Starting phenix.real_space_refine on Sat Apr 26 15:33:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggu_40021/04_2025/8ggu_40021.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggu_40021/04_2025/8ggu_40021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ggu_40021/04_2025/8ggu_40021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggu_40021/04_2025/8ggu_40021.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggu_40021/04_2025/8ggu_40021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggu_40021/04_2025/8ggu_40021.cif" } resolution = 3.4 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= 0.023 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 11 5.16 5 C 1374 2.51 5 N 326 2.21 5 O 342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 2053 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2038 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 7, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 109 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.88, per 1000 atoms: 1.40 Number of scatterers: 2053 At special positions: 0 Unit cell: (54.6651, 83.2992, 61.6067, 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 11 16.00 O 342 8.00 N 326 7.00 C 1374 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 276.0 milliseconds 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 0 sheets defined 88.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.698A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 4.175A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.692A 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 102 through 137 removed outlier: 3.709A pdb=" N CYS R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.531A pdb=" N ALA R 150 " --> pdb=" O THR R 146 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE R 153 " --> pdb=" O LYS R 149 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix removed outlier: 3.756A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 237 removed outlier: 3.889A pdb=" N ASP R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS R 235 " --> pdb=" O GLN R 231 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 299 removed outlier: 3.943A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.729A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN R 299 " --> pdb=" O VAL R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 327 removed outlier: 3.610A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY R 315 " --> pdb=" O LEU R 311 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR R 316 " --> pdb=" O ASN R 312 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 163 hydrogen bonds defined for protein. 489 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: 0.54 Time building geometry restraints manager: 0.70 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: 619 1.34 - 1.46: 435 1.46 - 1.58: 1039 1.58 - 1.70: 0 1.70 - 1.81: 15 Bond restraints: 2108 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.452 -0.055 2.00e-02 2.50e+03 7.51e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.577 -0.054 2.00e-02 2.50e+03 7.20e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.567 -0.047 2.00e-02 2.50e+03 5.59e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.441 -0.047 2.00e-02 2.50e+03 5.49e+00 bond pdb=" CAI G1I R 501 " pdb=" NAN G1I R 501 " ideal model delta sigma weight residual 1.451 1.485 -0.034 2.00e-02 2.50e+03 2.85e+00 ... (remaining 2103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 2764 1.11 - 2.22: 110 2.22 - 3.33: 15 3.33 - 4.43: 5 4.43 - 5.54: 6 Bond angle restraints: 2900 Sorted by residual: angle pdb=" C VAL R 87 " pdb=" CA VAL R 87 " pdb=" CB VAL R 87 " ideal model delta sigma weight residual 114.00 110.62 3.38 1.31e+00 5.83e-01 6.67e+00 angle pdb=" C VAL R 86 " pdb=" N VAL R 87 " pdb=" CA VAL R 87 " ideal model delta sigma weight residual 120.33 122.31 -1.98 8.00e-01 1.56e+00 6.10e+00 angle pdb=" N LYS R 97 " pdb=" CA LYS R 97 " pdb=" C LYS R 97 " ideal model delta sigma weight residual 113.72 110.89 2.83 1.52e+00 4.33e-01 3.47e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 118.17 -5.54 3.00e+00 1.11e-01 3.41e+00 angle pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sigma weight residual 110.89 115.93 -5.04 3.00e+00 1.11e-01 2.82e+00 ... (remaining 2895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.02: 1047 14.02 - 28.03: 101 28.03 - 42.05: 37 42.05 - 56.07: 5 56.07 - 70.09: 2 Dihedral angle restraints: 1192 sinusoidal: 364 harmonic: 828 Sorted by residual: dihedral pdb=" CA GLN R 170 " pdb=" C GLN R 170 " pdb=" N MET R 171 " pdb=" CA MET R 171 " ideal model delta harmonic sigma weight residual 180.00 162.06 17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA LEU R 302 " pdb=" C LEU R 302 " pdb=" N ILE R 303 " pdb=" CA ILE R 303 " ideal model delta harmonic sigma weight residual -180.00 -162.84 -17.16 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ALA R 59 " pdb=" C ALA R 59 " pdb=" N LYS R 60 " pdb=" CA LYS R 60 " ideal model delta harmonic sigma weight residual 180.00 -164.28 -15.72 0 5.00e+00 4.00e-02 9.89e+00 ... (remaining 1189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 227 0.031 - 0.062: 86 0.062 - 0.093: 36 0.093 - 0.124: 5 0.124 - 0.154: 1 Chirality restraints: 355 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 2.55 -0.15 2.00e-01 2.50e+01 5.97e-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 2.99e-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 2.76e-01 ... (remaining 352 not