Starting phenix.real_space_refine on Mon Feb 10 20:20:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggi_40009/02_2025/8ggi_40009.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggi_40009/02_2025/8ggi_40009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ggi_40009/02_2025/8ggi_40009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggi_40009/02_2025/8ggi_40009.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggi_40009/02_2025/8ggi_40009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggi_40009/02_2025/8ggi_40009.cif" } resolution = 3.5 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= 0.025 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 15 5.16 5 C 1470 2.51 5 N 348 2.21 5 O 370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2203 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 67 Chain: "R" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 17 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 2.79, per 1000 atoms: 1.27 Number of scatterers: 2203 At special positions: 0 Unit cell: (54.6651, 83.2992, 63.3421, 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 15 16.00 O 370 8.00 N 348 7.00 C 1470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=1.41 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 318.8 milliseconds 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 544 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'R' and resid 29 through 61 removed outlier: 3.553A pdb=" N VAL R 33 " --> pdb=" O ASP R 29 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU R 53 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE R 55 " --> pdb=" O ASN R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 97 removed outlier: 4.624A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 103 through 136 removed outlier: 4.114A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP R 109 " --> pdb=" O TRP R 105 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA R 134 " --> pdb=" O ASP R 130 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE R 135 " --> pdb=" O ARG R 131 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR R 136 " --> pdb=" O TYR R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 163 removed outlier: 3.657A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 178 through 186 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.686A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 238 removed outlier: 3.953A pdb=" N ARG R 221 " --> pdb=" O PHE R 217 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL R 222 " --> pdb=" O VAL R 218 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE R 223 " --> pdb=" O TYR R 219 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 280 Processing helix chain 'R' and resid 286 through 299 removed outlier: 3.692A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.569A pdb=" N GLY R 315 " --> pdb=" O LEU R 311 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 320 No H-bonds generated for 'chain 'R' and resid 318 through 320' Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 340 153 hydrogen bonds defined for protein. 459 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: 0.60 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 651 1.34 - 1.46: 581 1.46 - 1.58: 1004 1.58 - 1.70: 0 1.70 - 1.83: 21 Bond restraints: 2257 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.450 -0.053 2.00e-02 2.50e+03 6.97e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.439 -0.045 2.00e-02 2.50e+03 5.06e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.567 -0.044 2.00e-02 2.50e+03 4.87e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.563 -0.043 2.00e-02 2.50e+03 4.54e+00 bond pdb=" C CYS R 191 " pdb=" O CYS R 191 " ideal model delta sigma weight residual 1.235 1.220 0.015 7.50e-03 1.78e+04 4.18e+00 ... (remaining 2252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 3021 1.88 - 3.75: 44 3.75 - 5.63: 16 5.63 - 7.51: 3 7.51 - 9.38: 3 Bond angle restraints: 3087 Sorted by residual: angle pdb=" N THR R 189 " pdb=" CA THR R 189 " pdb=" C THR R 189 " ideal model delta sigma weight residual 114.04 104.66 9.38 1.24e+00 6.50e-01 5.73e+01 angle pdb=" N PHE R 193 " pdb=" CA PHE R 193 " pdb=" C PHE R 193 " ideal model delta sigma weight residual 108.67 116.73 -8.06 1.55e+00 4.16e-01 2.70e+01 angle pdb=" N CYS R 191 " pdb=" CA CYS R 191 " pdb=" C CYS R 191 " ideal model delta sigma weight residual 113.21 106.63 6.58 1.40e+00 5.10e-01 2.21e+01 angle pdb=" N CYS R 190 " pdb=" CA CYS R 190 " pdb=" C CYS R 190 " ideal model delta sigma weight residual 109.96 115.88 -5.92 1.50e+00 4.44e-01 1.56e+01 angle pdb=" N CYS R 191 " pdb=" CA CYS R 191 " pdb=" CB CYS R 191 " ideal model delta sigma weight residual 110.65 115.26 -4.61 1.71e+00 3.42e-01 7.28e+00 ... (remaining 3082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 1151 16.08 - 32.17: 122 32.17 - 48.25: 25 48.25 - 64.33: 3 64.33 - 80.42: 3 Dihedral angle restraints: 1304 sinusoidal: 467 harmonic: 837 Sorted by residual: dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual -180.00 -162.92 -17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA SER R 207 " pdb=" C SER R 207 " pdb=" N PHE R 208 " pdb=" CA PHE R 208 " ideal model delta harmonic sigma weight residual -180.00 -164.16 -15.84 0 5.00e+00 4.00e-02 1.00e+01 dihedral pdb=" CB MET R 171 " pdb=" CG MET R 171 " pdb=" SD MET R 171 " pdb=" CE MET R 171 " ideal model delta sinusoidal sigma weight residual 60.00 117.75 -57.75 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 1301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 232 0.033 - 0.066: 102 0.066 - 0.098: 33 0.098 - 0.131: 10 0.131 - 0.164: 1 Chirality restraints: 378 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.56 -0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA LEU R 287 " pdb=" N LEU R 287 " pdb=" C LEU R 287 " pdb=" CB LEU R 287 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.02e-01 chirality pdb=" CA PRO R 88 " pdb=" N PRO R 88 " pdb=" C PRO R 88 " pdb=" CB PRO R 88 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.96e-01 ... (remaining 375 not shown) Planarity restraints: 368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS R 190 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.12e+00 pdb=" C CYS R 190 " -0.043 2.00e-02 2.50e+03 pdb=" O CYS R 190 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS R 191 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU R 237 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.54e+00 pdb=" CD GLU R 237 " -0.021 2.00e-02 2.50e+03 pdb=" OE1 GLU R 237 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU R 237 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 313 " -0.006 2.00e-02 2.50e+03 7.40e-03 1.37e+00 pdb=" CG TRP R 313 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP R 313 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP R 313 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 313 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 313 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 313 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 313 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 313 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 313 " -0.000 2.00e-02 2.50e+03 ... (remaining 365 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 445 2.77 - 3.31: 2101 3.31 - 3.84: 3493 3.84 - 4.37: 3684 4.37 - 4.90: 6782 Nonbonded interactions: 16505 Sorted by model distance: nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.242 3.040 nonbonded pdb=" N GLU R 306 " pdb=" OE1 GLU R 306 " model vdw 2.333 3.120 nonbonded pdb=" OH TYR R 326 " pdb=" O HOH R 601 " model vdw 2.407 3.040 nonbonded pdb=" OH TYR R 209 " pdb=" O PHE R 290 " model vdw 2.450 3.040 nonbonded pdb=" O LEU R 64 " pdb=" ND2 ASN R 69 " model vdw 2.495 3.120 ... (remaining 16500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.120 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: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.040 Process input model: 11.880 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 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 0.053 2257 Z= 0.247 Angle : 0.692 9.382 3087 Z= 0.389 Chirality : 0.042 0.164 378 Planarity : 0.004 0.030 368 Dihedral : 13.755 80.416 754 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: 1.47 (0.51), residues: 280 helix: 1.60 (0.37), residues: 204 sheet: None (None), residues: 0 loop : -0.70 (0.71), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 313 HIS 0.005 0.002 HIS R 296 PHE 0.007 0.001 PHE R 193 TYR 0.007 0.001 TYR R 132 ARG 0.007 0.001 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.227 Fit side-chains REVERT: R 82 MET cc_start: 0.8318 (ttm) cc_final: 0.8052 (ttm) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1717 time to fit residues: 8.7008 Evaluate side-chains 34 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.112464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.095721 restraints weight = 3044.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.098169 restraints weight = 1732.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.099717 restraints weight = 1217.807| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2257 Z= 0.222 Angle : 0.526 7.099 3087 Z= 0.280 Chirality : 0.040 0.105 378 Planarity : 0.003 0.027 368 Dihedral : 4.595 20.606 316 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.33 % Allowed : 8.00 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.51), residues: 280 helix: 1.40 (0.36), residues: 221 sheet: None (None), residues: 0 loop : -0.56 (0.77), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.006 0.002 HIS R 178 PHE 0.009 0.001 PHE R 61 TYR 0.008 0.001 TYR R 132 ARG 0.001 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.237 Fit side-chains REVERT: R 279 MET cc_start: 0.8559 (mmm) cc_final: 0.8239 (mmm) outliers start: 3 outliers final: 2 residues processed: 38 average time/residue: 0.1912 time to fit residues: 8.3690 Evaluate side-chains 36 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.112640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.095508 restraints weight = 3075.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.097881 restraints weight = 1781.