Starting phenix.real_space_refine on Wed Sep 17 08:03:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m8j_23717/09_2025/7m8j_23717.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m8j_23717/09_2025/7m8j_23717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m8j_23717/09_2025/7m8j_23717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m8j_23717/09_2025/7m8j_23717.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m8j_23717/09_2025/7m8j_23717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m8j_23717/09_2025/7m8j_23717.map" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.008 sd= 0.083 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 14 5.16 5 C 2238 2.51 5 N 589 2.21 5 O 676 1.98 5 H 3398 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6915 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3541 Classifications: {'peptide': 224} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Chain: "H" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1799 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "L" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1575 Classifications: {'peptide': 109} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Time building chain proxies: 1.63, per 1000 atoms: 0.24 Number of scatterers: 6915 At special positions: 0 Unit cell: (100.1, 74.8, 94.6, 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 14 16.00 O 676 8.00 N 589 7.00 C 2238 6.00 H 3398 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.04 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: 0.62 Conformation dependent library (CDL) restraints added in 280.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 822 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 3.1% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 156 through 159 Processing helix chain 'H' and resid 29 through 37 Processing helix chain 'H' and resid 95 through 99 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.232A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.013A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.985A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.247A pdb=" N GLU H 11 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N MET H 39 " --> pdb=" O GLY H 55 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLY H 55 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TRP H 41 " --> pdb=" O MET H 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.020A pdb=" N VAL L 11 " --> pdb=" O THR L 125 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.020A pdb=" N VAL L 11 " --> pdb=" O THR L 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 24 removed outlier: 4.025A pdb=" N VAL L 19 " --> pdb=" O ILE L 91 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE L 91 " --> pdb=" O VAL L 19 " (cutoff:3.500A) 119 hydrogen bonds defined for protein. 282 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 3398 1.04 - 1.26: 569 1.26 - 1.47: 1552 1.47 - 1.69: 1466 1.69 - 1.91: 20 Bond restraints: 7005 Sorted by residual: bond pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " ideal model delta sigma weight residual 1.808 1.906 -0.098 3.30e-02 9.18e+02 8.80e+00 bond pdb=" CB CYS A 166 " pdb=" SG CYS A 166 " ideal model delta sigma weight residual 1.808 1.718 0.090 3.30e-02 9.18e+02 7.51e+00 bond pdb=" CG GLN H 72 " pdb=" CD GLN H 72 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 3.97e+00 bond pdb=" CB ASP A 111 " pdb=" CG ASP A 111 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.49e+00 bond pdb=" N GLN H 72 " pdb=" CA GLN H 72 " ideal model delta sigma weight residual 1.458 1.475 -0.017 1.23e-02 6.61e+03 1.84e+00 ... (remaining 7000 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 12031 1.70 - 3.40: 501 3.40 - 5.09: 47 5.09 - 6.79: 11 6.79 - 8.49: 2 Bond angle restraints: 12592 Sorted by residual: angle pdb=" N PHE H 71 " pdb=" CA PHE H 71 " pdb=" C PHE H 71 " ideal model delta sigma weight residual 113.28 119.15 -5.87 1.22e+00 6.72e-01 2.32e+01 angle pdb=" N CYS A 131 " pdb=" CA CYS A 131 " pdb=" C CYS A 131 " ideal model delta sigma weight residual 109.07 102.45 6.62 1.52e+00 4.33e-01 1.90e+01 angle pdb=" N THR A 167 " pdb=" CA THR A 167 " pdb=" C THR A 167 " ideal model delta sigma weight residual 110.80 118.99 -8.19 2.13e+00 2.20e-01 1.48e+01 angle pdb=" CA CYS A 131 " pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " ideal model delta sigma weight residual 114.40 122.89 -8.49 2.30e+00 1.89e-01 1.36e+01 angle pdb=" N LYS A 113 " pdb=" CA LYS A 113 " pdb=" CB LYS A 113 " ideal model delta sigma weight residual 110.39 116.08 -5.69 1.75e+00 3.27e-01 1.06e+01 ... (remaining 12587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3013 17.94 - 35.88: 250 35.88 - 53.81: 68 53.81 - 71.75: 21 71.75 - 89.69: 3 Dihedral angle