shown) Planarity restraints: 354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO R 168 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 281 " -0.005 2.00e-02 2.50e+03 9.96e-03 9.92e-01 pdb=" C THR R 281 " 0.017 2.00e-02 2.50e+03 pdb=" O THR R 281 " -0.006 2.00e-02 2.50e+03 pdb=" N PHE R 282 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " 0.015 5.00e-02 4.00e+02 2.20e-02 7.75e-01 pdb=" N PRO R 211 " -0.038 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " 0.012 5.00e-02 4.00e+02 ... (remaining 351 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 549 2.81 - 3.33: 2089 3.33 - 3.85: 3266 3.85 - 4.38: 3239 4.38 - 4.90: 5951 Nonbonded interactions: 15094 Sorted by model distance: nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.284 3.040 nonbonded pdb=" OD1 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.396 3.040 nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.477 3.040 nonbonded pdb=" O GLU R 62 " pdb=" NE2 GLN R 65 " model vdw 2.503 3.120 nonbonded pdb=" ND2 ASN R 103 " pdb=" O GLU R 188 " model vdw 2.580 3.120 ... (remaining 15089 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 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: 0.020 Set scattering table: 0.020 Process input model: 11.850 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 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 0.055 2109 Z= 0.198 Angle : 0.548 5.543 2902 Z= 0.305 Chirality : 0.038 0.154 355 Planarity : 0.003 0.039 354 Dihedral : 13.538 70.086 651 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: 1.90 (0.50), residues: 277 helix: 2.33 (0.35), residues: 214 sheet: None (None), residues: 0 loop : -2.78 (0.57), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 158 HIS 0.005 0.001 HIS R 296 PHE 0.008 0.001 PHE R 104 TYR 0.011 0.001 TYR R 185 ARG 0.001 0.000 ARG R 304 Details of bonding type rmsd hydrogen bonds : bond 0.15539 ( 163) hydrogen bonds : angle 4.82448 ( 489) SS BOND : bond 0.00302 ( 1) SS BOND : angle 0.46585 ( 2) covalent geometry : bond 0.00403 ( 2108) covalent geometry : angle 0.54846 ( 2900) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.225 Fit side-chains REVERT: R 105 TRP cc_start: 0.7474 (m100) cc_final: 0.7247 (m100) REVERT: R 159 ILE cc_start: 0.8391 (tt) cc_final: 0.8163 (tt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0732 time to fit residues: 4.4094 Evaluate side-chains 33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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: 0.6980 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 312 ASN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.182659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.167133 restraints weight = 3233.258| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.86 r_work: 0.3737 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2109 Z= 0.148 Angle : 0.502 4.781 2902 Z= 0.280 Chirality : 0.040 0.118 355 Planarity : 0.003 0.030 354 Dihedral : 5.172 19.385 309 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.31 % Allowed : 13.26 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.51), residues: 277 helix: 2.31 (0.35), residues: 220 sheet: None (None), residues: 0 loop : -2.43 (0.63), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.001 0.000 HIS R 296 PHE 0.010 0.001 PHE R 61 TYR 0.008 0.001 TYR R 185 ARG 0.001 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.05980 ( 163) hydrogen bonds : angle 3.91377 ( 489) SS BOND : bond 0.00247 ( 1) SS BOND : angle 0.55940 ( 2) covalent geometry : bond 0.00317 ( 2108) covalent geometry : angle 0.50235 ( 2900) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.245 Fit side-chains REVERT: R 105 TRP cc_start: 0.7564 (m100) cc_final: 0.7252 (m100) REVERT: R 159 ILE cc_start: 0.8430 (tt) cc_final: 0.8216 (tt) outliers start: 6 outliers final: 6 residues processed: 39 average time/residue: 0.0688 time to fit residues: 3.7539 Evaluate side-chains 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.0670 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 24 optimal weight: 0.1980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 103 ASN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.188510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.174787 restraints weight = 3142.453| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.38 r_work: 0.3799 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2109 Z= 0.116 Angle : 0.441 4.876 2902 Z= 0.249 Chirality : 0.038 0.117 355 Planarity : 0.003 0.025 354 Dihedral : 4.808 18.352 309 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.10 % Allowed : 18.23 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.51), residues: 277 helix: 2.47 (0.35), residues: 221 sheet: None (None), residues: 0 loop : -2.35 (0.64), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 99 HIS 0.002 0.001 HIS R 296 PHE 0.007 0.001 PHE R 61 TYR 0.006 0.001 TYR R 185 ARG 0.001 0.000 ARG R 175 Details of bonding type rmsd hydrogen bonds : bond 0.05008 ( 163) hydrogen bonds : angle 3.57151 ( 489) SS BOND : bond 0.00312 ( 1) SS BOND : angle 0.52778 ( 2) covalent geometry : bond 0.00222 ( 2108) covalent geometry : angle 0.44143 ( 2900) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.215 Fit side-chains REVERT: R 105 TRP cc_start: 0.7423 (m100) cc_final: 0.7113 (m100) REVERT: R 159 ILE cc_start: 0.8366 (tt) cc_final: 0.8162 (tt) outliers start: 2 outliers final: 2 residues processed: 39 average time/residue: 0.0690 time to fit residues: 3.7535 