Starting phenix.real_space_refine on Sun Mar 10 21:52:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rug_24705/03_2024/7rug_24705.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rug_24705/03_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_24705/03_2024/7rug_24705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rug_24705/03_2024/7rug_24705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rug_24705/03_2024/7rug_24705.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rug_24705/03_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-dev-5265/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: 3.18, per 1000 atoms: 0.59 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: 4.36 Conformation dependent library (CDL) restraints added in 677.1 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: 1.84 Time building geometry restraints manager: 4.51 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: 2349 15.36 - 30.72: 171 30.72 - 46.08: 50 46.08 - 61.44: 31 61.44 - 76.80: 4 Dihedral angle restraints: 2605 sinusoidal: 1323 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 2602 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: 0.440 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: 1.880 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 22.080 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.350 ------------------------------------------------------------------------------- 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 : 0.480 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: 0.2737 time to fit residues: 28.3179 Evaluate side-chains 65 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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: 5.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.1279 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= 0.157 Angle : 0.443 4.017 3774 Z= 0.251 Chirality : 0.034 0.114 427 Planarity : 0.004 0.032 440 Dihedral : 3.442 14.249 359 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: 3.83 (0.46), residues: 319 helix: 2.90 (0.30), residues: 259 sheet: None (None), residues: 0 loop : 0.85 (0.92), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 186 HIS 0.002 0.001 HIS A 184 PHE 0.025 0.001 PHE A 108 TYR 0.007 0.001 TYR A 225 ARG 0.006 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 80 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.454 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: 0.9306 (tm-30) cc_final: 0.8826 (tm-30) REVERT: A 188 GLU cc_start: 0.9038 (pt0) cc_final: 0.8341 (pt0) REVERT: A 244 ASN cc_start: 0.8676 (m-40) cc_final: 0.8348 (m-40) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1938 time to fit residues: 20.0724 Evaluate side-chains 68 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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: 10.0000 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2780 Z= 0.149 Angle : 0.446 3.951 3774 Z= 0.251 Chirality : 0.034 0.120 427 Planarity : 0.003 0.028 440 Dihedral : 3.412 13.198 359 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: 3.83 (0.46), residues: 319 helix: 2.95 (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 0.008 0.001 TRP A 186 HIS 0.007 0.002 HIS A 409 PHE 0.021 0.001 PHE A 112 TYR 0.007 0.001 TYR A 350 ARG 0.003 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 : 0.453 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: 0.9264 (tm-30) cc_final: 0.8873 (tm-30) REVERT: A 244 ASN cc_start: 0.8700 (m-40) cc_final: 0.8324 (m-40) REVERT: A 411 MET cc_start: 0.8443 (mtt) cc_final: 0.8199 (mtt) REVERT: A 420 MET cc_start: 0.8314 (ttt) cc_final: 0.8089 (ttt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1876 time to fit residues: 19.7086 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: 10.0000 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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: 0.6995 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2780 Z= 0.234 Angle : 0.515 4.452 3774 Z= 0.298 Chirality : 0.035 0.120 427 Planarity : 0.004 0.027 440 Dihedral : 3.649 13.603 359 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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 (0.45), residues: 319 helix: 2.32 (0.30), residues: 259 sheet: None (None), residues: 0 loop : 0.38 (0.88), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 284 HIS 0.003 0.001 HIS A 409 PHE 0.026 0.002 PHE A 112 TYR 0.011 0.001 TYR A 225 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 : 0.520 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: 0.9281 (tm-30) cc_final: 