restraints: 3355 sinusoidal: 1778 harmonic: 1577 Sorted by residual: dihedral pdb=" CA LYS A 97 " pdb=" C LYS A 97 " pdb=" N SER A 98 " pdb=" CA SER A 98 " ideal model delta harmonic sigma weight residual 180.00 -151.28 -28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA PHE H 71 " pdb=" C PHE H 71 " pdb=" N GLN H 72 " pdb=" CA GLN H 72 " ideal model delta harmonic sigma weight residual -180.00 -154.17 -25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA PRO A 217 " pdb=" C PRO A 217 " pdb=" N GLN A 218 " pdb=" CA GLN A 218 " ideal model delta harmonic sigma weight residual 180.00 154.34 25.66 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 3352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 341 0.044 - 0.088: 131 0.088 - 0.131: 53 0.131 - 0.175: 10 0.175 - 0.219: 3 Chirality restraints: 538 Sorted by residual: chirality pdb=" CG LEU A 249 " pdb=" CB LEU A 249 " pdb=" CD1 LEU A 249 " pdb=" CD2 LEU A 249 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA CYS A 131 " pdb=" N CYS A 131 " pdb=" C CYS A 131 " pdb=" CB CYS A 131 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA LYS A 113 " pdb=" N LYS A 113 " pdb=" C LYS A 113 " pdb=" CB LYS A 113 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.58e-01 ... (remaining 535 not shown) Planarity restraints: 1053 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 95 " 0.033 9.50e-02 1.11e+02 3.47e-02 2.44e+01 pdb=" NE ARG H 95 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG H 95 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG H 95 " -0.076 2.00e-02 2.50e+03 pdb=" NH2 ARG H 95 " -0.003 2.00e-02 2.50e+03 pdb="HH11 ARG H 95 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG H 95 " 0.058 2.00e-02 2.50e+03 pdb="HH21 ARG H 95 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG H 95 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 69 " 0.019 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C GLN H 69 " -0.064 2.00e-02 2.50e+03 pdb=" O GLN H 69 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS H 70 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 75 " 0.005 9.50e-02 1.11e+02 2.28e-02 1.16e+01 pdb=" NE ARG H 75 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG H 75 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG H 75 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG H 75 " -0.045 2.00e-02 2.50e+03 pdb="HH11 ARG H 75 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG H 75 " -0.013 2.00e-02 2.50e+03 pdb="HH21 ARG H 75 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 75 " 0.044 2.00e-02 2.50e+03 ... (remaining 1050 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 171 2.10 - 2.73: 11573 2.73 - 3.35: 17850 3.35 - 3.98: 22465 3.98 - 4.60: 35263 Nonbonded interactions: 87322 Sorted by model distance: nonbonded pdb=" OD2 ASP A 111 " pdb=" HZ1 LYS A 113 " model vdw 1.481 2.450 nonbonded pdb=" O ARG A 21 " pdb="HE22 GLN A 23 " model vdw 1.488 2.450 nonbonded pdb=" OD2 ASP A 111 " pdb=" HZ3 LYS A 113 " model vdw 1.573 2.450 nonbonded pdb=" O PRO L 15 " pdb="HE22 GLN L 17 " model vdw 1.659 2.450 nonbonded pdb=" OE1 GLN H 72 " pdb=" H GLN H 72 " model vdw 1.701 2.450 ... (remaining 87317 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 individual isotropic 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: 6.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.850 Find NCS groups from input model: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 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 : 0.006 0.098 3611 Z= 0.264 Angle : 0.977 10.056 4914 Z= 0.545 Chirality : 0.055 0.219 538 Planarity : 0.005 0.037 627 Dihedral : 14.719 89.686 1268 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.37), residues: 443 helix: None (None), residues: 0 sheet: 1.25 (0.38), residues: 172 loop : -1.30 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.008 ARG A 102 TYR 0.021 0.004 TYR H 28 PHE 0.016 0.003 PHE L 118 TRP 0.012 0.003 TRP L 41 HIS 0.013 0.003 HIS L 115 Details of bonding type rmsd covalent geometry : bond 0.00627 ( 3607) covalent geometry : angle 0.96043 ( 4906) SS BOND : bond 0.00791 ( 4) SS BOND : angle 4.60506 ( 8) hydrogen bonds : bond 0.25260 ( 115) hydrogen bonds : angle 8.71538 ( 282) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.192 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1261 time to fit residues: 6.8529 Evaluate side-chains 34 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.0980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 185 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.111953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.081333 restraints weight = 21348.956| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.51 r_work: 0.3101 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3611 