03 ... (remaining 754 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 639 2.25 - 2.83: 12403 2.83 - 3.42: 14521 3.42 - 4.01: 18216 4.01 - 4.60: 28153 Nonbonded interactions: 73932 Sorted by model distance: nonbonded pdb=" O ASP A 292 " pdb=" H ASN A 296 " model vdw 1.657 1.850 nonbonded pdb=" O CYS A 413 " pdb=" HG SER A 416 " model vdw 1.668 1.850 nonbonded pdb=" O TYR A 418 " pdb=" HG1 THR A 422 " model vdw 1.708 1.850 nonbonded pdb=" O ILE A 447 " pdb=" HG SER A 450 " model vdw 1.724 1.850 nonbonded pdb=" O SER A 288 " pdb="HD21 ASN A 296 " model vdw 1.728 1.850 ... (remaining 73927 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: 0.560 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: 0.080 Extract box with map and model: 1.950 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 21.610 Find NCS groups from input model: 0.090 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 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 : 0.003 0.021 2780 Z= 0.177 Angle : 0.498 4.253 3774 Z= 0.284 Chirality : 0.035 0.145 427 Planarity : 0.004 0.061 440 Dihedral : 12.584 76.800 950 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.46), residues: 319 helix: 2.50 (0.30), residues: 257 sheet: None (None), residues: 0 loop : 0.77 (0.90), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 284 HIS 0.005 0.001 HIS A 409 PHE 0.024 0.002 PHE A 112 TYR 0.013 0.001 TYR A 225 ARG 0.009 0.001 ARG L 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.9323 (tm-30) cc_final: 0.8826 (tm-30) REVERT: A 244 ASN cc_start: 0.8707 (m-40) cc_final: 0.8365 (m-40) REVERT: A 411 MET cc_start: 0.8543 (mtm) cc_final: 0.8319 (mtt) REVERT: A 420 MET cc_start: 0.8259 (ttt) cc_final: 0.8049 (ttt) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2430 time to fit residues: 24.6149 Evaluate side-chains 65 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2780 Z= 0.181 Angle : 0.461 4.067 3774 Z= 0.266 Chirality : 0.034 0.115 427 Planarity : 0.004 0.033 440 Dihedral : 3.511 14.648 359 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.46), residues: 319 helix: 2.75 (0.30), residues: 259 sheet: None (None), residues: 0 loop : 0.80 (0.91), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 186 HIS 0.003 0.001 HIS A 184 PHE 0.026 0.001 PHE A 108 TYR 0.008 0.001 TYR A 225 ARG 0.005 0.000 ARG L 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.9319 (tm-30) cc_final: 0.8840 (tm-30) REVERT: A 188 GLU cc_start: 0.9061 (pt0) cc_final: 0.8382 (pt0) REVERT: A 244 ASN cc_start: 0.8678 (m-40) cc_final: 0.8362 (m-40) REVERT: A 411 MET cc_start: 0.8584 (mtm) cc_final: 0.8379 (mtt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1991 time to fit residues: 20.0939 Evaluate side-chains 70 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 264 GLN ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2780 Z= 0.139 Angle : 0.441 3.906 3774 Z= 0.248 Chirality : 0.034 0.111 427 Planarity : 0.003 0.026 440 Dihedral : 3.417 13.212 359 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.81 (0.46), residues: 319 helix: 2.93 (0.30), residues: 259 sheet: None (None), residues: 0 loop : 0.62 (0.90), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 186 HIS 0.007 0.002 HIS A 409 PHE 0.023 0.001 PHE A 112 TYR 0.007 0.001 TYR A 350 ARG 0.002 0.000 ARG L 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.9264 (tm-30) cc_final: 0.8853 (tm-30) REVERT: A 244 ASN cc_start: 0.8659 (m-40) cc_final: 0.8287 (m-40) REVERT: A 411 MET cc_start: 0.8530 (mtm) cc_final: 0.8264 (mtt) REVERT: A 420 MET cc_start: 0.8327 (ttt) cc_final: 0.8081 (ttt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2014 time to fit residues: 21.0780 Evaluate side-chains 66 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2780 Z= 0.186 Angle : 0.463 4.174 3774 Z= 0.266 Chirality : 0.034 0.115 427 Planarity : 0.004 0.029 440 Dihedral : 3.461 13.056 359 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.45 (0.45), residues: 319 helix: 2.69 (0.30), residues: 259 sheet: None (None), residues: 0 loop : 0.41 (0.88), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 186 HIS 0.002 0.001 HIS A 184 PHE 0.026 0.001 PHE A 112 TYR 0.008 0.001 TYR L 111 ARG 0.002 0.000 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.9278 (tm-30) cc_final: 