Starting phenix.real_space_refine on Wed Mar 5 15:15:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggi_40009/03_2025/8ggi_40009.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggi_40009/03_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_40009/03_2025/8ggi_40009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggi_40009/03_2025/8ggi_40009.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggi_40009/03_2025/8ggi_40009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggi_40009/03_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-5624/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: 2.40, per 1000 atoms: 1.09 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: 0.61 Conformation dependent library (CDL) restraints added in 282.9 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: 0.22 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: 0.52 Time building geometry restraints manager: 0.73 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: 1.640 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.150 Find NCS groups from input model: 0.020 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.640 ------------------------------------------------------------------------------- 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 : 0.230 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: 0.1697 time to fit residues: 8.6340 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 : 0.227 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.095700 restraints weight = 3044.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.098110 restraints weight = 1737.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.099675 restraints weight = 1228.415| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 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 : 0.232 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: 0.1968 time to fit residues: 8.6454 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 : 0.187 ------------------------------------------------------------------------------- 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: 0.9990 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.114023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.096844 restraints weight = 3062.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.099314 restraints weight = 1753.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.100863 restraints weight = 1236.265| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2257 Z= 0.188 Angle : 0.504 9.317 3087 Z= 0.260 Chirality : 0.039 0.103 378 Planarity : 0.003 0.026 368 Dihedral : 4.470 17.436 316 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.22 % Allowed : 9.78 % Favored : 88.00 % 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: 1.53 (0.51), residues: 280 helix: 1.47 (0.36), residues: 221 sheet: None (None), residues: 0 loop : -0.59 (0.79), residues: 59 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 0.006 0.001 PHE R 332 TYR 0.006 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 41 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.230 Fit side-chains REVERT: R 279 MET cc_start: 0.8617 (mmm) cc_final: 0.8261 (mmm) outliers start: 5 outliers final: 3 residues processed: 39 average time/residue: 0.1823 time to fit residues: 8.2172 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 : 0.226 ------------------------------------------------------------------------------- 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: 1.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 0.0980 chunk 22 optimal weight: 0.4980 chunk 5 optimal weight: 0.0670 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 overall best weight: 0.3518 ------------------------------------------------------------------------------- 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 = 0.3225 r_free = 0.3225 target = 0.116354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.099409 restraints weight = 2947.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.101888 restraints weight = 1687.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.103466 restraints weight = 1186.301| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2257 Z= 0.146 Angle : 0.464 7.567 3087 Z= 0.242 Chirality : 0.038 0.101 378 Planarity : 0.003 0.025 368 Dihedral : 4.157 17.204 316 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.33 % Allowed : 11.56 % Favored : 87.11 % 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: 1.65 (0.51), residues: 280 helix: 1.55 (0.36), residues: 222 sheet: None (None), residues: 0 loop : -0.55 (0.78), residues: 58 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 0.005 0.001 PHE R 61 TYR 0.005 0.001 TYR R 132 ARG 0.003 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: 3 poor density : 36 time to evaluate : 0.227 Fit side-chains REVERT: R 279 MET cc_start: 0.8591 (mmm) cc_final: 0.8239 (mmm) outliers start: 3 outliers final: 2 residues processed: 38 average time/residue: 0.1749 time to fit residues: 7.7421 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 : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 195 THR 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: 1.9990 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 18 optimal weight: 0.0870 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3204 r_free = 0.3204 target = 0.114643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.097444 restraints weight = 3024.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.099929 restraints weight = 1742.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.101633 restraints weight = 1234.822| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2257 Z= 0.185 Angle : 0.479 7.950 3087 Z= 0.249 Chirality : 0.039 0.103 378 Planarity : 0.003 0.025 368 Dihedral : 4.165 17.272 316 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: 1.60 (0.51), residues: 280 helix: 1.55 (0.36), residues: 223 sheet: None (None), residues: 0 loop : -0.76 (0.76), residues: 57 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 0.006 0.001 PHE R 332 TYR 0.007 0.001 TYR R 132 ARG 0.006 0.001 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 40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.246 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 0.1727 time to fit residues: 7.8024 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 : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS 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: 0.5980 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 0.0870 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3208 r_free = 0.3208 target = 0.114987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.098004 restraints weight = 2980.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.100546 restraints weight = 1712.