Starting phenix.real_space_refine on Sat Apr 26 18:39:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xwf_38734/04_2025/8xwf_38734.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xwf_38734/04_2025/8xwf_38734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xwf_38734/04_2025/8xwf_38734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xwf_38734/04_2025/8xwf_38734.map" model { file = "/net/cci-nas-00/data/ceres_data/8xwf_38734/04_2025/8xwf_38734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xwf_38734/04_2025/8xwf_38734.cif" } resolution = 3.65 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= 1.000 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 21 5.16 5 C 2024 2.51 5 N 527 2.21 5 O 518 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: 3090 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 336 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 467 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 62} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2287 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 9, 'TRANS': 288} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 71 Time building chain proxies: 2.37, per 1000 atoms: 0.77 Number of scatterers: 3090 At special positions: 0 Unit cell: (68.475, 78.85, 94.4125, 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 21 16.00 O 518 8.00 N 527 7.00 C 2024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 35 " distance=2.03 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS D 51 " distance=2.03 Simple disulfide: pdb=" SG CYS R 39 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 196 " distance=2.04 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: 0.71 Conformation dependent library (CDL) restraints added in 457.6 milliseconds 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 798 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 65.8% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'E' and resid 19 through 21 No H-bonds generated for 'chain 'E' and resid 19 through 21' Processing helix chain 'E' and resid 56 through 69 removed outlier: 3.915A pdb=" N GLN E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 67 Processing helix chain 'R' and resid 44 through 76 removed outlier: 4.005A pdb=" N LYS R 48 " --> pdb=" O LEU R 44 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL R 52 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER R 76 " --> pdb=" O VAL R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 111 Proline residue: R 102 - end of helix Processing helix chain 'R' and resid 116 through 149 Processing helix chain 'R' and resid 154 through 160 removed outlier: 3.735A pdb=" N GLN R 157 " --> pdb=" O THR R 154 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR R 160 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 177 Processing helix chain 'R' and resid 177 through 183 removed outlier: 3.582A pdb=" N LEU R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 212 Processing helix chain 'R' and resid 212 through 218 removed outlier: 3.560A pdb=" N GLN R 216 " --> pdb=" O ARG R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 240 removed outlier: 3.789A pdb=" N LYS R 240 " --> pdb=" O ARG R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 279 Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 285 through 304 Processing helix chain 'R' and resid 304 through 315 removed outlier: 4.389A pdb=" N CYS R 308 " --> pdb=" O ILE R 304 " (cutoff:3.500A) Proline residue: R 311 - end of helix Processing helix chain 'R' and resid 318 through 329 removed outlier: 3.596A pdb=" N ARG R 322 " --> pdb=" O GLY R 318 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU R 329 " --> pdb=" O LEU R 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 49 through 52 removed outlier: 4.136A pdb=" N VAL E 40 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL D 40 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 184 through 187 217 hydrogen bonds defined for protein. 