0.8866 (tm-30) REVERT: A 188 GLU cc_start: 0.8977 (pt0) cc_final: 0.8264 (pt0) REVERT: A 244 ASN cc_start: 0.8616 (m110) cc_final: 0.8322 (m-40) REVERT: A 411 MET cc_start: 0.8563 (mtm) cc_final: 0.8285 (mtt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1966 time to fit residues: 20.1286 Evaluate side-chains 65 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2780 Z= 0.267 Angle : 0.569 5.981 3774 Z= 0.331 Chirality : 0.036 0.136 427 Planarity : 0.004 0.029 440 Dihedral : 3.885 13.990 359 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.45), residues: 319 helix: 1.74 (0.30), residues: 259 sheet: None (None), residues: 0 loop : 0.22 (0.88), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 284 HIS 0.010 0.002 HIS A 409 PHE 0.033 0.002 PHE A 112 TYR 0.019 0.002 TYR A 225 ARG 0.002 0.000 ARG L 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.9325 (tm-30) cc_final: 0.8855 (tm-30) REVERT: A 188 GLU cc_start: 0.9000 (pt0) cc_final: 0.8439 (pt0) REVERT: A 244 ASN cc_start: 0.8464 (m110) cc_final: 0.8221 (m110) REVERT: A 411 MET cc_start: 0.8641 (mtm) cc_final: 0.8364 (mtt) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1979 time to fit residues: 19.2509 Evaluate side-chains 62 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2780 Z= 0.208 Angle : 0.499 4.627 3774 Z= 0.292 Chirality : 0.035 0.115 427 Planarity : 0.004 0.026 440 Dihedral : 3.783 12.693 359 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.46), residues: 319 helix: 1.83 (0.30), residues: 258 sheet: None (None), residues: 0 loop : 0.30 (0.91), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 186 HIS 0.003 0.001 HIS A 184 PHE 0.028 0.002 PHE A 112 TYR 0.015 0.001 TYR A 225 ARG 0.002 0.000 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 MET cc_start: 0.8702 (mmm) cc_final: 0.7827 (mmm) REVERT: A 175 GLN cc_start: 0.9327 (tm-30) cc_final: 0.8856 (tm-30) REVERT: A 188 GLU cc_start: 0.8948 (pt0) cc_final: 0.8315 (pt0) REVERT: A 244 ASN cc_start: 0.8429 (m110) cc_final: 0.8142 (m110) REVERT: A 411 MET cc_start: 0.8643 (mtm) cc_final: 0.8362 (mtt) REVERT: A 421 MET cc_start: 0.7493 (tpt) cc_final: 0.7144 (tmm) REVERT: A 447 ILE cc_start: 0.8886 (tt) cc_final: 0.8588 (mt) REVERT: A 451 TRP cc_start: 0.8116 (m-10) cc_final: 0.7906 (m-10) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1973 time to fit residues: 20.2491 Evaluate side-chains 63 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 17 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2780 Z= 0.140 Angle : 0.446 3.803 3774 Z= 0.252 Chirality : 0.034 0.111 427 Planarity : 0.004 0.027 440 Dihedral : 3.552 12.202 359 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.16 (0.46), residues: 319 helix: 2.42 (0.30), residues: 260 sheet: None (None), residues: 0 loop : 0.67 (0.96), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 186 HIS 0.002 0.001 HIS A 263 PHE 0.027 0.001 PHE A 112 TYR 0.009 0.001 TYR A 225 ARG 0.003 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.9289 (t80) cc_final: 0.8939 (t80) REVERT: A 116 MET cc_start: 0.8439 (mmp) cc_final: 0.7658 (tpp) REVERT: A 165 MET cc_start: 0.8592 (mmm) cc_final: 0.7677 (mmm) REVERT: A 175 GLN cc_start: 0.9321 (tm-30) cc_final: 0.8952 (tm-30) REVERT: A 188 GLU cc_start: 0.8966 (pt0) cc_final: 0.8195 (pt0) REVERT: A 244 ASN cc_start: 0.8206 (m110) cc_final: 0.7952 (m110) REVERT: A 411 MET cc_start: 0.8591 (mtm) cc_final: 0.8318 (mtt) REVERT: A 421 MET cc_start: 0.7220 (tpt) cc_final: 0.6680 (tmm) REVERT: A 447 ILE cc_start: 0.8809 (tt) cc_final: 0.8461 (mt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1960 time to fit residues: 20.5125 Evaluate side-chains 67 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2780 Z= 0.229 Angle : 0.525 4.764 3774 Z= 0.306 Chirality : 0.035 0.114 427 Planarity : 0.004 0.025 440 Dihedral : 3.727 12.473 359 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.34 % Allowed : 0.34 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.46), residues: 319 helix: 1.96 (0.30), residues: 258 sheet: None (None), residues: 0 loop : 0.35 (0.93), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 459 HIS 0.004 0.001 HIS A 184 PHE 0.025 0.002 PHE A 112 TYR 0.018 0.001 TYR A 225 ARG 0.001 0.000 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 MET