0.8860 (tm-30) REVERT: A 188 GLU cc_start: 0.9008 (pt0) cc_final: 0.8393 (pt0) REVERT: A 244 ASN cc_start: 0.8669 (m110) cc_final: 0.8402 (m-40) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1950 time to fit residues: 20.1461 Evaluate side-chains 67 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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: 4.9990 chunk 12 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2780 Z= 0.197 Angle : 0.484 4.326 3774 Z= 0.279 Chirality : 0.035 0.114 427 Planarity : 0.004 0.026 440 Dihedral : 3.613 12.908 359 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: 2.89 (0.46), residues: 319 helix: 2.29 (0.30), residues: 259 sheet: None (None), residues: 0 loop : 0.31 (0.90), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 186 HIS 0.008 0.002 HIS A 409 PHE 0.028 0.002 PHE A 112 TYR 0.011 0.001 TYR A 225 ARG 0.002 0.000 ARG A 266 *********************** 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 79 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.436 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 165 MET cc_start: 0.8741 (mmm) cc_final: 0.7786 (mmm) REVERT: A 175 GLN cc_start: 0.9299 (tm-30) cc_final: 0.8842 (tm-30) REVERT: A 188 GLU cc_start: 0.8956 (pt0) cc_final: 0.8271 (pt0) REVERT: A 244 ASN cc_start: 0.8592 (m110) cc_final: 0.8301 (m110) REVERT: A 421 MET cc_start: 0.7482 (tpt) cc_final: 0.6922 (tmm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1967 time to fit residues: 20.1393 Evaluate side-chains 66 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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: 9.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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: 0.6967 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2780 Z= 0.166 Angle : 0.454 3.989 3774 Z= 0.260 Chirality : 0.034 0.111 427 Planarity : 0.003 0.026 440 Dihedral : 3.512 12.073 359 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: 3.11 (0.46), residues: 319 helix: 2.42 (0.30), residues: 260 sheet: None (None), residues: 0 loop : 0.44 (0.95), residues: 59 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 0.029 0.001 PHE A 112 TYR 0.009 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 80 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.330 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 165 MET cc_start: 0.8661 (mmm) cc_final: 0.7997 (mmm) REVERT: A 175 GLN cc_start: 0.9288 (tm-30) cc_final: 0.8837 (tm-30) REVERT: A 188 GLU cc_start: 0.8961 (pt0) cc_final: 0.8370 (pt0) REVERT: A 244 ASN cc_start: 0.8474 (m110) cc_final: 0.8199 (m110) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1947 time to fit residues: 20.1151 Evaluate side-chains 68 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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: 0.6980 chunk 26 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.6915 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2780 Z= 0.135 Angle : 0.431 4.184 3774 Z= 0.240 Chirality : 0.034 0.114 427 Planarity : 0.003 0.027 440 Dihedral : 3.428 11.541 359 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: 3.52 (0.47), residues: 319 helix: 2.73 (0.30), residues: 260 sheet: None (None), residues: 0 loop : 0.46 (0.94), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 186 HIS 0.003 0.001 HIS A 184 PHE 0.026 0.001 PHE A 112 TYR 0.011 0.001 TYR A 281 ARG 0.002 0.000 ARG A 266 *********************** 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 81 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.8431 (mmp) cc_final: 0.7638 (tpp) REVERT: A 165 MET cc_start: 0.8684 (mmm) cc_final: 0.7724 (mmm) REVERT: A 175 GLN cc_start: 0.9290 (tm-30) cc_final: 0.8804 (tm-30) REVERT: A 244 ASN cc_start: 0.8366 (m110) cc_final: 0.8027 (m110) REVERT: A 447 ILE cc_start: 0.8803 (tt) cc_final: 0.8461 (mt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1940 time to fit residues: 20.3986 Evaluate side-chains 69 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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: 5.9990 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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: 0.6962 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2780 Z= 0.171 Angle : 0.466 3.944 3774 Z= 0.264 Chirality : 0.034 0.105 427 Planarity : 0.003 0.025 440 Dihedral : 3.451 11.716 359 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % 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: 3.22 (0.47), residues: 319 helix: 2.49 (0.30), residues: 261 sheet: None (None), residues: 0 loop : 0.49 (0.98), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 459 HIS 0.003 0.001 HIS A 184 PHE 0.026 0.002 PHE A 112 TYR 0.010 0.001 TYR A 225 ARG 0.001 0.000 ARG A 100 *********************** 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 81 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.437 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: 0.8734 (mmm) cc_final: 0.8332 (mmm) REVERT: A 175 GLN cc_start: 0.9293 (tm-30) cc_final: 0.8862 (tm-30) REVERT: A 188 GLU cc_start: 0.8919 (pt0) cc_final: 0.8269 (pt0) REVERT: A 244 ASN cc_start: 0.8446 (m110) cc_final: 0.8124 (m110) REVERT: A 447 ILE cc_start: 0.8864 (tt) cc_final: 0.8568 (mt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2160 time to fit residues: 22.1788 Evaluate side-chains 70 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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: 0.9980 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 19 optimal weight: 0.0980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2780 Z= 0.146 Angle : 0.445 3.898 3774 Z= 0.249 Chirality : 0.034 0.111 427 Planarity : 0.004 0.033 440 Dihedral : 3.461 11.831 359 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: 3.48 (0.47), residues: 319 helix: 2.67 (0.30), residues: 261 sheet: None (None), residues: 0 loop : 0.55 (0.98), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 186 HIS 0.003 0.001 HIS A 184 PHE 0.022 0.001 PHE A 112 TYR 0.010 0.001 TYR A 214 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 81 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 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: A 116 MET cc_start: 0.8405 (mmp) cc_final: 0.7876 (tpp) REVERT: A 165 MET cc_start: 0.8726 (mmm) cc_final: 0.8305 (mmm) REVERT: A 175 GLN cc_start: 0.9327 (tm-30) cc_final: 0.8856 (tm-30) REVERT: A 188 GLU cc_start: 0.8954 (pt0) cc_final: 0.8229 (pt0) REVERT: A 244 ASN cc_start: 0.8358 (m110) cc_final: 0.8078 (m110) REVERT: A 447 ILE cc_start: 0.8832 (tt) cc_final: 0.8557 (mt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1997 time to fit residues: 20.9779 Evaluate side-chains 70 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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: 5.9990 chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2780 Z= 0.271 Angle : 0.569 4.329 3774 Z= 0.339 Chirality : 0.036 0.153 427 Planarity : 0.004 0.041 440 Dihedral : 3.834 12.786 359 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % 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: 2.04 (0.46), residues: 319 helix: 1.68 (0.30), residues: 260 sheet: None (None), residues: 0 loop : 0.05 (0.96), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 459 HIS 0.005 0.002 HIS A 409 PHE 0.028 0.002 PHE A 112 TYR 0.021 0.002 TYR A 225 ARG 0.001 0.000 ARG A 293 ********************** 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 79 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.444 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 165 MET cc_start: 0.8795 (mmm) cc_final: 0.8403 (mmm) REVERT: A 175 GLN cc_start: 0.9329 (tm-30) cc_final: 0.8822 (tm-30) REVERT: A 188 GLU cc_start: 0.9036 (pt0) cc_final: 0.8461 (pt0) REVERT: A 244 ASN cc_start: 0.8506 (m110) cc_final: 0.8181 (m110) REVERT: A 348 LEU cc_start: 0.9503 (tp) cc_final: 0.9266 (tp) REVERT: A 420 MET cc_start: 0.8308 (ttt) cc_final: 0.8105 (ttt) REVERT: A 447 ILE cc_start: 0.8901 (tt) cc_final: 0.8609 (mt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2019 time to fit residues: 20.9516 Evaluate side-chains 68 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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: 0.6980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.125359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.109014 restraints weight = 31878.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.113051 restraints weight = 15285.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.115525 restraints weight = 8693.395| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2780 Z= 0.143 Angle : 0.452 4.298 3774 Z= 0.256 Chirality : 0.035 0.113 427 Planarity : 0.003 0.029 440 Dihedral : 3.597 11.825 359 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % 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: 3.04 (0.47), residues: 319 helix: 2.38 (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 0.010 0.001 TRP A 186 HIS 0.002 0.001 HIS A 184 PHE 0.023 0.001 PHE A 112 TYR 0.009 0.001 TYR A 214 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: 1987.04 seconds wall clock time: 35 minutes 47.09 seconds (2147.09 seconds total)