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.102223 restraints weight = 1205.995| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2257 Z= 0.158 Angle : 0.480 8.243 3087 Z= 0.247 Chirality : 0.039 0.102 378 Planarity : 0.003 0.024 368 Dihedral : 4.174 17.243 316 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 : 0.44 % Allowed : 14.67 % Favored : 84.89 % 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: 1.60 (0.51), residues: 280 helix: 1.58 (0.36), residues: 224 sheet: None (None), residues: 0 loop : -0.95 (0.73), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.007 0.002 HIS R 296 PHE 0.006 0.001 PHE R 61 TYR 0.006 0.001 TYR R 132 ARG 0.004 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 36 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.250 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.1893 time to fit residues: 7.7468 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 : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 0.0020 chunk 8 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 = 0.3195 r_free = 0.3195 target = 0.113877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.097024 restraints weight = 3002.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.099533 restraints weight = 1703.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.101176 restraints weight = 1195.909| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2257 Z= 0.188 Angle : 0.489 8.524 3087 Z= 0.251 Chirality : 0.039 0.103 378 Planarity : 0.003 0.024 368 Dihedral : 4.201 17.211 316 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.78 % Allowed : 12.89 % Favored : 85.33 % 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: 1.56 (0.51), residues: 280 helix: 1.56 (0.36), residues: 224 sheet: None (None), residues: 0 loop : -1.04 (0.72), 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 0.006 0.001 PHE R 332 TYR 0.007 0.001 TYR R 132 ARG 0.006 0.001 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 39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.228 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 37 average time/residue: 0.1834 time to fit residues: 7.8277 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 : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.0470 chunk 23 optimal weight: 0.0980 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.3195 r_free = 0.3195 target = 0.114314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.096791 restraints weight = 3106.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.099533 restraints weight = 1678.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.101291 restraints weight = 1139.454| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1761 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= 0.181 Angle : 0.488 8.619 3087 Z= 0.251 Chirality : 0.039 0.103 378 Planarity : 0.003 0.028 368 Dihedral : 4.203 17.204 316 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.78 % Allowed : 12.89 % Favored : 85.33 % 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: 1.60 (0.51), residues: 280 helix: 1.60 (0.36), residues: 224 sheet: None (None), residues: 0 loop : -1.03 (0.72), residues: 56 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 0.006 0.001 PHE R 61 TYR 0.009 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 : 0.230 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 36 average time/residue: 0.1768 time to fit residues: 7.4142 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 : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL 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: 0.6980 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3188 r_free = 0.3188 target = 0.113535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.096430 restraints weight = 3030.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.098940 restraints weight = 1733.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.100486 restraints weight = 1220.576| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2257 Z= 0.210 Angle : 0.503 8.801 3087 Z= 0.258 Chirality : 0.040 0.105 378 Planarity : 0.003 0.031 368 Dihedral : 4.250 17.111 316 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.22 % Allowed : 14.22 % 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: 1.60 (0.51), residues: 280 helix: 1.58 (0.36), residues: 224 sheet: None (None), residues: 0 loop : -0.95 (0.73), residues: 56 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 0.009 0.001 PHE R 61 TYR 0.009 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 41 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.235 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 37 average time/residue: 0.2113 time to fit residues: 8.9975 Evaluate side-chains 40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL 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: 4.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3174 r_free = 0.3174 target = 0.112327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.095292 restraints weight = 3036.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.097779 restraints weight = 1749.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.099275 restraints weight = 1230.528| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1825 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= 0.248 Angle : 0.527 9.030 3087 Z= 0.271 Chirality : 0.041 0.108 378 Planarity : 0.003 0.031 368 Dihedral : 4.339 17.121 316 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.78 % Allowed : 13.78 % Favored : 84.44 % 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: 1.53 (0.51), residues: 280 helix: 1.52 (0.36), residues: 224 sheet: None (None), residues: 0 loop : -0.94 (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 0.011 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 40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.250 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 36 average time/residue: 0.1954 time to fit residues: 8.1133 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 : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL 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: 0.3980 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.0010 chunk 24 optimal weight: 0.0050 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 overall best weight: 0.2600 ------------------------------------------------------------------------------- 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 = 0.3228 r_free = 0.3228 target = 0.116772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.099557 restraints weight = 2967.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.101921 restraints weight = 1706.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.103681 restraints weight = 1220.423| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2257 Z= 0.140 Angle : 0.471 8.543 3087 Z= 0.242 Chirality : 0.038 0.102 378 Planarity : 0.003 0.031 368 Dihedral : 4.109 17.179 316 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.78 % Allowed : 13.78 % Favored : 84.44 % 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: 1.77 (0.51), residues: 280 helix: 1.71 (0.36), residues: 224 sheet: None (None), residues: 0 loop : -1.00 (0.74), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 109 HIS 0.004 0.001 HIS R 178 PHE 0.007 0.001 PHE R 61 TYR 0.006 0.001 TYR R 132 ARG 0.007 0.001 ARG R 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1228.97 seconds wall clock time: 21 minutes 49.17 seconds (1309.17 seconds total)