Starting phenix.real_space_refine on Tue Feb 11 11:01:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rug_24705/02_2025/7rug_24705.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rug_24705/02_2025/7rug_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/cci-nas-00/data/ceres_data/7rug_24705/02_2025/7rug_24705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rug_24705/02_2025/7rug_24705.map" model { file = "/net/cci-nas-00/data/ceres_data/7rug_24705/02_2025/7rug_24705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rug_24705/02_2025/7rug_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-5592/modules/chem_data/mon_lib" Total number of atoms: 5429 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5151 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 8, 'TRANS': 306} Chain breaks: 4 Chain: "L" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 278 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Time building chain proxies: 2.94, per 1000 atoms: 0.54 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: 1.27 Conformation dependent library (CDL) restraints added in 355.7 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: 0.35 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: 2.53 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 2723 1.03 - 1.23: 5 1.23 - 1.42: 1231 1.42 - 1.61: 1518 1.61 - 1.81: 31 Bond restraints: 5508 Sorted by residual: bond pdb=" CA ILE A 151 " pdb=" CB ILE A 151 " ideal model delta sigma weight residual 1.537 1.525 0.012 1.29e-02 6.01e+03 9.35e-01 bond pdb=" C TRP L 108 " pdb=" N TYR L 109 " ideal model delta sigma weight residual 1.335 1.323 0.012 1.35e-02 5.49e+03 7.39e-01 bond pdb=" CB TRP L 108 " pdb=" CG TRP L 108 " ideal model delta sigma weight residual 1.498 1.477 0.021 3.10e-02 1.04e+03 4.63e-01 bond pdb=" CG LEU A 206 " pdb=" CD2 LEU A 206 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 3.86e-01 bond pdb=" CA MET A 105 " pdb=" HA MET A 105 " ideal model delta sigma weight residual 0.970 0.958 0.012 2.00e-02 2.50e+03 3.51e-01 ... (remaining 5503 not shown) Histogram of bond angle deviations from ideal: 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: 0.700 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: 0.100 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.900 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.910 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.401 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: 0.2392 time to fit residues: 24.2199 Evaluate side-chains 65 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.125363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.108710 restraints weight = 30936.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.112921 restraints weight = 14307.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.115494 restraints weight = 7910.289| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 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 to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.408 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: 0.9367 (tm-30) cc_final: 0.8952 (tm-30) REVERT: A 188 GLU cc_start: 0.9038 (pt0) cc_final: 0.8438 (pt0) REVERT: A 244 ASN cc_start: 0.8759 (m-40) cc_final: 0.8468 (m-40) REVERT: A 411 MET cc_start: 0.8634 (mtm) cc_final: 0.8318 (mtt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1942 time to fit residues: 19.3658 Evaluate side-chains 68 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 21 optimal weight: 0.6980 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.125637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.108571 restraints weight = 29769.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.112789 restraints weight = 14070.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.115269 restraints weight = 7902.752| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.2011 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= 0.179 Angle : 0.479 4.030 3774 Z= 0.275 Chirality : 0.035 0.113 427 Planarity : 0.004 0.028 440 Dihedral : 3.537 13.032 359 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.77 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: 3.18 (0.45), residues: 319 helix: 2.52 (0.30), residues: 259 sheet: None (None), residues: 0 loop : 0.24 (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 0.025 0.002 PHE A 112 TYR 0.009 0.001 TYR A 225 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 76 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.457 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: 0.9360 (tm-30) cc_final: 0.8927 (tm-30) REVERT: A 188 GLU cc_start: 0.8972 (pt0) cc_final: 0.8319 (pt0) REVERT: A 244 ASN cc_start: 0.8786 (m-40) cc_final: 0.8535 (m110) REVERT: A 411 MET cc_start: 0.8638 (mtm) cc_final: 0.8393 (mtt) REVERT: A 420 MET cc_start: 0.8459 (ttt) cc_final: 0.8200 (ttt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1918 time to fit residues: 18.9533 Evaluate side-chains 65 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.125227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.108459 restraints weight = 29685.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.112669 restraints weight = 14065.