Starting phenix.real_space_refine on Wed Mar 5 14:18:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w3t_32293/03_2025/7w3t_32293.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w3t_32293/03_2025/7w3t_32293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w3t_32293/03_2025/7w3t_32293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w3t_32293/03_2025/7w3t_32293.map" model { file = "/net/cci-nas-00/data/ceres_data/7w3t_32293/03_2025/7w3t_32293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w3t_32293/03_2025/7w3t_32293.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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: 4 Type Number sf(0) Gaussians S 3 5.16 5 C 915 2.51 5 N 241 2.21 5 O 296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 1455 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1360 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 13, 'TRANS': 162} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.96, per 1000 atoms: 1.35 Number of scatterers: 1455 At special positions: 0 Unit cell: (66.843, 46.684, 55.172, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 3 16.00 O 296 8.00 N 241 7.00 C 915 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 67 " distance=2.03 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN B 186 " " NAG B1000 " - " ASN B 82 " " NAG B1001 " - " ASN B 106 " " NAG B1002 " - " ASN B 117 " " NAG B1003 " - " ASN B 152 " Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 212.7 milliseconds 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 330 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 3 sheets defined 27.8% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.574A pdb=" N GLN B 93 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 94 " --> pdb=" O LEU B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 94' Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.819A pdb=" N LEU B 115 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 142 removed outlier: 3.501A pdb=" N LEU B 142 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 removed outlier: 3.565A pdb=" N VAL B 166 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.503A pdb=" N PHE B 189 " --> pdb=" O ASN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.402A pdb=" N GLY B 85 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ILE B 107 " --> pdb=" O ARG B 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 65 through 66 removed outlier: 6.383A pdb=" N VAL B 76 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU B 100 " --> pdb=" O ASP B 125 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B 124 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ASN B 151 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 148 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 175 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 157 through 158 removed outlier: 6.452A pdb=" N GLY B 157 " --> pdb=" O THR B 180 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 27 hydrogen bonds defined for protein. 39 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.32 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 475 1.34 - 1.46: 267 1.46 - 1.57: 735 1.57 - 1.69: 0 1.69 - 1.81: 4 Bond restraints: 1481 Sorted by residual: bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.75e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C1 BMA A 3 " pdb=" C2 BMA A 3 " ideal model delta sigma weight residual 1.519 1.545 -0.026 2.00e-02 2.50e+03 1.65e+00 bond pdb=" C1 NAG B1003 " pdb=" O5 NAG B1003 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.55e+00 bond pdb=" C1 NAG B1000 " pdb=" O5 NAG B1000 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.46e+00 ... (remaining 1476 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 1908 1.43 - 2.86: 103 2.86 - 4.29: 10 4.29 - 5.72: 6 5.72 - 7.15: 2 Bond angle restraints: 2029 Sorted by residual: angle pdb=" CA PRO B 134 " pdb=" C PRO B 134 " pdb=" N ILE B 135 " ideal model delta sigma weight residual 114.74 116.95 -2.21 1.03e+00 9.43e-01 4.62e+00 angle pdb=" C3 BMA A 3 " pdb=" C2 BMA A 3 " pdb=" O2 BMA A 3 " ideal model delta sigma weight residual 112.95 106.58 6.37 3.00e+00 1.11e-01 4.50e+00 angle pdb=" CA LEU B 162 " pdb=" CB LEU B 162 " pdb=" CG LEU B 162 " ideal model delta sigma weight residual 116.30 123.45 -7.15 3.50e+00 8.16e-02 4.17e+00 angle pdb=" CA CYS B 60 " pdb=" CB CYS B 60 " pdb=" SG CYS B 60 " ideal model delta sigma weight residual 114.40 109.82 4.58 2.30e+00 1.89e-01 3.96e+00 angle pdb=" C LYS B 144 " pdb=" N LEU B 145 " pdb=" CA LEU B 145 " ideal model delta sigma weight residual 122.74 119.46 3.28 1.82e+00 3.02e-01 3.26e+00 ... (remaining 2024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 897 21.50 - 43.00: 71 43.00 - 64.50: 8 64.50 - 86.00: 8 86.00 - 107.50: 4 Dihedral angle restraints: 988 sinusoidal: 480 harmonic: 508 Sorted by residual: dihedral pdb=" CB CYS B 60 " pdb=" SG CYS B 60 " pdb=" SG CYS B 67 " pdb=" CB CYS B 67 " ideal model delta sinusoidal sigma weight residual 93.00 132.69 -39.69 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" O4 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C5 BMA A 3 " pdb=" O5 BMA A 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.79 107.50 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C3 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C5 BMA A 3 " pdb=" O5 BMA A 3 " ideal model delta sinusoidal sigma weight residual 47.62 -57.71 105.33 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 