Starting phenix.real_space_refine on Wed Feb 12 01:15:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m8j_23717/02_2025/7m8j_23717.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m8j_23717/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7m8j_23717/02_2025/7m8j_23717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m8j_23717/02_2025/7m8j_23717.map" model { file = "/net/cci-nas-00/data/ceres_data/7m8j_23717/02_2025/7m8j_23717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m8j_23717/02_2025/7m8j_23717.cif" } resolution = 3.48 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= -0.008 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.01, per 1000 atoms: 0.72 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: 1.55 Conformation dependent library (CDL) restraints added in 625.1 milliseconds 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: 0.67 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: 2.22 Time building geometry restraints manager: 1.90 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: 6.140 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: 0.120 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 20.060 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.400 ------------------------------------------------------------------------------- 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 3607 Z= 0.407 Angle : 0.960 8.488 4906 Z= 0.538 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 (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: -0.32 (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 TRP 0.012 0.003 TRP L 41 HIS 0.013 0.003 HIS L 115 PHE 0.016 0.003 PHE L 118 TYR 0.021 0.004 TYR H 28 ARG 0.045 0.008 ARG A 102 *********************** 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 : 0.554 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2686 time to fit residues: 14.6427 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 : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.0980 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.111416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.080402 restraints weight = 20978.248| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.56 r_work: 0.3076 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3607 Z= 0.252 Angle : 0.688 4.951 4906 Z= 0.378 Chirality : 0.046 0.147 538 Planarity : 0.004 0.026 627 Dihedral : 6.522 23.012 485 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.03 % Allowed : 7.24 % Favored : 91.73 % 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: -0.30 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 1.02 (0.39), residues: 171 loop : -1.08 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 104 HIS 0.008 0.002 HIS L 115 PHE 0.011 0.001 PHE A 92 TYR 0.011 0.002 TYR A 266 ARG 0.007 0.001 ARG A 21 *********************** 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 : 0.488 Fit side-chains REVERT: A 137 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.7997 (t0) REVERT: H 11 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7695 (mt-10) REVERT: H 90 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7118 (tm-30) outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 0.3027 time to fit residues: 15.7921 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 : 0.607 ------------------------------------------------------------------------------- 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 4 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 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 = 0.3737 r_free = 0.3737 target = 0.111516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.080975 restraints weight = 21312.517| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.50 r_work: 0.3094 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3607 Z= 0.236 Angle : 0.608 5.357 4906 Z= 0.331 Chirality : 0.044 0.142 538 Planarity : 0.003 0.025 627 Dihedral : 6.061 21.610 485 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.78 % Allowed : 9.56 % Favored : 89.66 % 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: -0.45 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 0.84 (0.39), residues: 171 loop : -1.12 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 104 HIS 0.006 0.001 HIS L 115 PHE 0.009 0.001 PHE A 86 TYR 0.011 0.002 TYR A 266 ARG 0.003 0.000 ARG A 78 *********************** 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 : 0.538 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 41 average time/residue: 0.2795 time to fit residues: 14.9356 Evaluate side-chains 35 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 20 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.111756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.080941 restraints weight = 21409.119| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.53 r_work: 0.3099 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3607 Z= 0.206 Angle : 0.568 5.326 4906 Z= 0.306 Chirality : 0.044 0.138 538 Planarity : 0.003 0.024 627 Dihedral : 5.612 20.177 485 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.03 % Allowed : 13.18 % Favored : 85.79 % 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: -0.48 (0.40), residues: 443 helix: None (None), residues: 0 sheet: 0.89 (0.38), residues: 167 loop : -1.17 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.006 0.001 HIS L 115 PHE 0.008 0.001 PHE A 86 TYR 0.010 0.001 TYR A 266 ARG 0.003 0.000 ARG A 78 *********************** 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 42 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.558 Fit side-chains REVERT: L 17 GLN cc_start: 0.8136 (mp10) cc_final: 0.7926 (mp10) outliers start: 4 outliers final: 3 residues processed: 41 average time/residue: 0.2690 time to fit residues: 14.3900 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 : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 112 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 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 = 0.3718 r_free = 0.3718 target = 0.110603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.079115 restraints weight = 21317.297| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.63 r_work: 0.3057 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3607 Z= 0.280 Angle : 0.587 6.639 4906 Z= 0.313 Chirality : 0.044 0.143 538 Planarity : 0.003 0.035 627 Dihedral : 5.492 20.092 485 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.29 % Allowed : 14.47 % Favored : 84.24 % 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: -0.58 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 0.83 (0.37), residues: 176 loop : -1.32 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.007 0.001 HIS L 115 PHE 0.014 0.002 PHE A 86 TYR 0.014 0.002 TYR A 266 ARG 0.003 0.000 ARG A 78 *********************** 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 43 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 40 average time/residue: 0.3039 time to fit residues: 15.6788 Evaluate side-chains 41 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 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 41 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 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 = 0.3706 r_free = 0.3706 target = 0.110309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.078845 restraints weight = 21138.702| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.59 r_work: 0.3044 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3607 Z= 0.233 Angle : 0.554 5.093 4906 Z= 0.297 Chirality : 0.043 0.139 538 Planarity : 0.003 0.032 627 Dihedral : 5.267 18.705 485 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.29 % Allowed : 15.25 % Favored : 83.46 % 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: -0.66 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 0.92 (0.38), residues: 164 loop : -1.39 