cc_start: 0.8687 (mmm) cc_final: 0.6998 (ttt) REVERT: A 175 GLN cc_start: 0.9361 (tm-30) cc_final: 0.8708 (tm-30) REVERT: A 184 HIS cc_start: 0.7890 (OUTLIER) cc_final: 0.7437 (t-170) REVERT: A 188 GLU cc_start: 0.8976 (pt0) cc_final: 0.8361 (pt0) REVERT: A 244 ASN cc_start: 0.8343 (m110) cc_final: 0.8055 (m110) REVERT: A 348 LEU cc_start: 0.9532 (tp) cc_final: 0.9315 (tp) REVERT: A 421 MET cc_start: 0.7328 (tpt) cc_final: 0.6596 (tmm) REVERT: A 447 ILE cc_start: 0.8878 (tt) cc_final: 0.8576 (mt) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.2061 time to fit residues: 21.5269 Evaluate side-chains 68 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2780 Z= 0.159 Angle : 0.458 3.838 3774 Z= 0.261 Chirality : 0.034 0.111 427 Planarity : 0.003 0.026 440 Dihedral : 3.591 12.758 359 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.47), residues: 319 helix: 2.33 (0.30), residues: 260 sheet: None (None), residues: 0 loop : 0.37 (0.97), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 451 HIS 0.002 0.001 HIS A 130 PHE 0.023 0.001 PHE A 112 TYR 0.013 0.001 TYR A 225 ARG 0.002 0.000 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.9274 (t80) cc_final: 0.8967 (t80) REVERT: A 165 MET cc_start: 0.8717 (mmm) cc_final: 0.7346 (ttt) REVERT: A 175 GLN cc_start: 0.9337 (tm-30) cc_final: 0.8875 (tm-30) REVERT: A 188 GLU cc_start: 0.8960 (pt0) cc_final: 0.8250 (pt0) REVERT: A 244 ASN cc_start: 0.8293 (m110) cc_final: 0.8010 (m110) REVERT: A 411 MET cc_start: 0.8686 (mtm) cc_final: 0.8384 (mtt) REVERT: A 447 ILE cc_start: 0.8823 (tt) cc_final: 0.8552 (mt) REVERT: A 453 CYS cc_start: 0.9165 (t) cc_final: 0.8952 (t) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1940 time to fit residues: 20.8526 Evaluate side-chains 68 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 3 optimal weight: 0.0060 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 overall best weight: 2.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2780 Z= 0.214 Angle : 0.516 4.108 3774 Z= 0.299 Chirality : 0.035 0.110 427 Planarity : 0.004 0.024 440 Dihedral : 3.689 12.983 359 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.34 % Allowed : 0.00 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.46), residues: 319 helix: 1.94 (0.30), residues: 260 sheet: None (None), residues: 0 loop : 0.24 (0.96), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 459 HIS 0.005 0.002 HIS A 184 PHE 0.024 0.002 PHE A 112 TYR 0.019 0.001 TYR A 225 ARG 0.001 0.000 ARG A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 MET cc_start: 0.8782 (mmm) cc_final: 0.8166 (mmm) REVERT: A 175 GLN cc_start: 0.9357 (tm-30) cc_final: 0.8860 (tm-30) REVERT: A 184 HIS cc_start: 0.7835 (OUTLIER) cc_final: 0.7087 (t-170) REVERT: A 188 GLU cc_start: 0.8924 (pt0) cc_final: 0.8372 (pt0) REVERT: A 244 ASN cc_start: 0.8336 (m110) cc_final: 0.8061 (m110) REVERT: A 411 MET cc_start: 0.8724 (mtm) cc_final: 0.8395 (mtt) REVERT: A 444 TRP cc_start: 0.7386 (m100) cc_final: 0.6355 (t60) REVERT: A 447 ILE cc_start: 0.8834 (tt) cc_final: 0.8531 (mt) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.2095 time to fit residues: 21.4988 Evaluate side-chains 71 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 1 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.0970 chunk 19 optimal weight: 0.0670 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.126771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.109622 restraints weight = 31370.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.113725 restraints weight = 15045.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.116258 restraints weight = 8603.986| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2780 Z= 0.134 Angle : 0.450 3.699 3774 Z= 0.245 Chirality : 0.034 0.111 427 Planarity : 0.003 0.026 440 Dihedral : 3.520 12.761 359 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.42 (0.47), residues: 319 helix: 2.63 (0.30), residues: 260 sheet: None (None), residues: 0 loop : 0.55 (0.98), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 186 HIS 0.002 0.001 HIS A 263 PHE 0.021 0.001 PHE A 112 TYR 0.009 0.001 TYR A 350 ARG 0.001 0.000 ARG A 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1999.44 seconds wall clock time: 36 minutes 4.62 seconds (2164.62 seconds total)