209 0.055 - 0.110: 44 0.110 - 0.165: 7 0.165 - 0.220: 3 0.220 - 0.275: 1 Chirality restraints: 264 Sorted by residual: chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C1 NAG B1000 " pdb=" ND2 ASN B 82 " pdb=" C2 NAG B1000 " pdb=" O5 NAG B1000 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 106 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 261 not shown) Planarity restraints: 263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 62 " 0.018 2.00e-02 2.50e+03 1.86e-02 8.63e+00 pdb=" CG TRP B 62 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP B 62 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 62 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 62 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 62 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 62 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 62 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 62 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 62 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 159 " -0.026 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO B 160 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 160 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 160 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 58 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.53e+00 pdb=" N PRO B 59 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 59 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 59 " -0.022 5.00e-02 4.00e+02 ... (remaining 260 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 321 2.79 - 3.32: 1407 3.32 - 3.84: 2237 3.84 - 4.37: 2594 4.37 - 4.90: 4242 Nonbonded interactions: 10801 Sorted by model distance: nonbonded pdb=" OD1 ASN B 68 " pdb=" OG SER B 72 " model vdw 2.259 3.040 nonbonded pdb=" O LEU B 162 " pdb=" OG1 THR B 165 " model vdw 2.278 3.040 nonbonded pdb=" O GLY B 187 " pdb=" OG SER B 190 " model vdw 2.338 3.040 nonbonded pdb=" O LEU B 145 " pdb=" OG SER B 168 " model vdw 2.366 3.040 nonbonded pdb=" O GLY B 85 " pdb=" N SER B 108 " model vdw 2.389 3.120 ... (remaining 10796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 11.160 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 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 : 0.004 0.033 1481 Z= 0.256 Angle : 0.731 7.147 2029 Z= 0.335 Chirality : 0.052 0.275 264 Planarity : 0.006 0.040 258 Dihedral : 17.978 107.496 655 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.63), residues: 174 helix: -2.58 (0.70), residues: 44 sheet: -2.90 (0.90), residues: 28 loop : -1.17 (0.65), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.006 TRP B 62 HIS 0.001 0.001 HIS B 64 PHE 0.007 0.001 PHE B 147 TYR 0.012 0.002 TYR B 127 ARG 0.001 0.000 ARG B 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8180 (m110) cc_final: 0.7686 (t0) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1095 time to fit residues: 5.2367 Evaluate side-chains 42 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 0.0370 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.0010 chunk 10 optimal weight: 0.6980 overall best weight: 0.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.126520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.105820 restraints weight = 2207.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.109299 restraints weight = 1229.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.111802 restraints weight = 816.406| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 1481 Z= 0.265 Angle : 0.708 9.049 2029 Z= 0.331 Chirality : 0.051 0.209 264 Planarity : 0.005 0.035 258 Dihedral : 11.464 56.589 329 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.62 % Allowed : 14.38 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.62), residues: 174 helix: -2.73 (0.70), residues: 44 sheet: -2.77 (0.88), residues: 29 loop : -1.24 (0.64), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 62 HIS 0.003 0.002 HIS B 64 PHE 0.013 0.002 PHE B 147 TYR 0.013 0.002 TYR B 103 ARG 0.003 0.001 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8180 (m110) cc_final: 0.7659 (t0) REVERT: B 127 TYR cc_start: 0.8720 (p90) cc_final: 0.8466 (p90) REVERT: B 161 MET cc_start: 0.5692 (mmp) cc_final: 0.5318 (mmp) outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.1014 time to fit residues: 5.1424 Evaluate side-chains 43 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 145 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 3 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105056 restraints weight = 2214.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108506 restraints weight = 1238.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110941 restraints weight = 823.142| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1481 Z= 0.227 Angle : 0.658 6.903 2029 Z= 0.317 Chirality : 0.050 0.222 264 Planarity : 0.005 0.037 258 Dihedral : 8.726 53.391 329 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.88 % Allowed : 16.88 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.63), residues: 174 helix: -2.72 (0.71), residues: 44 sheet: -2.72 (0.90), residues: 29 loop : -1.21 (0.64), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 62 HIS 0.002 0.001 HIS B 64 PHE 0.010 0.001 PHE B 147 TYR 0.010 0.002 TYR B 103 ARG 0.001 0.000 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8185 (m110) cc_final: 0.7669 (t0) REVERT: B 127 TYR cc_start: 0.8803 (p90) cc_final: 0.8484 (p90) REVERT: B 161 MET cc_start: 0.5684 (mmp) cc_final: 0.5160 (mmp) outliers start: 3 outliers final: 1 residues processed: 42 average time/residue: 0.1034 time to fit residues: 5.1507 Evaluate side-chains 40 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 16 optimal weight: 0.0030 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.125420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.105059 restraints weight = 2214.