Starting phenix.real_space_refine on Wed Mar 5 16:45:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6riu_4898/03_2025/6riu_4898.cif Found real_map, /net/cci-nas-00/data/ceres_data/6riu_4898/03_2025/6riu_4898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6riu_4898/03_2025/6riu_4898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6riu_4898/03_2025/6riu_4898.map" model { file = "/net/cci-nas-00/data/ceres_data/6riu_4898/03_2025/6riu_4898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6riu_4898/03_2025/6riu_4898.cif" } resolution = 3.9 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= 0.001 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 4 5.16 5 C 920 2.51 5 N 250 2.21 5 O 278 1.98 5 H 1430 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2882 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1441 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "B" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1441 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Time building chain proxies: 2.52, per 1000 atoms: 0.87 Number of scatterers: 2882 At special positions: 0 Unit cell: (69.828, 47.61, 49.726, 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 4 16.00 O 278 8.00 N 250 7.00 C 920 6.00 H 1430 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: 0.73 Conformation dependent library (CDL) restraints added in 197.1 milliseconds 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 340 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 90.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 1 through 17 removed outlier: 3.553A pdb=" N LYS A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU A 17 " --> pdb=" O GLN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 32 removed outlier: 3.757A pdb=" N ALA A 23 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 24 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 54 removed outlier: 4.196A pdb=" N TYR A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TRP A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 59 Processing helix chain 'A' and resid 60 through 73 removed outlier: 3.650A pdb=" N LEU A 67 " --> pdb=" O GLN A 63 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 Proline residue: A 77 - end of helix No H-bonds generated for 'chain 'A' and resid 74 through 79' Processing helix chain 'A' and resid 80 through 90 removed outlier: 4.275A pdb=" N VAL A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 17 removed outlier: 3.553A pdb=" N LYS B 9 " --> pdb=" O GLN B 5 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B 10 " --> pdb=" O GLU B 6 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 32 removed outlier: 3.758A pdb=" N ALA B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP B 29 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 54 removed outlier: 4.196A pdb=" N TYR B 42 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TRP B 43 " --> pdb=" O ASP B 39 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 59 Processing helix chain 'B' and resid 60 through 73 removed outlier: 3.650A pdb=" N LEU B 67 " --> pdb=" O GLN B 63 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 Proline residue: B 77 - end of helix No H-bonds generated for 'chain 'B' and resid 74 through 79' Processing helix chain 'B' and resid 80 through 90 removed outlier: 4.275A pdb=" N VAL B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) 75 hydrogen bonds defined for protein. 219 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 0.90 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: 1430 1.03 - 1.22: 3 1.22 - 1.42: 616 1.42 - 1.61: 853 1.61 - 1.80: 8 Bond restraints: 2910 Sorted by residual: bond pdb=" N GLY A 1 " pdb=" CA GLY A 1 " ideal model delta sigma weight residual 1.451 1.496 -0.045 1.60e-02 3.91e+03 7.95e+00 bond pdb=" N GLY B 1 " pdb=" CA GLY B 1 " ideal model delta sigma weight residual 1.451 1.496 -0.045 1.60e-02 3.91e+03 7.83e+00 bond pdb=" N LEU B 83 " pdb=" CA LEU B 83 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.23e-02 6.61e+03 7.01e+00 bond pdb=" N LEU A 83 " pdb=" CA LEU A 83 " ideal model delta sigma weight residual 1.458 1.491 -0.032 1.23e-02 6.61e+03 6.87e+00 bond pdb=" N LEU B 83 " pdb=" H LEU B 83 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.42e+00 ... (remaining 2905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 4702 2.12 - 4.24: 489 4.24 - 6.37: 41 6.37 - 8.49: 17 8.49 - 10.61: 5 Bond angle restraints: 5254 Sorted by residual: angle pdb=" N GLY B 61 " pdb=" CA GLY B 61 " pdb=" C GLY B 61 " ideal model delta sigma weight residual 112.49 103.08 9.41 1.21e+00 6.83e-01 6.04e+01 angle pdb=" N GLY A 61 " pdb=" CA GLY A 61 " pdb=" C GLY A 61 " ideal model delta sigma weight residual 112.49 103.14 9.35 1.21e+00 6.83e-01 5.97e+01 angle pdb=" N LYS B 9 " pdb=" CA LYS B 9 " pdb=" C LYS B 9 " ideal model delta sigma weight residual 112.89 106.94 5.95 1.24e+00 6.50e-01 2.30e+01 angle pdb=" N GLU B 36 " pdb=" CA GLU B 36 " pdb=" C GLU B 36 " ideal model delta sigma weight residual 110.58 117.63 -7.05 1.56e+00 4.11e-01 2.04e+01 angle pdb=" N VAL B 35 " pdb=" CA VAL B 35 " pdb=" C VAL B 35 " ideal model delta sigma weight residual 111.45 115.61 -4.16 9.30e-01 1.16e+00 2.01e+01 ... (remaining 5249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 