636 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: 0.86 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 964 1.34 - 1.46: 600 1.46 - 1.58: 1559 1.58 - 1.70: 0 1.70 - 1.83: 27 Bond restraints: 3150 Sorted by residual: bond pdb=" N GLY E 17 " pdb=" CA GLY E 17 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.37e+00 bond pdb=" N LYS D 65 " pdb=" CA LYS D 65 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.30e-02 5.92e+03 4.66e+00 bond pdb=" C PRO E 33 " pdb=" O PRO E 33 " ideal model delta sigma weight residual 1.237 1.213 0.025 1.26e-02 6.30e+03 3.81e+00 bond pdb=" CA LYS D 65 " pdb=" C LYS D 65 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.37e-02 5.33e+03 3.27e+00 bond pdb=" CA ILE R 46 " pdb=" CB ILE R 46 " ideal model delta sigma weight residual 1.540 1.522 0.018 1.17e-02 7.31e+03 2.35e+00 ... (remaining 3145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 4234 1.69 - 3.38: 53 3.38 - 5.07: 22 5.07 - 6.76: 0 6.76 - 8.45: 1 Bond angle restraints: 4310 Sorted by residual: angle pdb=" N LYS D 65 " pdb=" CA LYS D 65 " pdb=" C LYS D 65 " ideal model delta sigma weight residual 112.23 103.78 8.45 1.26e+00 6.30e-01 4.50e+01 angle pdb=" O GLY E 32 " pdb=" C GLY E 32 " pdb=" N PRO E 33 " ideal model delta sigma weight residual 121.77 118.46 3.31 1.00e+00 1.00e+00 1.09e+01 angle pdb=" O ILE D 66 " pdb=" C ILE D 66 " pdb=" N LEU D 67 " ideal model delta sigma weight residual 121.91 125.08 -3.17 9.80e-01 1.04e+00 1.05e+01 angle pdb=" N ILE D 66 " pdb=" CA ILE D 66 " pdb=" C ILE D 66 " ideal model delta sigma weight residual 110.42 107.33 3.09 9.60e-01 1.09e+00 1.04e+01 angle pdb=" N ILE R 317 " pdb=" CA ILE R 317 " pdb=" C ILE R 317 " ideal model delta sigma weight residual 112.98 109.08 3.90 1.25e+00 6.40e-01 9.72e+00 ... (remaining 4305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 1712 16.96 - 33.91: 143 33.91 - 50.86: 20 50.86 - 67.82: 5 67.82 - 84.77: 3 Dihedral angle restraints: 1883 sinusoidal: 660 harmonic: 1223 Sorted by residual: dihedral pdb=" CB CYS R 39 " pdb=" SG CYS R 39 " pdb=" SG CYS R 286 " pdb=" CB CYS R 286 " ideal model delta sinusoidal sigma weight residual 93.00 62.53 30.47 1 1.00e+01 1.00e-02 1.33e+01 dihedral pdb=" C LYS D 65 " pdb=" N LYS D 65 " pdb=" CA LYS D 65 " pdb=" CB LYS D 65 " ideal model delta harmonic sigma weight residual -122.60 -114.37 -8.23 0 2.50e+00 1.60e-01 1.08e+01 dihedral pdb=" CG ARG R 322 " pdb=" CD ARG R 322 " pdb=" NE ARG R 322 " pdb=" CZ ARG R 322 " ideal model delta sinusoidal sigma weight residual 90.00 133.99 -43.99 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 1880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 493 0.063 - 0.126: 57 0.126 - 0.188: 1 0.188 - 0.251: 0 0.251 - 0.314: 2 Chirality restraints: 553 Sorted by residual: chirality pdb=" CA ILE D 66 " pdb=" N ILE D 66 " pdb=" C ILE D 66 " pdb=" CB ILE D 66 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA LYS D 65 " pdb=" N LYS D 65 " pdb=" C LYS D 65 " pdb=" CB LYS D 65 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA GLU D 64 " pdb=" N GLU D 64 " pdb=" C GLU D 64 " pdb=" CB GLU D 64 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.37e-01 ... (remaining 550 not shown) Planarity restraints: 527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 310 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.89e+00 pdb=" N PRO R 311 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO R 311 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 311 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 30 " 0.016 5.00e-02 4.00e+02 2.44e-02 9.51e-01 pdb=" N PRO D 31 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO D 31 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 31 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 214 " 0.015 5.00e-02 4.00e+02 2.28e-02 8.35e-01 pdb=" N PRO R 215 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO R 215 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 215 " 0.013 5.00e-02 4.00e+02 ... (remaining 524 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1047 2.85 - 3.36: 3159 3.36 - 3.88: 4845 3.88 - 4.39: 5082 4.39 - 4.90: 9214 Nonbonded interactions: 23347 Sorted by model distance: nonbonded pdb=" OE1 GLN D 10 " pdb=" ND2 ASN R 191 " model vdw 2.340 3.120 nonbonded pdb=" O GLY R 201 " pdb=" OG1 THR R 204 " model vdw 2.341 3.040 nonbonded pdb=" NH2 ARG D 8 " pdb=" OD1 ASP R 293 " model vdw 2.379 3.120 nonbonded pdb=" O SER D 2 " pdb=" OG SER R 193 " model vdw 2.434 3.040 nonbonded pdb=" NE2 HIS D 34 " pdb=" OG SER R 189 " model vdw 2.442 3.120 ... (remaining 23342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.630 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 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 0.040 3154 Z= 0.196 Angle : 0.584 8.448 4318 Z= 0.364 Chirality : 0.043 0.314 553 Planarity : 0.004 