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.108447 restraints weight = 1257.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.110856 restraints weight = 842.532| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 1481 Z= 0.272 Angle : 0.666 5.967 2029 Z= 0.331 Chirality : 0.051 0.224 264 Planarity : 0.005 0.034 258 Dihedral : 7.316 53.084 329 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.25 % Allowed : 19.38 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.63), residues: 174 helix: -2.77 (0.70), residues: 44 sheet: -2.90 (0.97), residues: 27 loop : -1.30 (0.64), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 62 HIS 0.003 0.002 HIS B 64 PHE 0.012 0.002 PHE B 147 TYR 0.011 0.002 TYR B 103 ARG 0.002 0.001 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8156 (m110) cc_final: 0.7716 (t0) REVERT: B 127 TYR cc_start: 0.8807 (p90) cc_final: 0.8454 (p90) REVERT: B 161 MET cc_start: 0.5733 (mmp) cc_final: 0.5185 (mmp) outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 0.1132 time to fit residues: 5.7317 Evaluate side-chains 44 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.0770 chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.123962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.103447 restraints weight = 2243.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.106936 restraints weight = 1259.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.109239 restraints weight = 831.495| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 1481 Z= 0.334 Angle : 0.686 6.221 2029 Z= 0.340 Chirality : 0.051 0.221 264 Planarity : 0.005 0.031 258 Dihedral : 7.129 53.582 329 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.62 % Allowed : 20.62 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.63), residues: 174 helix: -2.97 (0.67), residues: 44 sheet: -2.95 (0.97), residues: 27 loop : -1.33 (0.64), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 62 HIS 0.003 0.002 HIS B 64 PHE 0.013 0.002 PHE B 147 TYR 0.013 0.002 TYR B 103 ARG 0.001 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.153 Fit side-chains REVERT: B 41 ASN cc_start: 0.8187 (m110) cc_final: 0.7708 (t0) REVERT: B 127 TYR cc_start: 0.8800 (p90) cc_final: 0.8445 (p90) REVERT: B 161 MET cc_start: 0.5847 (mmp) cc_final: 0.5303 (mmp) outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.1059 time to fit residues: 4.7293 Evaluate side-chains 40 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 10 optimal weight: 0.0170 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 0.1980 chunk 3 optimal weight: 0.0020 chunk 14 optimal weight: 0.0470 overall best weight: 0.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN ** B 153 ASN ** 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 = 0.3636 r_free = 0.3636 target = 0.126820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.106406 restraints weight = 2141.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.109994 restraints weight = 1196.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.112399 restraints weight = 793.066| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1481 Z= 0.172 Angle : 0.595 6.103 2029 Z= 0.297 Chirality : 0.047 0.202 264 Planarity : 0.005 0.031 258 Dihedral : 6.665 54.510 329 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.62 % Allowed : 21.25 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.64), residues: 174 helix: -2.63 (0.73), residues: 44 sheet: -2.91 (0.99), residues: 27 loop : -1.17 (0.64), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 62 HIS 0.001 0.001 HIS B 64 PHE 0.007 0.001 PHE B 147 TYR 0.005 0.001 TYR B 127 ARG 0.001 0.000 ARG B 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: B 40 THR cc_start: 0.8472 (m) cc_final: 0.8223 (t) REVERT: B 41 ASN cc_start: 0.8115 (m110) cc_final: 0.7641 (t0) REVERT: B 161 MET cc_start: 0.5764 (mmp) cc_final: 0.5196 (mmp) outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 0.1063 time to fit residues: 5.0250 Evaluate side-chains 41 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN B 178 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.121875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.101394 restraints weight = 2266.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.105132 restraints weight = 1232.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.107509 restraints weight = 806.526| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 1481 Z= 0.351 Angle : 0.671 6.134 2029 Z= 0.334 Chirality : 0.051 0.233 264 Planarity : 0.005 0.033 258 Dihedral : 6.892 53.720 329 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 1.88 % Allowed : 20.00 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.63), residues: 174 helix: -2.92 (0.68), residues: 44 sheet: -2.91 (0.98), residues: 27 loop : -1.27 (0.64), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP B 62 HIS 0.003 0.002 HIS B 64 PHE 0.015 0.002 PHE B 147 TYR 0.013 0.003 TYR B 103 ARG 0.002 0.001 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8193 (m110) cc_final: 0.7685 (t0) REVERT: B 161 MET cc_start: 0.5901 (mmp) cc_final: 0.5378 (mmp) outliers start: 3 outliers final: 2 residues processed: 43 average time/residue: 0.0999 time to fit residues: 5.0755 Evaluate side-chains 43 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 0.0670 chunk 2 optimal weight: 0.0970 chunk 12 optimal weight: 0.2980 chunk 14 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.123696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.103299 restraints weight = 2216.