1239 17.93 - 35.87: 71 35.87 - 53.80: 30 53.80 - 71.74: 8 71.74 - 89.67: 6 Dihedral angle restraints: 1354 sinusoidal: 742 harmonic: 612 Sorted by residual: dihedral pdb=" CA LEU A 74 " pdb=" C LEU A 74 " pdb=" N SER A 75 " pdb=" CA SER A 75 " ideal model delta harmonic sigma weight residual 180.00 156.03 23.97 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA LEU B 74 " pdb=" C LEU B 74 " pdb=" N SER B 75 " pdb=" CA SER B 75 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA LEU A 56 " pdb=" C LEU A 56 " pdb=" N ASP A 57 " pdb=" CA ASP A 57 " ideal model delta harmonic sigma weight residual 180.00 -162.27 -17.73 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 1351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 214 0.153 - 0.306: 4 0.306 - 0.459: 0 0.459 - 0.612: 0 0.612 - 0.765: 2 Chirality restraints: 220 Sorted by residual: chirality pdb=" CG LEU A 74 " pdb=" CB LEU A 74 " pdb=" CD1 LEU A 74 " pdb=" CD2 LEU A 74 " both_signs ideal model delta sigma weight residual False -2.59 -1.82 -0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" CG LEU B 74 " pdb=" CB LEU B 74 " pdb=" CD1 LEU B 74 " pdb=" CD2 LEU B 74 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" CA ALA A 34 " pdb=" N ALA A 34 " pdb=" C ALA A 34 " pdb=" CB ALA A 34 " both_signs ideal model delta sigma weight residual False 2.48 2.68 -0.20 2.00e-01 2.50e+01 9.89e-01 ... (remaining 217 not shown) Planarity restraints: 434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 59 " -0.018 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C MET B 59 " 0.065 2.00e-02 2.50e+03 pdb=" O MET B 59 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA B 60 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 59 " -0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C MET A 59 " 0.065 2.00e-02 2.50e+03 pdb=" O MET A 59 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA A 60 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 76 " 0.054 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO A 77 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 77 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 77 " 0.045 5.00e-02 4.00e+02 ... (remaining 431 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.00: 34 2.00 - 2.65: 4114 2.65 - 3.30: 8622 3.30 - 3.95: 10370 3.95 - 4.60: 15836 Nonbonded interactions: 38976 Sorted by model distance: nonbonded pdb=" OG SER A 75 " pdb=" HG SER B 75 " model vdw 1.355 2.450 nonbonded pdb=" O GLY B 30 " pdb=" HG SER B 33 " model vdw 1.488 2.450 nonbonded pdb=" O GLY A 30 " pdb=" HG SER A 33 " model vdw 1.520 2.450 nonbonded pdb=" OD1 ASP B 49 " pdb=" HH TYR B 64 " model vdw 1.659 2.450 nonbonded pdb=" O ILE A 87 " pdb=" HG1 THR A 91 " model vdw 1.713 2.450 ... (remaining 38971 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.960 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: 0.050 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.010 Find NCS groups from input model: 0.070 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 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 : 0.008 0.068 1480 Z= 0.527 Angle : 1.188 9.406 2006 Z= 0.756 Chirality : 0.089 0.765 220 Planarity : 0.011 0.081 260 Dihedral : 15.190 89.671 546 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % 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: -5.77 (0.42), residues: 178 helix: -3.50 (0.29), residues: 134 sheet: None (None), residues: 0 loop : -4.10 (0.72), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP B 79 HIS 0.000 0.000 HIS A 55 PHE 0.020 0.004 PHE A 41 TYR 0.005 0.002 TYR B 90 ARG 0.004 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.220 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 outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.4123 time to fit residues: 15.2411 Evaluate side-chains 27 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.070659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.061977 restraints weight = 38398.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.064085 restraints weight = 24222.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.065698 restraints weight = 16236.582| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1480 Z= 0.185 Angle : 0.677 6.614 2006 Z= 0.353 Chirality : 0.036 0.102 220 Planarity : 0.007 0.066 260 Dihedral : 6.019 22.474 196 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.66 % Allowed : 13.82 % Favored : 85.53 % 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: -3.97 (0.54), residues: 178 helix: -2.27 (0.37), residues: 138 sheet: None (None), residues: 0 loop : -3.18 (0.89), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 79 HIS 0.002 0.001 HIS B 55 PHE 0.009 0.002 PHE B 41 TYR 0.011 0.001 TYR B 42 ARG 0.002 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.239 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 outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.4712 time to fit residues: 13.3227 Evaluate side-chains 25 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 14 optimal weight: 4.9990 chunk 11 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 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 = 0.3829 r_free = 0.3829 target = 0.069935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.061380 restraints weight = 39674.