0.034 527 Dihedral : 13.120 84.772 1073 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.43), residues: 412 helix: 2.68 (0.33), residues: 258 sheet: 1.33 (0.69), residues: 49 loop : 0.45 (0.63), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 104 HIS 0.003 0.001 HIS R 242 PHE 0.009 0.001 PHE R 220 TYR 0.006 0.001 TYR R 160 ARG 0.003 0.000 ARG R 185 Details of bonding type rmsd hydrogen bonds : bond 0.09586 ( 217) hydrogen bonds : angle 4.91654 ( 636) SS BOND : bond 0.00325 ( 4) SS BOND : angle 1.66181 ( 8) covalent geometry : bond 0.00354 ( 3150) covalent geometry : angle 0.58035 ( 4310) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 187 VAL cc_start: 0.9330 (t) cc_final: 0.9090 (m) REVERT: R 243 MET cc_start: 0.7788 (mtm) cc_final: 0.7332 (ptp) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1238 time to fit residues: 16.2303 Evaluate side-chains 69 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 36 optimal weight: 0.4980 chunk 11 optimal weight: 20.0000 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 GLN R 66 ASN R 89 ASN R 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.118986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.091405 restraints weight = 6267.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.093816 restraints weight = 3294.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.095413 restraints weight = 2201.250| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3154 Z= 0.135 Angle : 0.567 6.633 4318 Z= 0.287 Chirality : 0.041 0.154 553 Planarity : 0.004 0.030 527 Dihedral : 3.683 16.379 441 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.45 % Allowed : 14.42 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.43), residues: 412 helix: 2.90 (0.33), residues: 261 sheet: 1.42 (0.71), residues: 49 loop : 0.53 (0.66), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 112 HIS 0.002 0.001 HIS E 19 PHE 0.005 0.001 PHE R 183 TYR 0.008 0.001 TYR R 86 ARG 0.010 0.001 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.04646 ( 217) hydrogen bonds : angle 4.09498 ( 636) SS BOND : bond 0.00320 ( 4) SS BOND : angle 2.07867 ( 8) covalent geometry : bond 0.00292 ( 3150) covalent geometry : angle 0.56064 ( 4310) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: D 44 LEU cc_start: 0.8856 (mt) cc_final: 0.8396 (tp) REVERT: D 52 LEU cc_start: 0.9113 (mt) cc_final: 0.8853 (mt) REVERT: R 240 LYS cc_start: 0.8546 (mtpp) cc_final: 0.8163 (mtmm) REVERT: R 262 LEU cc_start: 0.8326 (tp) cc_final: 0.8098 (mt) outliers start: 11 outliers final: 9 residues processed: 76 average time/residue: 0.1412 time to fit residues: 13.2068 Evaluate side-chains 68 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 51 CYS Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 9 CYS Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 227 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 2 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 25 optimal weight: 0.0060 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 0.0870 chunk 8 optimal weight: 0.0000 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.126223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.102584 restraints weight = 6333.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.102812 restraints weight = 4077.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.103758 restraints weight = 3006.039| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3154 Z= 0.121 Angle : 0.551 6.852 4318 Z= 0.279 Chirality : 0.039 0.143 553 Planarity : 0.004 0.050 527 Dihedral : 3.700 20.250 441 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.76 % Allowed : 16.93 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.42), residues: 412 helix: 2.85 (0.32), residues: 260 sheet: 1.12 (0.72), residues: 50 loop : 0.36 (0.61), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 112 HIS 0.008 0.001 HIS D 34 PHE 0.004 0.001 PHE R 130 TYR 0.008 0.001 TYR R 86 ARG 0.016 0.001 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 217) hydrogen bonds : angle 3.93097 ( 636) SS BOND : bond 0.00375 ( 4) SS BOND : angle 1.47106 ( 8) covalent geometry : bond 0.00259 ( 3150) covalent geometry : angle 0.54752 ( 4310) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: D 24 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7782 (tm-30) REVERT: R 240 LYS cc_start: 0.8301 (mtpp) cc_final: 0.8049 (mtmm) outliers start: 12 outliers final: 8 residues processed: 74 average time/residue: 0.1234 time to fit residues: 11.4091 Evaluate side-chains 75 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 51 CYS Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 9 CYS Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 141 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 0.0040 chunk 18 optimal weight: 0.5980 chunk 22 optimal weight: 0.0970 chunk 3 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 GLN D 22 ASN R 110 ASN ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.125928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.102399 restraints weight = 6400.