Starting phenix.real_space_refine on Mon Feb 10 19:28:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w3t_32293/02_2025/7w3t_32293.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w3t_32293/02_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_32293/02_2025/7w3t_32293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w3t_32293/02_2025/7w3t_32293.map" model { file = "/net/cci-nas-00/data/ceres_data/7w3t_32293/02_2025/7w3t_32293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w3t_32293/02_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): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 2.04, per 1000 atoms: 1.40 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: 0.54 Conformation dependent library (CDL) restraints added in 173.8 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: 0.22 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: 0.58 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: 0.620 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.830 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.240 ------------------------------------------------------------------------------- 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 : 0.133 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: 0.1118 time to fit residues: 5.3060 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 : 0.165 ------------------------------------------------------------------------------- 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 = 0.105812 restraints weight = 2207.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.109332 restraints weight = 1228.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.111802 restraints weight = 815.652| |-----------------------------------------------------------------------------| 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 : 11.465 56.595 329 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 : 0.150 Fit side-chains revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8180 (m110) cc_final: 0.7658 (t0) REVERT: B 127 TYR cc_start: 0.8721 (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: 0.1007 time to fit residues: 5.0937 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 : 0.150 ------------------------------------------------------------------------------- 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: 0.1980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 12 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 overall best weight: 0.2718 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.126704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.106366 restraints weight = 2213.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.109784 restraints weight = 1241.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.112227 restraints weight = 827.158| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1481 Z= 0.205 Angle : 0.648 6.721 2029 Z= 0.312 Chirality : 0.050 0.222 264 Planarity : 0.005 0.035 258 Dihedral : 8.567 53.587 329 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.88 % Allowed : 17.50 % 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: -2.86 (0.63), residues: 174 helix: -2.68 (0.72), residues: 44 sheet: -2.69 (0.90), residues: 29 loop : -1.19 (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 0.009 0.001 PHE B 147 TYR 0.009 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 : 0.153 Fit side-chains revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8168 (m110) cc_final: 0.7669 (t0) REVERT: B 123 SER cc_start: 0.7836 (t) cc_final: 0.7512 (t) REVERT: B 127 TYR cc_start: 0.8796 (p90) cc_final: 0.8463 (p90) REVERT: B 161 MET cc_start: 0.5662 (mmp) cc_final: 0.5135 (mmp) outliers start: 3 outliers final: 1 residues processed: 42 average time/residue: 0.0980 time to fit residues: 4.9195 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 : 0.164 ------------------------------------------------------------------------------- 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: 0.0980 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.0470 chunk 7 optimal weight: 0.3980 overall best weight: 0.3878 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.125896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105366 restraints weight = 2225.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108811 restraints weight = 1255.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.111223 restraints weight = 838.173| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1378 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= 0.254 Angle : 0.653 6.050 2029 Z= 0.325 Chirality : 0.050 0.223 264 Planarity : 0.005 0.032 258 Dihedral : 7.261 53.097 329 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.58 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: -2.97 (0.63), residues: 174 helix: -2.72 (0.71), residues: 44 sheet: -2.90 (0.97), residues: 27 loop : -1.29 (0.64), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 62 HIS 0.002 0.002 HIS B 64 PHE 0.011 0.002 PHE B 147 TYR 0.011 0.002 TYR B 103 ARG 0.002 0.000 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 44 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8146 (m110) cc_final: 0.7693 (t0) REVERT: B 127 TYR cc_start: 0.8803 (p90) cc_final: 0.8461 (p90) REVERT: B 161 MET cc_start: 0.5747 (mmp) cc_final: 0.5210 (mmp) outliers start: 2 outliers final: 1 residues processed: 42 average time/residue: 0.1072 time to fit residues: 5.3243 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 : 0.162 ------------------------------------------------------------------------------- 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: 0.4980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.0070 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 chunk 7 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 overall best weight: 0.3998 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.125246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.104863 restraints weight = 2248.