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 104 HIS 0.005 0.001 HIS L 115 PHE 0.010 0.001 PHE A 86 TYR 0.010 0.001 TYR H 103 ARG 0.003 0.000 ARG A 78 *********************** 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 41 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.575 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 39 average time/residue: 0.3090 time to fit residues: 15.4146 Evaluate side-chains 40 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 115 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 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 = 0.3700 r_free = 0.3700 target = 0.109871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.078091 restraints weight = 20954.363| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.58 r_work: 0.3028 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3607 Z= 0.281 Angle : 0.572 5.150 4906 Z= 0.308 Chirality : 0.044 0.144 538 Planarity : 0.003 0.033 627 Dihedral : 5.280 19.339 485 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.33 % Allowed : 16.54 % Favored : 81.14 % 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: -0.71 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 0.76 (0.37), residues: 181 loop : -1.45 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 104 HIS 0.005 0.001 HIS L 115 PHE 0.014 0.002 PHE A 86 TYR 0.012 0.001 TYR A 266 ARG 0.005 0.001 ARG A 214 *********************** 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: 9 poor density : 40 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: H 97 GLU cc_start: 0.8631 (mp0) cc_final: 0.8162 (pp20) outliers start: 9 outliers final: 8 residues processed: 45 average time/residue: 0.2839 time to fit residues: 16.4661 Evaluate side-chains 45 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 28 TYR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 57 ASN Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 115 HIS Chi-restraints excluded: chain L residue 122 THR 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 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 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 = 0.3708 r_free = 0.3708 target = 0.110306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.078687 restraints weight = 21241.384| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.60 r_work: 0.3045 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3607 Z= 0.218 Angle : 0.548 5.098 4906 Z= 0.292 Chirality : 0.043 0.140 538 Planarity : 0.003 0.030 627 Dihedral : 5.164 19.684 485 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.33 % Allowed : 16.80 % Favored : 80.88 % 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: -0.72 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 0.76 (0.37), residues: 181 loop : -1.48 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 104 HIS 0.005 0.001 HIS L 115 PHE 0.010 0.001 PHE A 86 TYR 0.009 0.001 TYR H 103 ARG 0.003 0.000 ARG A 78 *********************** 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 50 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8864 (tp30) cc_final: 0.8474 (tp30) outliers start: 9 outliers final: 7 residues processed: 45 average time/residue: 0.2910 time to fit residues: 16.8464 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 : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 28 TYR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 5 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 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 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 = 0.3697 r_free = 0.3697 target = 0.109747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.077993 restraints weight = 21366.922| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.60 r_work: 0.3031 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3607 Z= 0.279 Angle : 0.567 5.760 4906 Z= 0.304 Chirality : 0.044 0.146 538 Planarity : 0.003 0.031 627 Dihedral : 5.190 20.048 485 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.33 % Allowed : 17.31 % Favored : 80.36 % 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: -0.78 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 0.74 (0.37), residues: 181 loop : -1.53 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 104 HIS 0.006 0.001 HIS L 115 PHE 0.013 0.002 PHE A 86 TYR 0.012 0.001 TYR H 103 ARG 0.004 0.000 ARG A 78 *********************** 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 49 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8876 (tp30) cc_final: 0.8515 (tp30) REVERT: A 185 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.6124 (t0) REVERT: A 187 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7582 (mttp) REVERT: H 97 GLU cc_start: 0.8643 (mp0) cc_final: 0.8200 (pp20) outliers start: 9 outliers final: 7 residues processed: 45 average time/residue: 0.3064 time to fit residues: 17.7104 Evaluate side-chains 47 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 28 TYR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 5 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 42 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 0.0970 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 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 = 0.3707 r_free = 0.3707 target = 0.110372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.078511 restraints weight = 21625.675| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.63 r_work: 0.3030 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3607 Z= 0.232 Angle : 0.551 5.080 4906 Z= 0.295 Chirality : 0.043 0.141 538 Planarity : 0.003 0.029 627 Dihedral : 5.091 20.561 485 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.07 % Allowed : 17.31 % 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 (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: -0.76 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 0.79 (0.38), residues: 181 loop : -1.55 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.005 0.001 HIS L 115 PHE 0.010 0.001 PHE A 86 TYR 0.009 0.001 TYR H 103 ARG 0.004 0.000 ARG A 78 ********************** 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 48 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8843 (tp30) cc_final: 0.8493 (tp30) REVERT: A 185 ASN cc_start: 0.7401 (OUTLIER) cc_final: 0.6214 (t0) REVERT: H 97 GLU cc_start: 0.8559 (mp0) cc_final: 0.7965 (pp20) outliers start: 8 outliers final: 7 residues processed: 45 average time/residue: 0.2922 time to fit residues: 16.9599 Evaluate side-chains 47 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 28 TYR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 5 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 27 optimal weight: 0.0060 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 35 optimal weight: 0.0980 chunk 16 optimal weight: 0.4980 chunk 9 optimal weight: 0.0570 chunk 34 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 overall best weight: 0.2314 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.111928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.080738 restraints weight = 20980.538| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 3.56 r_work: 0.3081 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3607 Z= 0.147 Angle : 0.516 5.091 4906 Z= 0.273 Chirality : 0.043 0.142 538 Planarity : 0.003 0.024 627 Dihedral : 4.787 19.492 485 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.55 % Allowed : 17.57 % Favored : 80.88 % 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: -0.66 (0.39), residues: 443 helix: None (None), residues: 0 sheet: 1.10 (0.38), residues: 171 loop : -1.58 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 104 HIS 0.004 0.001 HIS L 115 PHE 0.008 0.001 PHE A 92 TYR 0.007 0.001 TYR A 91 ARG 0.004 0.000 ARG A 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4369.36 seconds wall clock time: 77 minutes 42.44 seconds (4662.44 seconds total)