Starting phenix.real_space_refine on Fri May 9 13:15:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggu_40021/05_2025/8ggu_40021.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggu_40021/05_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_40021/05_2025/8ggu_40021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggu_40021/05_2025/8ggu_40021.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggu_40021/05_2025/8ggu_40021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggu_40021/05_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-5687/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: 2.55, per 1000 atoms: 1.24 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 278.3 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: 0.53 Time building geometry restraints manager: 0.68 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: 1.510 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.040 Process input model: 11.270 Find NCS groups from input model: 0.030 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.670 ------------------------------------------------------------------------------- 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 : 0.211 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: 0.0691 time to fit residues: 4.1914 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 : 0.216 ------------------------------------------------------------------------------- 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: 0.7980 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 = 0.4076 r_free = 0.4076 target = 0.185821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.169743 restraints weight = 3194.186| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.66 r_work: 0.3717 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 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 4.763 2902 Z= 0.280 Chirality : 0.040 0.118 355 Planarity : 0.003 0.030 354 Dihedral : 5.172 19.388 309 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 3.91443 ( 489) SS BOND : bond 0.00249 ( 1) SS BOND : angle 0.55945 ( 2) covalent geometry : bond 0.00317 ( 2108) covalent geometry : angle 0.50208 ( 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 : 0.227 Fit side-chains REVERT: R 105 TRP cc_start: 0.7583 (m100) cc_final: 0.7260 (m100) REVERT: R 159 ILE cc_start: 0.8408 (tt) cc_final: 0.8193 (tt) outliers start: 6 outliers final: 6 residues processed: 39 average time/residue: 0.0683 time to fit residues: 3.7035 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 : 0.231 ------------------------------------------------------------------------------- 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: 0.7980 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.0170 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.187666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.175221 restraints weight = 3238.968| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.15 r_work: 0.3821 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2109 Z= 0.119 Angle : 0.449 5.018 2902 Z= 0.253 Chirality : 0.038 0.117 355 Planarity : 0.003 0.025 354 Dihedral : 4.832 18.653 309 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.10 % Allowed : 18.78 % Favored : 80.11 % 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: 2.31 (0.51), residues: 277 helix: 2.42 (0.35), residues: 221 sheet: None (None), residues: 0 loop : -2.36 (0.64), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.001 0.001 HIS R 296 PHE 0.008 0.001 PHE R 61 TYR 0.010 0.001 TYR R 185 ARG 0.001 0.000 ARG R 175 Details of bonding type rmsd hydrogen bonds : bond 0.05178 ( 163) hydrogen bonds : angle 3.59868 ( 489) SS BOND : bond 0.00299 ( 1) SS BOND : angle 0.53786 ( 2) covalent geometry : bond 0.00235 ( 2108) covalent geometry : angle 0.44900 ( 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 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.230 Fit side-chains REVERT: R 159 ILE cc_start: 0.8398 (tt) cc_final: 0.8189 (tt) outliers start: 2 outliers final: 2 residues processed: 38 average time/residue: 0.0709 time to fit residues: 3.7092 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 0.0770 chunk 24 optimal weight: 0.0010 chunk 27 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 13 optimal weight: 0.0070 chunk 5 optimal weight: 0.0970 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.1560 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.192028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.178536 restraints weight = 3234.819| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.68 r_work: 0.3885 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1786 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= 0.097 Angle : 0.407 4.955 2902 Z= 0.226 Chirality : 0.037 0.115 355 Planarity : 0.003 0.023 354 Dihedral : 4.446 17.173 309 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.66 % Allowed : 19.34 % 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: 2.82 (0.35), residues: 218 sheet: None (None), residues: 0 loop : -2.64 (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 296 PHE 0.007 0.001 PHE R 61 TYR 0.003 0.000 TYR R 185 ARG 0.001 0.000 ARG R 304 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 163) hydrogen bonds : angle 3.27151 ( 489) SS BOND : bond 0.00390 ( 1) SS BOND : angle 0.53574 ( 2) covalent geometry : bond 0.00174 ( 2108) covalent geometry : angle 0.40669 ( 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 45 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.213 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 44 average time/residue: 0.0696 time to fit residues: 4.2073 Evaluate side-chains 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 LEU 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: 0.0570 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.187545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.172421 restraints weight = 3208.893| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.78 r_work: 0.3786 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1685 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= 0.130 Angle : 0.458 5.061 2902 Z= 0.255 Chirality : 0.039 0.117 355 Planarity : 0.003 0.023 354 Dihedral : 4.619 18.580 309 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.97 % Allowed : 18.23 % Favored : 76.80 % 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: 2.80 (0.36), residues: 216 sheet: None (None), residues: 0 loop : -2.58 (0.59), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 PHE 0.008 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 0.05154 ( 163) hydrogen bonds : angle 3.44536 ( 489) SS BOND : bond 0.00278 ( 1) SS BOND : angle 0.58867 ( 2) covalent geometry : bond 0.00280 ( 2108) covalent geometry : angle 0.45778 ( 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 : 0.223 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 42 average time/residue: 0.0683 time to fit residues: 3.9389 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 : 0.225 ------------------------------------------------------------------------------- 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: 0.9980 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 0 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 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 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.183254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.167952 restraints weight = 3173.490| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 3.04 r_work: 0.3763 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2109 Z= 0.144 Angle : 0.478 5.048 2902 Z= 0.265 Chirality : 0.039 0.120 355 Planarity : 0.003 0.025 354 Dihedral : 4.759 19.512 309 