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.108356 restraints weight = 1259.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.110694 restraints weight = 834.616| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 1481 Z= 0.262 Angle : 0.641 6.085 2029 Z= 0.318 Chirality : 0.050 0.218 264 Planarity : 0.005 0.029 258 Dihedral : 6.983 53.959 329 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % 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: -2.95 (0.63), residues: 174 helix: -2.71 (0.71), residues: 44 sheet: -2.91 (0.97), residues: 27 loop : -1.27 (0.63), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 62 HIS 0.002 0.002 HIS B 64 PHE 0.011 0.002 PHE B 147 TYR 0.011 0.002 TYR B 103 ARG 0.002 0.000 ARG B 149 *********************** 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 42 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.163 Fit side-chains REVERT: B 41 ASN cc_start: 0.8147 (m110) cc_final: 0.7684 (t0) REVERT: B 127 TYR cc_start: 0.8782 (p90) cc_final: 0.8418 (p90) REVERT: B 161 MET cc_start: 0.5804 (mmp) cc_final: 0.5233 (mmp) outliers start: 1 outliers final: 1 residues processed: 41 average time/residue: 0.1000 time to fit residues: 4.8441 Evaluate side-chains 42 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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: 0.8980 chunk 16 optimal weight: 0.4980 chunk 10 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 0.0870 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 chunk 0 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 overall best weight: 0.2156 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.126744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.106586 restraints weight = 2140.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.110200 restraints weight = 1188.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112617 restraints weight = 786.972| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1481 Z= 0.190 Angle : 0.598 5.909 2029 Z= 0.297 Chirality : 0.048 0.240 264 Planarity : 0.004 0.029 258 Dihedral : 6.664 54.356 329 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.25 % Allowed : 20.00 % 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: -2.79 (0.64), residues: 174 helix: -2.56 (0.74), residues: 44 sheet: -2.85 (0.99), residues: 27 loop : -1.17 (0.63), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 62 HIS 0.001 0.001 HIS B 64 PHE 0.008 0.001 PHE B 147 TYR 0.007 0.001 TYR B 103 ARG 0.001 0.000 ARG B 149 *********************** 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 41 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: B 40 THR cc_start: 0.8479 (m) cc_final: 0.8236 (t) REVERT: B 41 ASN cc_start: 0.8109 (m110) cc_final: 0.7650 (t0) REVERT: B 161 MET cc_start: 0.5749 (mmp) cc_final: 0.5156 (mmp) outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.1105 time to fit residues: 5.1702 Evaluate side-chains 41 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.123521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.102667 restraints weight = 2249.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.106464 restraints weight = 1223.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108877 restraints weight = 799.666| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 1481 Z= 0.290 Angle : 0.629 5.658 2029 Z= 0.314 Chirality : 0.050 0.233 264 Planarity : 0.005 0.030 258 Dihedral : 6.761 53.897 329 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 1.88 % Allowed : 19.38 % 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: -2.87 (0.64), residues: 174 helix: -2.69 (0.72), residues: 44 sheet: -2.92 (0.98), residues: 27 loop : -1.17 (0.64), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 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 0.001 0.000 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 43 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8171 (m110) cc_final: 0.7671 (t0) REVERT: B 148 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7989 (tp) REVERT: B 161 MET cc_start: 0.5886 (mmp) cc_final: 0.5332 (mmp) outliers start: 3 outliers final: 1 residues processed: 42 average time/residue: 0.1140 time to fit residues: 5.6040 Evaluate side-chains 44 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 148 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.2980 chunk 12 optimal weight: 0.0980 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 0.0470 overall best weight: 0.2478 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.124235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.103775 restraints weight = 2214.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.107528 restraints weight = 1199.