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 24 optimal weight: 0.0060 chunk 27 optimal weight: 0.6980 chunk 14 optimal weight: 0.0770 chunk 13 optimal weight: 0.0050 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 overall best weight: 0.1968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 293 ASN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.192095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.178541 restraints weight = 3243.312| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.63 r_work: 0.3876 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2109 Z= 0.096 Angle : 0.408 4.948 2902 Z= 0.226 Chirality : 0.037 0.115 355 Planarity : 0.003 0.022 354 Dihedral : 4.413 16.825 309 Min Nonbonded Distance : 2.669 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.21 % Allowed : 18.78 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.51), residues: 277 helix: 2.83 (0.35), residues: 218 sheet: None (None), residues: 0 loop : -2.66 (0.55), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 109 HIS 0.002 0.001 HIS R 93 PHE 0.008 0.001 PHE R 61 TYR 0.003 0.000 TYR R 185 ARG 0.000 0.000 ARG R 175 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 163) hydrogen bonds : angle 3.25710 ( 489) SS BOND : bond 0.00320 ( 1) SS BOND : angle 0.42972 ( 2) covalent geometry : bond 0.00173 ( 2108) covalent geometry : angle 0.40821 ( 2900) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.211 Fit side-chains REVERT: R 105 TRP cc_start: 0.7267 (m100) cc_final: 0.7024 (m100) outliers start: 4 outliers final: 4 residues processed: 42 average time/residue: 0.0683 time to fit residues: 3.9177 Evaluate side-chains 42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.187429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.173473 restraints weight = 3191.032| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.42 r_work: 0.3804 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2109 Z= 0.132 Angle : 0.466 5.117 2902 Z= 0.258 Chirality : 0.039 0.115 355 Planarity : 0.003 0.023 354 Dihedral : 4.635 18.484 309 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 4.97 % Allowed : 17.68 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.52), residues: 277 helix: 2.75 (0.36), residues: 216 sheet: None (None), residues: 0 loop : -2.54 (0.61), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 158 HIS 0.002 0.001 HIS R 296 PHE 0.007 0.001 PHE R 61 TYR 0.008 0.001 TYR R 199 ARG 0.001 0.000 ARG R 151 Details of bonding type rmsd hydrogen bonds : bond 0.05254 ( 163) hydrogen bonds : angle 3.47060 ( 489) SS BOND : bond 0.00207 ( 1) SS BOND : angle 0.54426 ( 2) covalent geometry : bond 0.00285 ( 2108) covalent geometry : angle 0.46574 ( 2900) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.212 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 42 average time/residue: 0.0650 time to fit residues: 3.7710 Evaluate side-chains 43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 0 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.184491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.169628 restraints weight = 3179.412| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.56 r_work: 0.3755 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2109 Z= 0.136 Angle : 0.466 5.020 2902 Z= 0.259 Chirality : 0.039 0.119 355 Planarity : 0.003 0.024 354 Dihedral : 4.723 19.265 309 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 6.08 % Allowed : 18.78 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.52), residues: 277 helix: 2.66 (0.36), residues: 216 sheet: None (None), residues: 0 loop : -2.60 (0.61), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 99 HIS 0.002 0.001 HIS R 296 PHE 0.007 0.001 PHE R 61 TYR 0.009 0.001 TYR R 185 ARG 0.000 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.05450 ( 163) hydrogen bonds : angle 3.48801 ( 489) SS BOND : bond 0.00242 ( 1) SS BOND : angle 0.67687 ( 2) covalent geometry : bond 0.00296 ( 2108) covalent geometry : angle 0.46589 ( 2900) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.259 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 42 average time/residue: 0.0722 time to fit residues: 4.1749 Evaluate side-chains 45 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 291 ILE Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.181325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.167648 restraints weight = 3201.827| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.18 r_work: 0.3768 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2109 Z= 0.151 Angle : 0.486 5.018 2902 Z= 0.270 Chirality : 0.040 0.119 355 Planarity : 0.003 0.025 354 Dihedral : 4.809 19.689 309 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 6.08 % Allowed : 19.89 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.52), residues: 277 helix: 2.57 (0.36), residues: 216 sheet: None (None), residues: 0 loop : -2.61 (0.62), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 99 HIS 0.002 0.001 HIS R 296 PHE 0.008 0.001 PHE R 282 TYR 0.008 0.001 TYR R 199 ARG 0.000 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.05778 ( 163) hydrogen bonds : angle 3.57431 ( 489) SS BOND : bond 0.00257 ( 1) SS BOND : angle 0.76647 ( 2) covalent geometry : bond 0.00337 ( 2108) covalent geometry : angle 0.48561 ( 2900) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.272 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 42 average time/residue: 0.0758 time to fit residues: 4.3668 Evaluate side-chains 