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.103927 restraints weight = 3477.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.104417 restraints weight = 2274.536| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3154 Z= 0.111 Angle : 0.522 6.675 4318 Z= 0.260 Chirality : 0.039 0.152 553 Planarity : 0.004 0.042 527 Dihedral : 3.572 17.154 441 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.82 % Allowed : 18.81 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.42), residues: 412 helix: 2.85 (0.32), residues: 260 sheet: 1.01 (0.84), residues: 43 loop : 0.38 (0.57), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 112 HIS 0.006 0.001 HIS D 34 PHE 0.004 0.001 PHE R 130 TYR 0.008 0.001 TYR R 86 ARG 0.008 0.001 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 217) hydrogen bonds : angle 3.81891 ( 636) SS BOND : bond 0.00268 ( 4) SS BOND : angle 1.16576 ( 8) covalent geometry : bond 0.00237 ( 3150) covalent geometry : angle 0.52041 ( 4310) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.341 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 75 average time/residue: 0.1345 time to fit residues: 12.6493 Evaluate side-chains 70 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 141 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.0060 chunk 9 optimal weight: 0.0270 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 overall best weight: 0.7656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.118425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.091321 restraints weight = 6435.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.093795 restraints weight = 3378.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.095210 restraints weight = 2240.452| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3154 Z= 0.124 Angle : 0.556 7.789 4318 Z= 0.276 Chirality : 0.039 0.153 553 Planarity : 0.004 0.049 527 Dihedral : 3.555 15.977 441 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.70 % Allowed : 19.44 % Favored : 75.86 % 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: 2.96 (0.41), residues: 412 helix: 2.79 (0.32), residues: 260 sheet: 1.02 (0.84), residues: 43 loop : 0.32 (0.56), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 112 HIS 0.008 0.001 HIS D 34 PHE 0.006 0.001 PHE R 183 TYR 0.008 0.001 TYR R 86 ARG 0.005 0.000 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 217) hydrogen bonds : angle 3.90200 ( 636) SS BOND : bond 0.00268 ( 4) SS BOND : angle 1.20098 ( 8) covalent geometry : bond 0.00281 ( 3150) covalent geometry : angle 0.55454 ( 4310) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 6 GLU cc_start: 0.8233 (mt-10) cc_final: 0.8018 (mt-10) outliers start: 15 outliers final: 12 residues processed: 75 average time/residue: 0.1149 time to fit residues: 11.0218 Evaluate side-chains 78 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 9 CYS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 227 MET Chi-restraints excluded: chain R residue 237 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.0370 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 306 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.116253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.088513 restraints weight = 6648.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.090982 restraints weight = 3435.