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.109934 restraints weight = 776.967| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1691 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= 0.200 Angle : 0.596 5.288 2029 Z= 0.296 Chirality : 0.048 0.219 264 Planarity : 0.004 0.029 258 Dihedral : 6.575 54.314 329 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.88 % Allowed : 18.75 % 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: -2.70 (0.65), residues: 174 helix: -2.54 (0.74), residues: 44 sheet: -2.83 (1.00), residues: 27 loop : -1.07 (0.65), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 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 0.001 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 43 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: B 40 THR cc_start: 0.8473 (m) cc_final: 0.8220 (t) REVERT: B 41 ASN cc_start: 0.8148 (m110) cc_final: 0.7637 (t0) REVERT: B 161 MET cc_start: 0.5831 (mmp) cc_final: 0.5291 (mmp) outliers start: 3 outliers final: 2 residues processed: 41 average time/residue: 0.1034 time to fit residues: 4.9993 Evaluate side-chains 42 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.121570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.100790 restraints weight = 2248.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.104600 restraints weight = 1229.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.107045 restraints weight = 800.700| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 1481 Z= 0.378 Angle : 0.686 6.289 2029 Z= 0.340 Chirality : 0.052 0.230 264 Planarity : 0.005 0.033 258 Dihedral : 6.883 53.914 329 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 1.25 % Allowed : 18.12 % 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: -3.01 (0.63), residues: 174 helix: -2.95 (0.68), residues: 44 sheet: -2.83 (1.00), residues: 27 loop : -1.24 (0.64), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.005 TRP B 62 HIS 0.003 0.002 HIS B 64 PHE 0.016 0.002 PHE B 147 TYR 0.014 0.003 TYR B 103 ARG 0.002 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: 2 poor density : 38 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: B 41 ASN cc_start: 0.8209 (m110) cc_final: 0.7713 (t0) REVERT: B 161 MET cc_start: 0.5927 (mmp) cc_final: 0.5389 (mmp) outliers start: 2 outliers final: 2 residues processed: 38 average time/residue: 0.1141 time to fit residues: 5.0912 Evaluate side-chains 41 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 0 optimal weight: 0.0980 chunk 5 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 8 optimal weight: 0.0670 chunk 4 optimal weight: 0.8980 overall best weight: 0.2718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 ASN ** 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 = 0.3590 r_free = 0.3590 target = 0.123300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.102588 restraints weight = 2260.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.106287 restraints weight = 1227.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.108819 restraints weight = 801.037| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 1481 Z= 0.211 Angle : 0.612 5.266 2029 Z= 0.303 Chirality : 0.049 0.218 264 Planarity : 0.005 0.030 258 Dihedral : 6.617 54.371 329 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % 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: -2.79 (0.65), residues: 174 helix: -2.70 (0.71), residues: 44 sheet: -2.72 (1.04), residues: 27 loop : -1.13 (0.65), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP B 62 HIS 0.003 0.002 HIS B 64 PHE 0.008 0.001 PHE B 147 TYR 0.008 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 43 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: B 40 THR cc_start: 0.8484 (m) cc_final: 0.8219 (t) REVERT: B 41 ASN cc_start: 0.8145 (m110) cc_final: 0.7663 (t0) REVERT: B 161 MET cc_start: 0.5847 (mmp) cc_final: 0.5316 (mmp) outliers start: 2 outliers final: 2 residues processed: 41 average time/residue: 0.1051 time to fit residues: 5.0767 Evaluate side-chains 41 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 0.0770 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 1 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 overall best weight: 0.3338 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.122962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.102070 restraints weight = 2305.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.105899 restraints weight = 1246.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.108475 restraints weight = 808.172| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1846 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= 0.236 Angle : 0.619 5.256 2029 Z= 0.308 Chirality : 0.049 0.218 264 Planarity : 0.005 0.031 258 Dihedral : 6.608 54.098 329 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.25 % Allowed : 20.62 % 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: -2.72 (0.65), residues: 174 helix: -2.67 (0.73), residues: 44 sheet: -2.90 (1.04), residues: 26 loop : -1.02 (0.65), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.006 TRP B 62 HIS 0.002 0.001 HIS B 64 PHE 0.009 0.001 PHE B 147 TYR 0.009 0.002 TYR B 103 ARG 0.001 0.000 ARG B 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1116.36 seconds wall clock time: 20 minutes 23.08 seconds (1223.08 seconds total)