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.063425 restraints weight = 25220.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.064951 restraints weight = 17165.949| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1480 Z= 0.177 Angle : 0.606 6.793 2006 Z= 0.323 Chirality : 0.036 0.104 220 Planarity : 0.006 0.059 260 Dihedral : 5.239 18.765 196 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.32 % Allowed : 17.76 % Favored : 80.92 % 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: -3.31 (0.57), residues: 178 helix: -1.68 (0.40), residues: 140 sheet: None (None), residues: 0 loop : -3.52 (0.94), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 79 HIS 0.001 0.001 HIS B 55 PHE 0.005 0.001 PHE B 41 TYR 0.005 0.001 TYR A 90 ARG 0.001 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.218 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 outliers start: 2 outliers final: 2 residues processed: 25 average time/residue: 0.5018 time to fit residues: 13.6520 Evaluate side-chains 25 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.071471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.062738 restraints weight = 39419.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.064865 restraints weight = 25385.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.066432 restraints weight = 17419.444| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1480 Z= 0.146 Angle : 0.565 6.795 2006 Z= 0.295 Chirality : 0.034 0.104 220 Planarity : 0.006 0.057 260 Dihedral : 4.915 16.852 196 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.32 % Allowed : 19.08 % Favored : 79.61 % 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: -2.68 (0.60), residues: 178 helix: -1.53 (0.38), residues: 160 sheet: None (None), residues: 0 loop : -1.87 (1.80), residues: 18 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 79 HIS 0.001 0.000 HIS B 55 PHE 0.006 0.001 PHE B 41 TYR 0.004 0.001 TYR B 42 ARG 0.001 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.235 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 outliers start: 2 outliers final: 2 residues processed: 26 average time/residue: 0.4210 time to fit residues: 11.9654 Evaluate side-chains 24 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.071803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.063293 restraints weight = 36594.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.065502 restraints weight = 23165.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.067069 restraints weight = 15437.479| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 1480 Z= 0.147 Angle : 0.549 7.126 2006 Z= 0.288 Chirality : 0.035 0.100 220 Planarity : 0.005 0.055 260 Dihedral : 4.641 15.953 196 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.63 % Allowed : 20.39 % Favored : 76.97 % 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: -2.31 (0.62), residues: 178 helix: -1.23 (0.39), residues: 164 sheet: None (None), residues: 0 loop : -2.44 (2.00), residues: 14 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 4 HIS 0.001 0.001 HIS B 55 PHE 0.005 0.001 PHE B 41 TYR 0.007 0.001 TYR A 90 ARG 0.002 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.221 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: B 67 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8793 (pp) outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.4357 time to fit residues: 11.4252 Evaluate side-chains 26 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 67 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 0.0670 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.070839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.062870 restraints weight = 36861.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.064897 restraints weight = 23117.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.066361 restraints weight = 15445.180| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1480 Z= 0.147 Angle : 0.517 4.696 2006 Z= 0.277 Chirality : 0.034 0.103 220 Planarity : 0.005 0.053 260 Dihedral : 4.477 15.552 196 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.97 % Allowed : 19.74 % Favored : 78.29 % 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: -1.90 (0.63), residues: 178 helix: -0.97 (0.39), residues: 164 sheet: None (None), residues: 0 loop : -2.32 (2.12), residues: 14 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 79 HIS 0.001 0.000 HIS B 55 PHE 0.004 0.001 PHE B 41 TYR 0.003 0.001 TYR B 90 ARG 0.001 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.217 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 outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 0.4458 time to fit residues: 11.1700 Evaluate side-chains 23 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 0.0980 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.078185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.070435 restraints weight = 45952.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.072307 restraints weight = 26627.