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 291 ILE Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.0370 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.0870 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.185774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.169881 restraints weight = 3359.334| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.71 r_work: 0.3759 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 : 0.002 0.026 2109 Z= 0.116 Angle : 0.443 4.959 2902 Z= 0.247 Chirality : 0.038 0.119 355 Planarity : 0.003 0.025 354 Dihedral : 4.705 19.071 309 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.87 % Allowed : 23.20 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.52), residues: 277 helix: 2.67 (0.36), residues: 217 sheet: None (None), residues: 0 loop : -2.49 (0.63), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 99 HIS 0.002 0.001 HIS R 296 PHE 0.007 0.001 PHE R 61 TYR 0.006 0.001 TYR R 185 ARG 0.000 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.05212 ( 163) hydrogen bonds : angle 3.45233 ( 489) SS BOND : bond 0.00298 ( 1) SS BOND : angle 0.67702 ( 2) covalent geometry : bond 0.00227 ( 2108) covalent geometry : angle 0.44283 ( 2900) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.188 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 41 average time/residue: 0.0638 time to fit residues: 3.6785 Evaluate side-chains 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.0000 chunk 4 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.0370 chunk 1 optimal weight: 0.8980 overall best weight: 0.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.184855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.170914 restraints weight = 3415.381| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.90 r_work: 0.3797 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2109 Z= 0.117 Angle : 0.442 4.986 2902 Z= 0.246 Chirality : 0.038 0.118 355 Planarity : 0.003 0.025 354 Dihedral : 4.677 18.873 309 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.42 % Allowed : 23.20 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.52), residues: 277 helix: 2.68 (0.36), residues: 217 sheet: None (None), residues: 0 loop : -2.48 (0.64), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 PHE 0.007 0.001 PHE R 61 TYR 0.006 0.001 TYR R 199 ARG 0.000 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.05115 ( 163) hydrogen bonds : angle 3.43568 ( 489) SS BOND : bond 0.00298 ( 1) SS BOND : angle 0.63118 ( 2) covalent geometry : bond 0.00233 ( 2108) covalent geometry : angle 0.44171 ( 2900) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.219 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 42 average time/residue: 0.0796 time to fit residues: 4.4682 Evaluate side-chains 45 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 0.0000 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 26 optimal weight: 0.0470 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 overall best weight: 0.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.188910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.173899 restraints weight = 3287.505| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.84 r_work: 0.3811 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2109 Z= 0.104 Angle : 0.424 4.944 2902 Z= 0.236 Chirality : 0.038 0.115 355 Planarity : 0.003 0.025 354 Dihedral : 4.546 17.933 309 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.31 % Allowed : 23.76 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.52), residues: 277 helix: 2.83 (0.36), residues: 217 sheet: None (None), residues: 0 loop : -2.42 (0.64), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 PHE 0.007 0.001 PHE R 61 TYR 0.004 0.001 TYR R 308 ARG 0.000 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.04445 ( 163) hydrogen bonds : angle 3.30040 ( 489) SS BOND : bond 0.00333 ( 1) SS BOND : angle 0.54664 ( 2) covalent geometry : bond 0.00183 ( 2108) covalent geometry : angle 0.42344 ( 2900) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.235 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 41 average time/residue: 0.0694 time to fit residues: 3.9440 Evaluate side-chains 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 0.0970 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 13 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.186189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.171830 restraints weight = 3217.223| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.87 r_work: 0.3788 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2109 Z= 0.117 Angle : 0.439 5.009 2902 Z= 0.244 Chirality : 0.038 0.116 355 Planarity : 0.003 0.025 354 Dihedral : 4.547 18.255 309 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.42 % Allowed : 23.20 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.52), residues: 277 helix: 2.76 (0.36), residues: 217 sheet: None (None), residues: 0 loop : -2.44 (0.65), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.002 0.001 HIS R 296 PHE 0.008 0.001 PHE R 61 TYR 0.015 0.001 TYR R 185 ARG 0.000 0.000 ARG R 304 Details of bonding type rmsd hydrogen bonds : bond 0.04867 ( 163) hydrogen bonds : angle 3.40668 ( 489) SS BOND : bond 0.00281 ( 1) SS BOND : angle 0.59433 ( 2) covalent geometry : bond 0.00241 ( 2108) covalent geometry : angle 0.43902 ( 2900) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1545.76 seconds wall clock time: 27 minutes 13.79 seconds (1633.79 seconds total)