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 6.08 % Allowed : 20.44 % Favored : 73.48 % 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: 2.35 (0.51), residues: 277 helix: 2.62 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -2.64 (0.60), 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 61 TYR 0.010 0.001 TYR R 185 ARG 0.000 0.000 ARG R 151 Details of bonding type rmsd hydrogen bonds : bond 0.05591 ( 163) hydrogen bonds : angle 3.52231 ( 489) SS BOND : bond 0.00256 ( 1) SS BOND : angle 0.73278 ( 2) covalent geometry : bond 0.00321 ( 2108) covalent geometry : angle 0.47761 ( 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 : 0.255 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 42 average time/residue: 0.0675 time to fit residues: 3.8783 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 : 0.222 ------------------------------------------------------------------------------- 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: 0.7980 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.184627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.169434 restraints weight = 3303.796| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.76 r_work: 0.3755 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2109 Z= 0.141 Angle : 0.475 5.047 2902 Z= 0.264 Chirality : 0.039 0.118 355 Planarity : 0.003 0.026 354 Dihedral : 4.783 19.590 309 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 6.63 % Allowed : 20.99 % 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: 2.35 (0.51), residues: 277 helix: 2.60 (0.35), 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 0.008 0.001 PHE R 61 TYR 0.008 0.001 TYR R 185 ARG 0.000 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.05668 ( 163) hydrogen bonds : angle 3.55735 ( 489) SS BOND : bond 0.00281 ( 1) SS BOND : angle 0.75904 ( 2) covalent geometry : bond 0.00312 ( 2108) covalent geometry : angle 0.47458 ( 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 48 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.226 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 42 average time/residue: 0.0674 time to fit residues: 3.8873 Evaluate side-chains 46 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 26 optimal weight: 0.0040 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.0070 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.5212 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.182691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.168472 restraints weight = 3375.019| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.97 r_work: 0.3804 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1793 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= 0.122 Angle : 0.450 4.996 2902 Z= 0.251 Chirality : 0.038 0.121 355 Planarity : 0.003 0.025 354 Dihedral : 4.728 19.231 309 Min Nonbonded Distance : 2.650 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: 2.45 (0.52), residues: 277 helix: 2.64 (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 199 ARG 0.000 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.05362 ( 163) hydrogen bonds : angle 3.48743 ( 489) SS BOND : bond 0.00303 ( 1) SS BOND : angle 0.70249 ( 2) covalent geometry : bond 0.00247 ( 2108) covalent geometry : angle 0.45027 ( 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 45 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.235 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 42 average time/residue: 0.0717 time to fit residues: 4.1308 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 : 0.231 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 1 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.186804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.170839 restraints weight = 3438.339| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.74 r_work: 0.3783 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1832 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= 0.119 Angle : 0.444 4.990 2902 Z= 0.248 Chirality : 0.038 0.119 355 Planarity : 0.003 0.025 354 Dihedral : 4.693 18.940 309 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: 2.67 (0.36), residues: 217 sheet: None (None), residues: 0 loop : -2.48 (0.63), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 105 HIS 0.002 0.001 HIS R 296 PHE 0.008 0.001 PHE R 104 TYR 0.006 0.001 TYR R 199 ARG 0.000 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.05175 ( 163) hydrogen bonds : angle 3.44885 ( 489) SS BOND : bond 0.00322 ( 1) SS BOND : angle 0.70077 ( 2) covalent geometry : bond 0.00237 ( 2108) covalent geometry : angle 0.44408 ( 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 : 0.235 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 42 average time/residue: 0.0697 time to fit residues: 4.0152 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 : 0.227 ------------------------------------------------------------------------------- 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: 0.9980 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 0.0770 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.186777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.171258 restraints weight = 3302.806| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.71 r_work: 0.3775 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2109 Z= 0.130 Angle : 0.457 5.039 2902 Z= 0.255 Chirality : 0.039 0.118 355 Planarity : 0.003 0.025 354 Dihedral : 4.713 19.010 309 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.42 % Allowed : 23.76 % Favored : 71.82 % 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: 2.43 (0.52), residues: 277 helix: 2.62 (0.36), residues: 217 sheet: None (None), residues: 0 loop : -2.48 (0.63), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 105 HIS 0.002 0.001 HIS R 296 PHE 0.009 0.001 PHE R 104 TYR 0.007 0.001 TYR R 199 ARG 0.000 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.05328 ( 163) hydrogen bonds : angle 3.49422 ( 489) SS BOND : bond 0.00307 ( 1) SS BOND : angle 0.72118 ( 2) covalent geometry : bond 0.00273 ( 2108) covalent geometry : angle 0.45681 ( 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 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.246 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 41 average time/residue: 0.0694 time to fit residues: 3.9460 Evaluate side-chains 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 15 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 13 optimal weight: 0.0470 chunk 22 optimal weight: 0.9990 overall best weight: 0.4880 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.186700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.171811 restraints weight = 3304.362| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.77 r_work: 0.3795 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1880 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= 0.119 Angle : 0.445 5.012 2902 Z= 0.248 Chirality : 0.038 0.117 355 Planarity : 0.003 0.025 354 Dihedral : 4.678 18.795 309 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 5.52 % Allowed : 23.20 % Favored : 71.27 % 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: 2.52 (0.52), residues: 277 helix: 2.68 (0.36), residues: 217 sheet: None (None), residues: 0 loop : -2.43 (0.65), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 105 HIS 0.002 0.001 HIS R 296 PHE 0.010 0.001 PHE R 104 TYR 0.006 0.001 TYR R 199 ARG 0.000 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.05149 ( 163) hydrogen bonds : angle 3.45406 ( 489) SS BOND : bond 0.00314 ( 1) SS BOND : angle 0.68711 ( 2) covalent geometry : bond 0.00238 ( 2108) covalent geometry : angle 0.44439 ( 2900) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1434.61 seconds wall clock time: 25 minutes 36.52 seconds (1536.52 seconds total)