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.073598 restraints weight = 16898.545| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1480 Z= 0.139 Angle : 0.505 4.140 2006 Z= 0.270 Chirality : 0.034 0.102 220 Planarity : 0.005 0.051 260 Dihedral : 4.370 15.087 196 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.97 % Allowed : 22.37 % Favored : 75.66 % 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: -1.54 (0.63), residues: 178 helix: -0.79 (0.39), residues: 168 sheet: None (None), residues: 0 loop : -1.50 (3.08), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 4 HIS 0.001 0.001 HIS B 55 PHE 0.004 0.001 PHE B 41 TYR 0.004 0.001 TYR B 90 ARG 0.001 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.196 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 outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 0.4381 time to fit residues: 10.9966 Evaluate side-chains 23 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.077294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.069894 restraints weight = 44816.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.071720 restraints weight = 26318.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.072979 restraints weight = 16859.793| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1480 Z= 0.149 Angle : 0.518 3.713 2006 Z= 0.278 Chirality : 0.035 0.114 220 Planarity : 0.005 0.050 260 Dihedral : 4.296 14.763 196 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.97 % Allowed : 22.37 % Favored : 75.66 % 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: -1.45 (0.62), residues: 178 helix: -0.43 (0.40), residues: 156 sheet: None (None), residues: 0 loop : -3.86 (1.45), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 4 HIS 0.001 0.001 HIS B 55 PHE 0.005 0.001 PHE A 41 TYR 0.005 0.001 TYR B 90 ARG 0.001 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.203 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 outliers start: 3 outliers final: 2 residues processed: 22 average time/residue: 0.4760 time to fit residues: 11.4087 Evaluate side-chains 23 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.078708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.071077 restraints weight = 44594.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.072928 restraints weight = 25948.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.074206 restraints weight = 16485.244| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1480 Z= 0.136 Angle : 0.518 6.531 2006 Z= 0.269 Chirality : 0.034 0.101 220 Planarity : 0.005 0.049 260 Dihedral : 4.240 14.277 196 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.32 % Allowed : 23.03 % Favored : 75.66 % 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: -0.89 (0.63), residues: 178 helix: -0.33 (0.39), residues: 168 sheet: None (None), residues: 0 loop : -2.11 (2.72), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 4 HIS 0.001 0.000 HIS A 55 PHE 0.005 0.001 PHE A 41 TYR 0.004 0.001 TYR A 42 ARG 0.001 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.217 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 outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.4418 time to fit residues: 11.0724 Evaluate side-chains 24 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.078989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.071327 restraints weight = 45398.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.073180 restraints weight = 26497.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.074469 restraints weight = 16778.727| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1480 Z= 0.129 Angle : 0.519 6.025 2006 Z= 0.266 Chirality : 0.034 0.099 220 Planarity : 0.005 0.049 260 Dihedral : 4.071 13.386 196 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.97 % Allowed : 21.71 % Favored : 76.32 % 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: -0.56 (0.63), residues: 178 helix: -0.09 (0.40), residues: 168 sheet: None (None), residues: 0 loop : -2.78 (2.29), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 79 HIS 0.001 0.000 HIS A 55 PHE 0.005 0.001 PHE B 41 TYR 0.003 0.001 TYR B 90 ARG 0.001 0.000 ARG A 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.216 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 outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.4290 time to fit residues: 11.2546 Evaluate side-chains 24 residues out of total 152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain B residue 6 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.078069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.070563 restraints weight = 44003.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.072406 restraints weight = 25826.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.073675 restraints weight = 16425.394| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.6041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1480 Z= 0.140 Angle : 0.521 5.813 2006 Z= 0.271 Chirality : 0.034 0.102 220 Planarity : 0.005 0.048 260 Dihedral : 4.046 12.864 196 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.97 % Allowed : 22.37 % Favored : 75.66 % 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: -0.49 (0.63), residues: 178 helix: -0.04 (0.40), residues: 168 sheet: None (None), residues: 0 loop : -2.87 (2.23), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 4 HIS 0.001 0.000 HIS A 55 PHE 0.005 0.001 PHE B 41 TYR 0.004 0.001 TYR B 90 ARG 0.001 0.000 ARG A 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2028.21 seconds wall clock time: 35 minutes 8.23 seconds (2108.23 seconds total)