Z= 0.156 Angle : 0.683 4.913 4914 Z= 0.374 Chirality : 0.046 0.144 538 Planarity : 0.004 0.026 627 Dihedral : 6.478 22.757 485 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.03 % Allowed : 6.98 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 1.03 (0.39), residues: 171 loop : -1.05 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 21 TYR 0.011 0.002 TYR A 266 PHE 0.012 0.001 PHE A 92 TRP 0.011 0.001 TRP A 104 HIS 0.009 0.002 HIS L 115 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 3607) covalent geometry : angle 0.67986 ( 4906) SS BOND : bond 0.00455 ( 4) SS BOND : angle 1.74813 ( 8) hydrogen bonds : bond 0.05743 ( 115) hydrogen bonds : angle 6.52334 ( 282) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.200 Fit side-chains REVERT: A 137 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.7988 (t0) REVERT: H 90 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7040 (tm-30) outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 0.1449 time to fit residues: 7.5285 Evaluate side-chains 36 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain L residue 112 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 0.0970 chunk 43 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.111790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.081271 restraints weight = 21273.266| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.49 r_work: 0.3101 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3611 Z= 0.144 Angle : 0.604 5.353 4914 Z= 0.328 Chirality : 0.044 0.142 538 Planarity : 0.003 0.024 627 Dihedral : 6.006 21.375 485 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.78 % Allowed : 9.82 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 0.85 (0.38), residues: 171 loop : -1.07 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.011 0.001 TYR A 266 PHE 0.009 0.001 PHE A 86 TRP 0.008 0.001 TRP A 104 HIS 0.006 0.001 HIS L 115 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 3607) covalent geometry : angle 0.60172 ( 4906) SS BOND : bond 0.00465 ( 4) SS BOND : angle 1.41535 ( 8) hydrogen bonds : bond 0.05034 ( 115) hydrogen bonds : angle 6.10244 ( 282) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.198 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 41 average time/residue: 0.1265 time to fit residues: 6.7676 Evaluate side-chains 36 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain L residue 57 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.0010 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.1980 chunk 22 optimal weight: 0.7980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.112074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.081452 restraints weight = 21193.374| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.51 r_work: 0.3107 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3611 Z= 0.123 Angle : 0.564 5.279 4914 Z= 0.304 Chirality : 0.044 0.139 538 Planarity : 0.003 0.024 627 Dihedral : 5.551 19.618 485 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.78 % Allowed : 12.66 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.40), residues: 443 helix: None (None), residues: 0 sheet: 0.93 (0.38), residues: 167 loop : -1.12 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.009 0.001 TYR A 266 PHE 0.007 0.001 PHE A 92 TRP 0.007 0.001 TRP A 104 HIS 0.005 0.001 HIS L 115 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 3607) covalent geometry : angle 0.56240 ( 4906) SS BOND : bond 0.00416 ( 4) SS BOND : angle 1.14382 ( 8) hydrogen bonds : bond 0.04247 ( 115) hydrogen bonds : angle 5.77601 ( 282) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.201 Fit side-chains REVERT: A 96 GLU cc_start: 0.8775 (tp30) cc_final: 0.8515 (tp30) REVERT: H 62 ASP cc_start: 0.9193 (OUTLIER) cc_final: 0.8990 (t70) REVERT: L 17 GLN cc_start: 0.8112 (mp10) cc_final: 0.7880 (mp10) outliers start: 3 outliers final: 2 residues processed: 41 average time/residue: 0.1328 time to fit residues: 7.0699 Evaluate side-chains 38 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain L residue 57 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.111016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.080060 restraints weight = 21311.637| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.53 r_work: 0.3080 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3611 Z= 0.167 Angle : 0.580 6.833 4914 Z= 0.309 Chirality : 0.044 0.144 538 Planarity : 0.003 0.033 627 Dihedral : 5.423 19.487 485 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.81 % Allowed : 13.70 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 0.79 (0.38), residues: 167 loop : -1.22 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.013 0.001 TYR A 266 PHE 0.013 0.001 PHE A 86 TRP 0.007 0.001 TRP A 104 HIS 0.007 0.001 