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.099498 restraints weight = 1254.545| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2257 Z= 0.231 Angle : 0.524 9.469 3087 Z= 0.271 Chirality : 0.040 0.104 378 Planarity : 0.003 0.027 368 Dihedral : 4.550 17.717 316 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.22 % Allowed : 10.22 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.51), residues: 280 helix: 1.41 (0.36), residues: 221 sheet: None (None), residues: 0 loop : -0.61 (0.79), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.007 0.002 HIS R 296 PHE 0.007 0.001 PHE R 332 TYR 0.007 0.001 TYR R 132 ARG 0.003 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.246 Fit side-chains REVERT: R 279 MET cc_start: 0.8594 (mmm) cc_final: 0.8224 (mmm) outliers start: 5 outliers final: 3 residues processed: 37 average time/residue: 0.1953 time to fit residues: 8.3510 Evaluate side-chains 37 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 3 optimal weight: 0.0370 chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.114789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.097954 restraints weight = 2965.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.100346 restraints weight = 1685.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.102029 restraints weight = 1198.212| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2257 Z= 0.166 Angle : 0.476 7.801 3087 Z= 0.248 Chirality : 0.038 0.102 378 Planarity : 0.003 0.026 368 Dihedral : 4.241 17.295 316 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.78 % Allowed : 10.67 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.51), residues: 280 helix: 1.52 (0.36), residues: 221 sheet: None (None), residues: 0 loop : -0.61 (0.78), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.004 0.001 HIS R 178 PHE 0.005 0.001 PHE R 61 TYR 0.007 0.001 TYR R 132 ARG 0.004 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.213 Fit side-chains REVERT: R 279 MET cc_start: 0.8624 (mmm) cc_final: 0.8257 (mmm) outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 0.1787 time to fit residues: 7.6390 Evaluate side-chains 38 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.113048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.095911 restraints weight = 3044.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.098416 restraints weight = 1746.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.099930 restraints weight = 1235.063| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2257 Z= 0.232 Angle : 0.518 10.258 3087 Z= 0.265 Chirality : 0.040 0.106 378 Planarity : 0.003 0.026 368 Dihedral : 4.342 17.375 316 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.33 % Allowed : 12.89 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.51), residues: 280 helix: 1.45 (0.35), residues: 223 sheet: None (None), residues: 0 loop : -0.66 (0.80), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.005 0.002 HIS R 296 PHE 0.007 0.001 PHE R 332 TYR 0.009 0.001 TYR R 132 ARG 0.003 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.241 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 38 average time/residue: 0.1914 time to fit residues: 8.3687 Evaluate side-chains 36 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 0.0570 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.113289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.096489 restraints weight = 3012.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.098958 restraints weight = 1716.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.100597 restraints weight = 1202.311| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2257 Z= 0.180 Angle : 0.497 9.629 3087 Z= 0.254 Chirality : 0.039 0.103 378 Planarity : 0.003 0.026 368 Dihedral : 4.230 17.349 316 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.89 % Allowed : 13.33 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.51), residues: 280 helix: 1.55 (0.36), residues: 223 sheet: None (None), residues: 0 loop : -0.79 (0.75), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.004 0.002 HIS R 178 PHE 0.006 0.001 PHE R 61 TYR 0.007 0.001 TYR R 132 ARG 0.006 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.237 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 37 average time/residue: 0.1949 time to fit residues: 8.3255 Evaluate side-chains 37 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 0.0570 chunk 26 optimal weight: 0.0040 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 overall best weight: 0.3310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.114809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.097772 restraints weight = 2996.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.100265 restraints weight = 1715.