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.115272 restraints weight = 7876.029| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2780 Z= 0.192 Angle : 0.481 4.532 3774 Z= 0.276 Chirality : 0.035 0.111 427 Planarity : 0.003 0.028 440 Dihedral : 3.514 13.199 359 Min Nonbonded Distance : 2.400 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: 3.05 (0.45), residues: 319 helix: 2.45 (0.30), residues: 259 sheet: None (None), residues: 0 loop : 0.07 (0.83), 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 0.025 0.002 PHE A 112 TYR 0.008 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 76 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.405 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: 0.9356 (tm-30) cc_final: 0.8882 (tm-30) REVERT: A 188 GLU cc_start: 0.8955 (pt0) cc_final: 0.8394 (pt0) REVERT: A 244 ASN cc_start: 0.8785 (m-40) cc_final: 0.8567 (m110) REVERT: A 411 MET cc_start: 0.8626 (mtm) cc_final: 0.8378 (mtt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2239 time to fit residues: 21.7172 Evaluate side-chains 66 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.127869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.110783 restraints weight = 29010.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.115194 restraints weight = 13414.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.117971 restraints weight = 7418.158| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.2601 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= 0.145 Angle : 0.444 3.820 3774 Z= 0.250 Chirality : 0.035 0.118 427 Planarity : 0.003 0.029 440 Dihedral : 3.421 13.372 359 Min Nonbonded Distance : 2.336 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: 3.42 (0.45), residues: 319 helix: 2.72 (0.30), residues: 259 sheet: None (None), residues: 0 loop : 0.17 (0.84), residues: 60 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 0.027 0.001 PHE A 112 TYR 0.008 0.001 TYR L 111 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 78 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 MET cc_start: 0.8759 (mmm) cc_final: 0.7762 (mmm) REVERT: A 175 GLN cc_start: 0.9348 (tm-30) cc_final: 0.8934 (tm-30) REVERT: A 244 ASN cc_start: 0.8720 (m110) cc_final: 0.8394 (m110) REVERT: A 411 MET cc_start: 0.8584 (mtm) cc_final: 0.8340 (mtt) REVERT: A 421 MET cc_start: 0.7416 (tpt) cc_final: 0.6896 (tmm) REVERT: A 447 ILE cc_start: 0.8873 (tt) cc_final: 0.8592 (mt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1968 time to fit residues: 20.0259 Evaluate side-chains 67 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 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 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 = 0.3937 r_free = 0.3937 target = 0.124168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.107380 restraints weight = 31260.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.111357 restraints weight = 14779.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.113836 restraints weight = 8428.296| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2780 Z= 0.206 Angle : 0.496 4.237 3774 Z= 0.285 Chirality : 0.035 0.115 427 Planarity : 0.004 0.029 440 Dihedral : 3.524 13.763 359 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.32 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: 3.02 (0.46), residues: 319 helix: 2.41 (0.31), residues: 261 sheet: None (None), residues: 0 loop : 0.08 (0.88), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 459 HIS 0.002 0.001 HIS A 184 PHE 0.028 0.002 PHE A 112 TYR 0.011 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 76 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.392 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 165 MET cc_start: 0.8779 (mmm) cc_final: 0.8155 (mmm) REVERT: A 175 GLN cc_start: 0.9367 (tm-30) cc_final: 0.8916 (tm-30) REVERT: A 188 GLU cc_start: 0.9027 (pt0) cc_final: 0.8376 (pt0) REVERT: A 244 ASN cc_start: 0.8670 (m110) cc_final: 0.8310 (m110) REVERT: A 411 MET cc_start: 0.8664 (mtm) cc_final: 0.8389 (mtt) REVERT: A 447 ILE cc_start: 0.8855 (tt) cc_final: 0.8581 (mt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2009 time to fit residues: 19.7720 Evaluate side-chains 65 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 2 optimal weight: 0.0270 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7440 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.126777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.109622 restraints weight = 29620.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.113880 restraints weight = 13864.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.116323 restraints weight = 7768.487| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.3087 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= 0.136 Angle : 0.437 4.022 3774 Z= 0.242 Chirality : 0.034 0.113 427 Planarity : 0.003 0.032 440 Dihedral : 3.363 13.965 359 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.46), residues: 319 helix: 2.79 (0.30), residues: 261 sheet: None (None), residues: 0 loop : 0.29 (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 0.027 0.001 PHE A 112 TYR 0.009 0.001 TYR A 350 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 to be fit. rotamer outliers: 0 poor density : 78 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: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.8448 (mmp) cc_final: 0.7410 (tpp) REVERT: A 165 MET cc_start: 0.8756 (mmm) cc_final: 0.7758 (mmm) REVERT: A 175 GLN cc_start: 0.9384 (tm-30) cc_final: 0.8928 (tm-30) REVERT: A 244 ASN cc_start: 0.8560 (m110) cc_final: 0.8197 (m110) REVERT: A 411 MET cc_start: 0.8623 (mtm) cc_final: 0.8271 (mtt) REVERT: A 447 ILE cc_start: 0.8790 (tt) cc_final: 0.8577 (mt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2004 time to fit residues: 20.1906 Evaluate side-chains 69 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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: 0.5980 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.125286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.108682 restraints weight = 30995.