HIS L 115 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 3607) covalent geometry : angle 0.57850 ( 4906) SS BOND : bond 0.00562 ( 4) SS BOND : angle 1.27553 ( 8) hydrogen bonds : bond 0.04756 ( 115) hydrogen bonds : angle 5.71851 ( 282) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: H 62 ASP cc_start: 0.9241 (OUTLIER) cc_final: 0.9020 (t70) outliers start: 7 outliers final: 6 residues processed: 39 average time/residue: 0.1348 time to fit residues: 6.9056 Evaluate side-chains 41 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 112 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.110846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.079231 restraints weight = 20985.001| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.59 r_work: 0.3056 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3611 Z= 0.139 Angle : 0.550 5.060 4914 Z= 0.294 Chirality : 0.043 0.139 538 Planarity : 0.003 0.032 627 Dihedral : 5.212 18.235 485 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.03 % Allowed : 15.76 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 0.95 (0.38), residues: 162 loop : -1.33 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.009 0.001 TYR A 266 PHE 0.009 0.001 PHE A 86 TRP 0.007 0.001 TRP A 104 HIS 0.005 0.001 HIS L 115 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 3607) covalent geometry : angle 0.54867 ( 4906) SS BOND : bond 0.00414 ( 4) SS BOND : angle 1.07204 ( 8) hydrogen bonds : bond 0.04252 ( 115) hydrogen bonds : angle 5.56971 ( 282) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8906 (tp30) cc_final: 0.8523 (tp30) REVERT: H 62 ASP cc_start: 0.9279 (OUTLIER) cc_final: 0.8694 (t70) outliers start: 4 outliers final: 3 residues processed: 41 average time/residue: 0.1260 time to fit residues: 6.7638 Evaluate side-chains 39 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain L residue 57 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 13 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 0.0570 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.0010 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 9 optimal weight: 0.0070 overall best weight: 0.3122 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.112212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.080658 restraints weight = 20980.181| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.60 r_work: 0.3079 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 3611 Z= 0.101 Angle : 0.526 5.170 4914 Z= 0.279 Chirality : 0.043 0.140 538 Planarity : 0.003 0.028 627 Dihedral : 4.926 17.010 485 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.81 % Allowed : 15.50 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 1.09 (0.38), residues: 164 loop : -1.31 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.006 0.001 TYR H 103 PHE 0.007 0.001 PHE A 92 TRP 0.007 0.001 TRP A 104 HIS 0.004 0.001 HIS L 115 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 3607) covalent geometry : angle 0.52571 ( 4906) SS BOND : bond 0.00375 ( 4) SS BOND : angle 0.88102 ( 8) hydrogen bonds : bond 0.03546 ( 115) hydrogen bonds : angle 5.35930 ( 282) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8781 (tp30) cc_final: 0.8458 (tp30) REVERT: H 62 ASP cc_start: 0.9260 (OUTLIER) cc_final: 0.8742 (t70) REVERT: H 97 GLU cc_start: 0.8653 (mp0) cc_final: 0.8135 (pp20) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.1325 time to fit residues: 8.1798 Evaluate side-chains 44 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain H residue 28 TYR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 115 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 29 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.111349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.079744 restraints weight = 21247.392| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.60 r_work: 0.3066 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3611 Z= 0.130 Angle : 0.541 4.941 4914 Z= 0.287 Chirality : 0.043 0.139 538 Planarity : 0.003 0.028 627 Dihedral : 4.919 17.787 485 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.81 % Allowed : 16.54 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.40), residues: 443 helix: None (None), residues: 0 sheet: 1.00 (0.38), residues: 182 loop : -1.31 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.009 0.001 TYR A 266 PHE 0.009 0.001 PHE A 86 TRP 0.005 0.001 TRP A 104 HIS 0.004 0.001 HIS L 115 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 3607) covalent geometry : angle 0.54005 ( 4906) SS BOND : bond 0.00498 ( 4) SS BOND : angle 1.05520 ( 8) hydrogen bonds : bond 0.03903 ( 115) hydrogen bonds : angle 5.35590 ( 282) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8836 (tp30) cc_final: 0.8508 (tp30) REVERT: A 185 ASN