Starting phenix.real_space_refine on Mon Sep 23 21:07:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rug_24705/09_2024/7rug_24705.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rug_24705/09_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_24705/09_2024/7rug_24705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rug_24705/09_2024/7rug_24705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rug_24705/09_2024/7rug_24705.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rug_24705/09_2024/7rug_24705.cif" } 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. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 3.26, per 1000 atoms: 0.60 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 396.6 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: 0.45 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: 1.88 Time building geometry restraints manager: 1.81 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: 0.00 - 0.85: 8849 0.85 - 1.70: 974 1.70 - 2.55: 65 2.55 - 3.40: 13 3.40 - 4.25: 11 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 2.450 nonbonded pdb=" O CYS A 413 " pdb=" HG SER A 416 " model vdw 1.668 2.450 nonbonded pdb=" O TYR A 418 " pdb=" HG1 THR A 422 " model vdw 1.708 2.450 nonbonded pdb=" O ILE A 447 " pdb=" HG SER A 450 " model vdw 1.724 2.450 nonbonded pdb=" O SER A 288 " pdb="HD21 ASN A 296 " model vdw 1.728 2.450 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.770 Find NCS groups from input model: 0.040 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.550 ------------------------------------------------------------------------------- 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 : 0.428 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: 0.2363 time to fit residues: 24.0243 Evaluate side-chains 65 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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: 5.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2780 Z= 0.230 Angle : 0.508 4.278 3774 Z= 0.296 Chirality : 0.035 0.121 427 Planarity : 0.004 0.036 440 Dihedral : 3.573 14.045 359 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.87 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: 3.14 (0.45), residues: 319 helix: 2.44 (0.30), residues: 259 sheet: None (None), residues: 0 loop : 0.52 (0.87), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 186 HIS 0.003 0.001 HIS A 184 PHE 0.027 0.002 PHE A 108 TYR 0.011 0.001 TYR A 225 ARG 0.006 0.001 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 77 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 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: symmetry clash revert: symmetry clash REVERT: A 175 GLN cc_start: 0.9311 (tm-30) cc_final: 0.8880 (tm-30) REVERT: A 188 GLU cc_start: 0.9045 (pt0) cc_final: 0.8431 (pt0) REVERT: A 244 ASN cc_start: 0.8695 (m-40) cc_final: 0.8404 (m-40) REVERT: A 411 MET cc_start: 0.8599 (mtm) cc_final: 0.8267 (mtt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1927 time to fit residues: 19.3770 Evaluate side-chains 68 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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: 0.9980 chunk 9 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.6930 moved from start: 0.1959 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= 0.158 Angle : 0.464 4.244 3774 Z= 0.263 Chirality : 0.035 0.117 427 Planarity : 0.004 0.026 440 Dihedral : 3.477 12.675 359 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: 3.43 (0.45), residues: 319 helix: 2.70 (0.30), residues: 259 sheet: None (None), residues: 0 loop : 0.30 (0.85), 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 0.024 0.001 PHE A 112 TYR 0.008 0.001 TYR L 111 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 77 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.445 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: 0.9287 (tm-30) cc_final: 0.8810 (tm-30) REVERT: A 188 GLU cc_start: 0.8981 (pt0) cc_final: 0.8249 (pt0) REVERT: A 244 ASN cc_start: 0.8711 (m-40) cc_final: 0.8490 (m110) REVERT: A 411 MET cc_start: 0.8570 (mtm) cc_final: 0.8330 (mtt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1867 time to fit residues: 18.7894 Evaluate side-chains 67 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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: 7.