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.101958 restraints weight = 1210.941| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2257 Z= 0.143 Angle : 0.478 8.759 3087 Z= 0.245 Chirality : 0.038 0.104 378 Planarity : 0.003 0.025 368 Dihedral : 4.197 17.265 316 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.44 % Allowed : 15.56 % Favored : 84.00 % 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: 1.62 (0.51), residues: 280 helix: 1.60 (0.36), residues: 224 sheet: None (None), residues: 0 loop : -1.00 (0.73), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.006 0.002 HIS R 296 PHE 0.006 0.001 PHE R 61 TYR 0.005 0.001 TYR R 132 ARG 0.005 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.223 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 36 average time/residue: 0.1804 time to fit residues: 7.5413 Evaluate side-chains 36 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 24 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.113997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.096692 restraints weight = 3091.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.099163 restraints weight = 1763.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.100875 restraints weight = 1247.281| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2257 Z= 0.184 Angle : 0.490 8.761 3087 Z= 0.251 Chirality : 0.039 0.103 378 Planarity : 0.003 0.027 368 Dihedral : 4.200 17.330 316 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.78 % Allowed : 15.11 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.51), residues: 280 helix: 1.62 (0.36), residues: 224 sheet: None (None), residues: 0 loop : -0.90 (0.75), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.004 0.002 HIS R 296 PHE 0.008 0.001 PHE R 61 TYR 0.007 0.001 TYR R 132 ARG 0.006 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.243 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 37 average time/residue: 0.1939 time to fit residues: 8.2692 Evaluate side-chains 38 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.113155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.096087 restraints weight = 3036.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.098556 restraints weight = 1731.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.100188 restraints weight = 1227.469| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2257 Z= 0.220 Angle : 0.508 8.882 3087 Z= 0.260 Chirality : 0.040 0.105 378 Planarity : 0.003 0.030 368 Dihedral : 4.268 17.252 316 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.78 % Allowed : 14.67 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.51), residues: 280 helix: 1.59 (0.36), residues: 224 sheet: None (None), residues: 0 loop : -0.89 (0.75), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.004 0.001 HIS R 178 PHE 0.008 0.001 PHE R 61 TYR 0.011 0.001 TYR R 132 ARG 0.007 0.001 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.257 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 37 average time/residue: 0.1987 time to fit residues: 8.4828 Evaluate side-chains 38 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.112400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.095363 restraints weight = 3034.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.097659 restraints weight = 1738.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.099365 restraints weight = 1245.265| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2257 Z= 0.245 Angle : 0.523 9.058 3087 Z= 0.269 Chirality : 0.040 0.107 378 Planarity : 0.004 0.032 368 Dihedral : 4.333 17.169 316 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.33 % Allowed : 14.67 % Favored : 84.00 % 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: 1.55 (0.51), residues: 280 helix: 1.53 (0.36), residues: 224 sheet: None (None), residues: 0 loop : -0.88 (0.76), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.005 0.002 HIS R 296 PHE 0.008 0.001 PHE R 61 TYR 0.011 0.001 TYR R 132 ARG 0.007 0.001 ARG R 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.255 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 35 average time/residue: 0.1948 time to fit residues: 7.9269 Evaluate side-chains 36 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 THR Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 5 optimal weight: 0.2980 chunk 14 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.114412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.097269 restraints weight = 3006.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.099555 restraints weight = 1735.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.101284 restraints weight = 1249.805| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2257 Z= 0.170 Angle : 0.487 8.733 3087 Z= 0.250 Chirality : 0.039 0.103 378 Planarity : 0.003 0.031 368 Dihedral : 4.214 17.267 316 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.33 % Allowed : 14.67 % Favored : 84.00 % 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: 1.69 (0.51), residues: 280 helix: 1.64 (0.36), residues: 224 sheet: None (None), residues: 0 loop : -0.92 (0.75), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.004 0.002 HIS R 178 PHE 0.007 0.001 PHE R 61 TYR 0.009 0.001 TYR R 132 ARG 0.008 0.001 ARG R 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1156.32 seconds wall clock time: 21 minutes 24.90 seconds (1284.90 seconds total)