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.092560 restraints weight = 2270.473| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3154 Z= 0.157 Angle : 0.593 7.508 4318 Z= 0.297 Chirality : 0.041 0.157 553 Planarity : 0.004 0.037 527 Dihedral : 3.630 15.634 441 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.39 % Allowed : 20.69 % Favored : 74.92 % 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: 2.74 (0.41), residues: 412 helix: 2.57 (0.32), residues: 260 sheet: 1.01 (0.83), residues: 43 loop : 0.34 (0.57), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 112 HIS 0.005 0.001 HIS D 34 PHE 0.009 0.001 PHE R 183 TYR 0.010 0.001 TYR R 55 ARG 0.004 0.000 ARG R 185 Details of bonding type rmsd hydrogen bonds : bond 0.04636 ( 217) hydrogen bonds : angle 3.96047 ( 636) SS BOND : bond 0.00357 ( 4) SS BOND : angle 1.45010 ( 8) covalent geometry : bond 0.00363 ( 3150) covalent geometry : angle 0.59063 ( 4310) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: D 6 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8123 (mt-10) REVERT: D 44 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8269 (tp) outliers start: 14 outliers final: 11 residues processed: 72 average time/residue: 0.1230 time to fit residues: 11.2631 Evaluate side-chains 74 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 227 MET Chi-restraints excluded: chain R residue 237 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.116184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.088868 restraints weight = 6442.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.091178 restraints weight = 3393.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.092804 restraints weight = 2280.438| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3154 Z= 0.156 Angle : 0.626 11.961 4318 Z= 0.307 Chirality : 0.041 0.159 553 Planarity : 0.003 0.019 527 Dihedral : 3.645 15.729 441 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.08 % Allowed : 21.63 % Favored : 74.29 % 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: 2.75 (0.41), residues: 412 helix: 2.59 (0.32), residues: 260 sheet: 0.83 (0.83), residues: 43 loop : 0.41 (0.59), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 112 HIS 0.003 0.001 HIS D 34 PHE 0.008 0.001 PHE R 183 TYR 0.007 0.001 TYR R 86 ARG 0.011 0.001 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.04517 ( 217) hydrogen bonds : angle 3.98896 ( 636) SS BOND : bond 0.00262 ( 4) SS BOND : angle 1.32673 ( 8) covalent geometry : bond 0.00364 ( 3150) covalent geometry : angle 0.62366 ( 4310) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: D 6 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8143 (mt-10) REVERT: D 44 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8253 (tp) REVERT: R 94 ASP cc_start: 0.8878 (m-30) cc_final: 0.8610 (t0) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.1206 time to fit residues: 11.0482 Evaluate side-chains 74 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 237 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 25 optimal weight: 0.0000 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.0770 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.118108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.090608 restraints weight = 6464.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.093170 restraints weight = 3336.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.094669 restraints weight = 2193.642| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3154 Z= 0.118 Angle : 0.606 11.161 4318 Z= 0.297 Chirality : 0.040 0.154 553 Planarity : 0.003 0.022 527 Dihedral : 3.572 15.541 441 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.13 % Allowed : 23.51 % Favored : 73.35 % 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: 2.69 (0.42), residues: 412 helix: 2.66 (0.32), residues: 256 sheet: 0.74 (0.85), residues: 43 loop : 0.16 (0.56), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 112 HIS 0.004 0.001 HIS D 34 PHE 0.004 0.001 PHE R 130 TYR 0.006 0.001 TYR R 86 ARG 0.006 0.001 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.04068 ( 217) hydrogen bonds : angle 3.87618 ( 636) SS BOND : bond 0.00243 ( 4) SS BOND : angle 1.15081 ( 8) covalent geometry : bond 0.00259 ( 3150) covalent geometry : angle 0.60440 ( 4310) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: D 6 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8143 (mt-10) REVERT: R 94 ASP cc_start: 0.8879 (m-30) cc_final: 0.8556 (t0) REVERT: R 274 ASP cc_start: 0.8988 (t0) cc_final: 0.8781 (t0) REVERT: R 314 TYR cc_start: 0.9056 (m-80) cc_final: 0.8668 (m-80) outliers start: 10 outliers final: 8 residues processed: 70 average time/residue: 0.1046 time to fit residues: 9.6750 Evaluate side-chains 72 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 279 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 4 optimal weight: 0.0370 chunk 13 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.118433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.091029 restraints weight = 6450.