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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: 0.7003 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2780 Z= 0.246 Angle : 0.540 5.070 3774 Z= 0.313 Chirality : 0.036 0.120 427 Planarity : 0.004 0.029 440 Dihedral : 3.679 13.418 359 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.43 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: 2.61 (0.45), residues: 319 helix: 2.10 (0.30), residues: 259 sheet: None (None), residues: 0 loop : 0.14 (0.84), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 284 HIS 0.003 0.001 HIS A 257 PHE 0.030 0.002 PHE A 112 TYR 0.012 0.001 TYR A 225 ARG 0.002 0.000 ARG L 105 *********************** 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 77 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.435 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: 0.9327 (tm-30) cc_final: 0.8861 (tm-30) REVERT: A 188 GLU cc_start: 0.9013 (pt0) cc_final: 0.8478 (pt0) REVERT: A 411 MET cc_start: 0.8635 (mtm) cc_final: 0.8356 (mtt) REVERT: A 420 MET cc_start: 0.8435 (ttt) cc_final: 0.8175 (ttt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2180 time to fit residues: 21.3711 Evaluate side-chains 62 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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: 1.9990 chunk 12 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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: 0.6952 moved from start: 0.3018 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= 0.166 Angle : 0.465 3.791 3774 Z= 0.268 Chirality : 0.035 0.119 427 Planarity : 0.004 0.028 440 Dihedral : 3.521 13.633 359 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: 3.01 (0.45), residues: 319 helix: 2.41 (0.30), residues: 259 sheet: None (None), residues: 0 loop : 0.14 (0.85), 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 0.027 0.001 PHE A 112 TYR 0.010 0.001 TYR A 214 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 74 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 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: A 165 MET cc_start: 0.8719 (mmm) cc_final: 0.7738 (mmm) REVERT: A 175 GLN cc_start: 0.9329 (tm-30) cc_final: 0.8857 (tm-30) REVERT: A 188 GLU cc_start: 0.8968 (pt0) cc_final: 0.8354 (pt0) REVERT: A 411 MET cc_start: 0.8577 (mtm) cc_final: 0.8323 (mtt) REVERT: A 421 MET cc_start: 0.7367 (tpt) cc_final: 0.6802 (tmm) REVERT: A 447 ILE cc_start: 0.8886 (tt) cc_final: 0.8549 (mt) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1966 time to fit residues: 19.0536 Evaluate side-chains 66 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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: 3.9990 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 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: 0.6954 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2780 Z= 0.178 Angle : 0.472 4.113 3774 Z= 0.272 Chirality : 0.035 0.114 427 Planarity : 0.004 0.030 440 Dihedral : 3.487 14.036 359 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.06 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: 3.01 (0.46), residues: 319 helix: 2.40 (0.30), residues: 261 sheet: None (None), residues: 0 loop : 0.11 (0.90), residues: 58 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 0.027 0.001 PHE A 112 TYR 0.010 0.001 TYR A 214 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 74 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.441 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 165 MET cc_start: 0.8679 (mmm) cc_final: 0.7922 (mmm) REVERT: A 175 GLN cc_start: 0.9335 (tm-30) cc_final: 0.8859 (tm-30) REVERT: A 188 GLU cc_start: 0.9015 (pt0) cc_final: 0.8329 (pt0) REVERT: A 411 MET cc_start: 0.8590 (mtm) cc_final: 0.8314 (mtt) REVERT: A 421 MET cc_start: 0.7224 (tpt) cc_final: 0.6488 (tmm) REVERT: A 447 ILE cc_start: 0.8856 (tt) cc_final: 0.8515 (mt) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2007 time to fit residues: 19.2618 Evaluate side-chains 64 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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: 0.6955 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2780 Z= 0.166 Angle : 0.465 4.443 3774 Z= 0.266 Chirality : 0.035 0.115 427 Planarity : 0.003 0.030 440 Dihedral : 3.470 14.316 359 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: 3.13 (0.46), residues: 319 helix: 2.47 (0.30), residues: 261 sheet: None (None), residues: 0 loop : 0.22 (0.92), 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 0.024 0.001 PHE A 112 TYR 0.009 0.001 TYR A 214 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 78 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.420 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: 0.8707 (mmm) cc_final: 0.7907 (mmm) REVERT: A 175 GLN cc_start: 0.9370 (tm-30) cc_final: 0.8911 (tm-30) REVERT: A 188 GLU cc_start: 0.8982 (pt0) cc_final: 0.8296 (pt0) REVERT: A 219 ILE cc_start: 0.8093 (mm) cc_final: 0.7703 (tp) REVERT: A 411 MET cc_start: 0.8593 (mtm) cc_final: 0.8326 (mtt) REVERT: A 447 ILE cc_start: 0.8857 (tt) cc_final: 0.8535 (mt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1940 time to fit residues: 19.6330 Evaluate side-chains 68 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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: 6.9990 chunk 2 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.3457 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= 0.141 Angle : 0.443 3.717 3774 Z= 0.249 Chirality : 0.034 0.113 427 Planarity : 0.003 0.032 440 Dihedral : 3.384 14.412 359 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.95 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: 3.42 (0.46), residues: 319 helix: 2.68 (0.30), residues: 261 sheet: None (None), residues: 0 loop : 0.29 (0.93), residues: 