cc_start: 0.7243 (OUTLIER) cc_final: 0.6141 (t0) REVERT: H 62 ASP cc_start: 0.9261 (OUTLIER) cc_final: 0.8743 (t70) outliers start: 7 outliers final: 4 residues processed: 45 average time/residue: 0.1295 time to fit residues: 7.5772 Evaluate side-chains 43 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain H residue 28 TYR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 115 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 15 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.111025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.079256 restraints weight = 21206.458| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.61 r_work: 0.3055 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3611 Z= 0.142 Angle : 0.548 5.815 4914 Z= 0.292 Chirality : 0.043 0.143 538 Planarity : 0.003 0.028 627 Dihedral : 4.932 19.667 485 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.81 % Allowed : 16.80 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 0.88 (0.38), residues: 181 loop : -1.30 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.010 0.001 TYR A 266 PHE 0.010 0.001 PHE A 86 TRP 0.006 0.001 TRP H 118 HIS 0.005 0.001 HIS L 115 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 3607) covalent geometry : angle 0.54701 ( 4906) SS BOND : bond 0.00448 ( 4) SS BOND : angle 1.06902 ( 8) hydrogen bonds : bond 0.04081 ( 115) hydrogen bonds : angle 5.35749 ( 282) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8858 (tp30) cc_final: 0.8535 (tp30) REVERT: A 185 ASN cc_start: 0.7255 (OUTLIER) cc_final: 0.6147 (t0) REVERT: H 62 ASP cc_start: 0.9251 (OUTLIER) cc_final: 0.8760 (t70) REVERT: H 97 GLU cc_start: 0.8717 (mp0) cc_final: 0.8229 (pp20) outliers start: 7 outliers final: 4 residues processed: 46 average time/residue: 0.1361 time to fit residues: 7.9989 Evaluate side-chains 44 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain H residue 28 TYR Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 115 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 0.0570 chunk 27 optimal weight: 0.0270 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 35 optimal weight: 0.0670 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 0.1894 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.113182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.081508 restraints weight = 21131.699| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.62 r_work: 0.3092 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3611 Z= 0.094 Angle : 0.524 5.291 4914 Z= 0.276 Chirality : 0.043 0.141 538 Planarity : 0.003 0.024 627 Dihedral : 4.690 18.983 485 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.03 % Allowed : 18.35 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.40), residues: 443 helix: None (None), residues: 0 sheet: 1.10 (0.38), residues: 182 loop : -1.30 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 78 TYR 0.006 0.001 TYR A 91 PHE 0.007 0.001 PHE A 92 TRP 0.008 0.001 TRP A 104 HIS 0.003 0.001 HIS L 115 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 3607) covalent geometry : angle 0.52302 ( 4906) SS BOND : bond 0.00373 ( 4) SS BOND : angle 0.85564 ( 8) hydrogen bonds : bond 0.03172 ( 115) hydrogen bonds : angle 5.17977 ( 282) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 185 ASN cc_start: 0.7227 (OUTLIER) cc_final: 0.6107 (t0) outliers start: 4 outliers final: 3 residues processed: 43 average time/residue: 0.1417 time to fit residues: 7.8017 Evaluate side-chains 40 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain H residue 28 TYR Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 115 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.112139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.080374 restraints weight = 21193.733| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.62 r_work: 0.3072 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.003 0.035 3611 Z= 0.125 Angle : 0.542 6.395 4914 Z= 0.285 Chirality : 0.043 0.141 538 Planarity : 0.003 0.027 627 Dihedral : 4.721 19.636 485 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.29 % Allowed : 18.86 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.40), residues: 443 helix: None (None), residues: 0 sheet: 1.03 (0.38), residues: 184 loop : -1.30 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 78 TYR 0.008 0.001 TYR H 103 PHE 0.009 0.001 PHE A 86 TRP 0.005 0.001 TRP H 118 HIS 0.004 0.001 HIS L 115 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3607) covalent geometry : angle 0.54130 ( 4906) SS BOND : bond 0.00409 ( 4) SS BOND : angle 0.98420 ( 8) hydrogen bonds : bond 0.03729 ( 115) hydrogen bonds : angle 5.20696 ( 282) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2473.08 seconds wall clock time: 42 minutes 46.75 seconds (2566.75 seconds total)