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.093476 restraints weight = 3383.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.095121 restraints weight = 2259.184| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3154 Z= 0.119 Angle : 0.613 10.935 4318 Z= 0.298 Chirality : 0.040 0.153 553 Planarity : 0.003 0.021 527 Dihedral : 3.490 15.048 441 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.51 % Allowed : 24.45 % Favored : 73.04 % 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 (0.42), residues: 412 helix: 2.67 (0.32), residues: 256 sheet: 0.81 (0.87), residues: 43 loop : 0.13 (0.55), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 112 HIS 0.003 0.001 HIS D 34 PHE 0.005 0.001 PHE R 183 TYR 0.006 0.001 TYR R 55 ARG 0.006 0.000 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 217) hydrogen bonds : angle 3.85325 ( 636) SS BOND : bond 0.00241 ( 4) SS BOND : angle 1.17682 ( 8) covalent geometry : bond 0.00264 ( 3150) covalent geometry : angle 0.61154 ( 4310) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: D 6 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8179 (mt-10) REVERT: R 94 ASP cc_start: 0.8836 (m-30) cc_final: 0.8558 (t0) outliers start: 8 outliers final: 8 residues processed: 70 average time/residue: 0.1053 time to fit residues: 9.6798 Evaluate side-chains 71 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 279 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 0.0010 chunk 35 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.117778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.089973 restraints weight = 6400.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.092486 restraints weight = 3317.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.093992 restraints weight = 2192.299| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3154 Z= 0.137 Angle : 0.640 10.744 4318 Z= 0.312 Chirality : 0.040 0.150 553 Planarity : 0.003 0.019 527 Dihedral : 3.509 14.995 441 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.82 % Allowed : 24.45 % Favored : 72.73 % 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: 2.68 (0.42), residues: 412 helix: 2.66 (0.32), residues: 256 sheet: 0.78 (0.88), residues: 43 loop : 0.11 (0.56), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 112 HIS 0.004 0.001 HIS R 242 PHE 0.006 0.001 PHE R 183 TYR 0.008 0.001 TYR R 55 ARG 0.006 0.000 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 217) hydrogen bonds : angle 3.94330 ( 636) SS BOND : bond 0.00262 ( 4) SS BOND : angle 1.26495 ( 8) covalent geometry : bond 0.00316 ( 3150) covalent geometry : angle 0.63835 ( 4310) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: R 94 ASP cc_start: 0.8886 (m-30) cc_final: 0.8563 (t0) outliers start: 9 outliers final: 9 residues processed: 67 average time/residue: 0.1078 time to fit residues: 9.5666 Evaluate side-chains 72 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 279 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.117495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.089888 restraints weight = 6464.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.092353 restraints weight = 3308.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.094056 restraints weight = 2185.500| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3154 Z= 0.124 Angle : 0.633 10.613 4318 Z= 0.308 Chirality : 0.040 0.153 553 Planarity : 0.003 0.034 527 Dihedral : 3.506 15.310 441 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.45 % Allowed : 23.82 % Favored : 72.73 % 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: 2.58 (0.42), residues: 412 helix: 2.67 (0.32), residues: 251 sheet: 0.41 (0.88), residues: 45 loop : 0.13 (0.54), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 112 HIS 0.003 0.001 HIS D 34 PHE 0.005 0.001 PHE R 130 TYR 0.007 0.001 TYR R 55 ARG 0.006 0.001 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 217) hydrogen bonds : angle 3.90844 ( 636) SS BOND : bond 0.00261 ( 4) SS BOND : angle 1.20677 ( 8) covalent geometry : bond 0.00281 ( 3150) covalent geometry : angle 0.63155 ( 4310) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1388.67 seconds wall clock time: 24 minutes 46.86 seconds (1486.86 seconds total)