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.112899 restraints weight = 14601.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.115190 restraints weight = 8210.531| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2780 Z= 0.166 Angle : 0.452 3.882 3774 Z= 0.258 Chirality : 0.034 0.113 427 Planarity : 0.003 0.034 440 Dihedral : 3.365 14.056 359 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.39 (0.46), residues: 319 helix: 2.69 (0.30), residues: 260 sheet: None (None), residues: 0 loop : 0.14 (0.92), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 281 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 to be fit. 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: A 116 MET cc_start: 0.8497 (mmp) cc_final: 0.7518 (tpp) REVERT: A 165 MET cc_start: 0.8741 (mmm) cc_final: 0.8328 (mmm) REVERT: A 175 GLN cc_start: 0.9386 (tm-30) cc_final: 0.8934 (tm-30) REVERT: A 188 GLU cc_start: 0.9038 (pt0) cc_final: 0.8332 (pt0) REVERT: A 244 ASN cc_start: 0.8625 (m110) cc_final: 0.8276 (m110) REVERT: A 411 MET cc_start: 0.8618 (mtm) cc_final: 0.8347 (mtt) REVERT: A 447 ILE cc_start: 0.8834 (tt) cc_final: 0.8590 (mt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2204 time to fit residues: 22.2110 Evaluate side-chains 67 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.124386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.108267 restraints weight = 31586.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.112284 restraints weight = 14914.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.114678 restraints weight = 8460.061| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.3394 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= 0.192 Angle : 0.476 3.883 3774 Z= 0.274 Chirality : 0.035 0.116 427 Planarity : 0.004 0.031 440 Dihedral : 3.500 14.341 359 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.50 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: 3.20 (0.46), residues: 319 helix: 2.52 (0.30), residues: 261 sheet: None (None), residues: 0 loop : 0.24 (0.93), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 459 HIS 0.002 0.001 HIS A 184 PHE 0.022 0.002 PHE A 112 TYR 0.015 0.001 TYR A 225 ARG 0.001 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 78 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.414 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 112 PHE cc_start: 0.9206 (m-80) cc_final: 0.8984 (m-10) REVERT: A 165 MET cc_start: 0.8812 (mmm) cc_final: 0.7994 (mmm) REVERT: A 175 GLN cc_start: 0.9371 (tm-30) cc_final: 0.8899 (tm-30) REVERT: A 188 GLU cc_start: 0.9028 (pt0) cc_final: 0.8374 (pt0) REVERT: A 244 ASN cc_start: 0.8617 (m110) cc_final: 0.8259 (m110) REVERT: A 411 MET cc_start: 0.8707 (mtm) cc_final: 0.8421 (mtt) REVERT: A 447 ILE cc_start: 0.8862 (tt) cc_final: 0.8638 (mt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2020 time to fit residues: 20.5907 Evaluate side-chains 67 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 17 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.127148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.109803 restraints weight = 31772.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.114186 restraints weight = 14636.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.116737 restraints weight = 8108.397| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2780 Z= 0.146 Angle : 0.459 4.416 3774 Z= 0.258 Chirality : 0.035 0.149 427 Planarity : 0.003 0.034 440 Dihedral : 3.430 14.291 359 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.95 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: 3.35 (0.46), residues: 319 helix: 2.66 (0.30), residues: 260 sheet: None (None), residues: 0 loop : 0.14 (0.91), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 451 HIS 0.003 0.001 HIS A 184 PHE 0.024 0.001 PHE A 112 TYR 0.010 0.001 TYR A 350 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 to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.567 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 112 PHE cc_start: 0.9221 (m-80) cc_final: 0.9017 (m-10) REVERT: A 116 MET cc_start: 0.8448 (mmp) cc_final: 0.7571 (tpp) REVERT: A 165 MET cc_start: 0.8785 (mmm) cc_final: 0.7970 (mmm) REVERT: A 175 GLN cc_start: 0.9444 (tm-30) cc_final: 0.8971 (tm-30) REVERT: A 188 GLU cc_start: 0.8984 (pt0) cc_final: 0.8322 (pt0) REVERT: A 244 ASN cc_start: 0.8584 (m110) cc_final: 0.8244 (m110) REVERT: A 411 MET cc_start: 0.8711 (mtm) cc_final: 0.8380 (mtt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1992 time to fit residues: 19.8622 Evaluate side-chains 69 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.125448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.109259 restraints weight = 32907.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.113282 restraints weight = 15301.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.115618 restraints weight = 8642.190| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2780 Z= 0.191 Angle : 0.493 4.512 3774 Z= 0.283 Chirality : 0.035 0.120 427 Planarity : 0.004 0.032 440 Dihedral : 3.461 14.438 359 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.43 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 (0.46), residues: 319 helix: 2.44 (0.30), residues: 260 sheet: None (None), residues: 0 loop : 0.06 (0.90), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 459 HIS 0.003 0.001 HIS A 184 PHE 0.023 0.001 PHE A 112 TYR 0.015 0.001 TYR A 225 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: 2336.32 seconds wall clock time: 41 minutes 53.42 seconds (2513.42 seconds total)