58 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 0.009 0.001 TYR A 350 ARG 0.002 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 77 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.448 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: 0.8490 (mmp) cc_final: 0.7655 (tpp) REVERT: A 165 MET cc_start: 0.8683 (mmm) cc_final: 0.8021 (mmm) REVERT: A 175 GLN cc_start: 0.9355 (tm-30) cc_final: 0.8923 (tm-30) REVERT: A 188 GLU cc_start: 0.8967 (pt0) cc_final: 0.8288 (pt0) REVERT: A 219 ILE cc_start: 0.8028 (mm) cc_final: 0.7652 (tp) REVERT: A 244 ASN cc_start: 0.9075 (m-40) cc_final: 0.8871 (m110) REVERT: A 411 MET cc_start: 0.8572 (mtm) cc_final: 0.8311 (mtt) REVERT: A 447 ILE cc_start: 0.8815 (tt) cc_final: 0.8502 (mt) REVERT: A 453 CYS cc_start: 0.9164 (t) cc_final: 0.8961 (t) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1983 time to fit residues: 19.8130 Evaluate side-chains 68 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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: 7.9990 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.3663 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 : 0.488 4.201 3774 Z= 0.280 Chirality : 0.036 0.141 427 Planarity : 0.004 0.034 440 Dihedral : 3.469 14.578 359 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.06 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: 3.07 (0.46), residues: 319 helix: 2.43 (0.30), residues: 260 sheet: None (None), residues: 0 loop : 0.25 (0.93), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 459 HIS 0.003 0.001 HIS A 184 PHE 0.027 0.002 PHE A 112 TYR 0.011 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 77 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.443 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 116 MET cc_start: 0.8532 (mmp) cc_final: 0.7810 (tpp) REVERT: A 165 MET cc_start: 0.8698 (mmm) cc_final: 0.7969 (mmm) REVERT: A 175 GLN cc_start: 0.9369 (tm-30) cc_final: 0.8895 (tm-30) REVERT: A 188 GLU cc_start: 0.9011 (pt0) cc_final: 0.8325 (pt0) REVERT: A 219 ILE cc_start: 0.8014 (mm) cc_final: 0.7655 (tp) REVERT: A 411 MET cc_start: 0.8663 (mtm) cc_final: 0.8358 (mtt) REVERT: A 447 ILE cc_start: 0.8819 (tt) cc_final: 0.8501 (mt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1966 time to fit residues: 19.4965 Evaluate side-chains 67 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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: 3.9990 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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: 0.7021 moved from start: 0.3892 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= 0.215 Angle : 0.523 4.776 3774 Z= 0.303 Chirality : 0.036 0.123 427 Planarity : 0.004 0.031 440 Dihedral : 3.641 15.006 359 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.35 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: 2.74 (0.46), residues: 319 helix: 2.19 (0.30), residues: 260 sheet: None (None), residues: 0 loop : 0.17 (0.93), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 459 HIS 0.003 0.001 HIS A 184 PHE 0.026 0.002 PHE A 112 TYR 0.018 0.002 TYR A 225 ARG 0.002 0.000 ARG A 266 ********************** 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 77 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.440 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: 0.8805 (mmm) cc_final: 0.8030 (mmm) REVERT: A 175 GLN cc_start: 0.9461 (tm-30) cc_final: 0.8925 (tm-30) REVERT: A 188 GLU cc_start: 0.9011 (pt0) cc_final: 0.8379 (pt0) REVERT: A 219 ILE cc_start: 0.8041 (mm) cc_final: 0.7653 (tp) REVERT: A 244 ASN cc_start: 0.8844 (m110) cc_final: 0.8496 (m110) REVERT: A 411 MET cc_start: 0.8665 (mtm) cc_final: 0.8302 (mtt) REVERT: A 447 ILE cc_start: 0.8850 (tt) cc_final: 0.8592 (mt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1895 time to fit residues: 19.0300 Evaluate side-chains 65 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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: 2.9990 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.125076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.108283 restraints weight = 31120.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.112481 restraints weight = 14264.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.114925 restraints weight = 7772.208| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.4038 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= 0.169 Angle : 0.482 4.355 3774 Z= 0.275 Chirality : 0.036 0.131 427 Planarity : 0.003 0.033 440 Dihedral : 3.537 14.960 359 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.32 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: 2.98 (0.46), residues: 319 helix: 2.38 (0.30), residues: 260 sheet: None (None), residues: 0 loop : 0.16 (0.91), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 451 HIS 0.003 0.001 HIS A 184 PHE 0.024 0.001 PHE A 112 TYR 0.013 0.001 TYR A 214 ARG 0.002 0.000 ARG A 266 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1929.60 seconds wall clock time: 34 minutes 11.28 seconds (2051.28 seconds total)