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.107023 restraints weight = 1203.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.109489 restraints weight = 784.928| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 1481 Z= 0.206 Angle : 0.618 5.591 2029 Z= 0.303 Chirality : 0.048 0.218 264 Planarity : 0.005 0.030 258 Dihedral : 6.649 54.380 329 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.62 % Allowed : 21.88 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.64), residues: 174 helix: -2.68 (0.72), residues: 44 sheet: -2.88 (1.00), residues: 27 loop : -1.15 (0.65), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 62 HIS 0.002 0.001 HIS B 64 PHE 0.008 0.001 PHE B 147 TYR 0.007 0.002 TYR B 103 ARG 0.003 0.000 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: B 40 THR cc_start: 0.8479 (m) cc_final: 0.8216 (t) REVERT: B 41 ASN cc_start: 0.8148 (m110) cc_final: 0.7632 (t0) REVERT: B 161 MET cc_start: 0.5816 (mmp) cc_final: 0.5247 (mmp) outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 0.1050 time to fit residues: 4.9696 Evaluate side-chains 38 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 0 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 0.0870 chunk 15 optimal weight: 0.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.123153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.102230 restraints weight = 2238.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.106002 restraints weight = 1220.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.108438 restraints weight = 798.548| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 1481 Z= 0.243 Angle : 0.623 5.269 2029 Z= 0.308 Chirality : 0.049 0.220 264 Planarity : 0.005 0.031 258 Dihedral : 6.632 54.044 329 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 23.12 % Favored : 76.88 % 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: -2.81 (0.65), residues: 174 helix: -2.68 (0.72), residues: 44 sheet: -2.81 (1.03), residues: 27 loop : -1.14 (0.65), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP B 62 HIS 0.002 0.001 HIS B 64 PHE 0.010 0.002 PHE B 147 TYR 0.010 0.002 TYR B 103 ARG 0.001 0.000 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: B 40 THR cc_start: 0.8496 (m) cc_final: 0.8232 (t) REVERT: B 41 ASN cc_start: 0.8164 (m110) cc_final: 0.7655 (t0) REVERT: B 161 MET cc_start: 0.5880 (mmp) cc_final: 0.5357 (mmp) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0967 time to fit residues: 4.5413 Evaluate side-chains 39 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 2 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 4 optimal weight: 0.0470 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN ** B 153 ASN ** 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 = 0.3602 r_free = 0.3602 target = 0.124211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.104269 restraints weight = 2214.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.107899 restraints weight = 1227.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110259 restraints weight = 804.043| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 1481 Z= 0.288 Angle : 0.649 5.750 2029 Z= 0.322 Chirality : 0.050 0.225 264 Planarity : 0.005 0.031 258 Dihedral : 6.721 54.100 329 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 22.50 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.64), residues: 174 helix: -2.83 (0.70), residues: 44 sheet: -2.82 (1.02), residues: 27 loop : -1.26 (0.64), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.006 TRP B 62 HIS 0.003 0.002 HIS B 64 PHE 0.012 0.002 PHE B 147 TYR 0.012 0.002 TYR B 103 ARG 0.002 0.000 ARG B 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8154 (m110) cc_final: 0.7710 (t0) REVERT: B 161 MET cc_start: 0.5877 (mmp) cc_final: 0.5386 (mmp) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1105 time to fit residues: 4.9258 Evaluate side-chains 37 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 0.0470 chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN ** B 153 ASN ** 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 = 0.3601 r_free = 0.3601 target = 0.124266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.103939 restraints weight = 2245.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.107640 restraints weight = 1232.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.110105 restraints weight = 801.431| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 1481 Z= 0.268 Angle : 0.667 8.106 2029 Z= 0.333 Chirality : 0.050 0.220 264 Planarity : 0.005 0.032 258 Dihedral : 6.715 54.280 329 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 23.12 % Favored : 76.88 % 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: -2.95 (0.64), residues: 174 helix: -2.79 (0.70), residues: 44 sheet: -3.16 (1.00), residues: 26 loop : -1.17 (0.63), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.006 TRP B 62 HIS 0.003 0.002 HIS B 64 PHE 0.010 0.002 PHE B 147 TYR 0.011 0.002 TYR B 103 ARG 0.002 0.000 ARG B 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1137.77 seconds wall clock time: 20 minutes 8.85 seconds (1208.85 seconds total)