Starting phenix.real_space_refine on Wed Mar 5 17:26:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xwf_38734/03_2025/8xwf_38734.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xwf_38734/03_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_38734/03_2025/8xwf_38734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xwf_38734/03_2025/8xwf_38734.map" model { file = "/net/cci-nas-00/data/ceres_data/8xwf_38734/03_2025/8xwf_38734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xwf_38734/03_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-5624/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: 0.72 Conformation dependent library (CDL) restraints added in 362.3 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: 0.82 Time building geometry restraints manager: 0.86 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: 0.610 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.720 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.420 ------------------------------------------------------------------------------- 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 3150 Z= 0.233 Angle : 0.580 8.448 4310 Z= 0.363 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 *********************** 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 : 0.340 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: 0.1213 time to fit residues: 15.8784 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 : 0.330 ------------------------------------------------------------------------------- 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 3150 Z= 0.195 Angle : 0.561 6.633 4310 Z= 0.284 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 *********************** 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 : 0.321 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: 0.1364 time to fit residues: 12.7763 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 : 0.352 ------------------------------------------------------------------------------- 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: 0.0030 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 overall best weight: 0.3984 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.126416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.102811 restraints weight = 6350.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.103037 restraints weight = 4115.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.104171 restraints weight = 3030.205| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3150 Z= 0.174 Angle : 0.543 6.602 4310 Z= 0.275 Chirality : 0.039 0.143 553 Planarity : 0.004 0.045 527 Dihedral : 3.699 20.534 441 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.99 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: 3.06 (0.42), residues: 412 helix: 2.83 (0.32), residues: 260 sheet: 1.11 (0.72), residues: 50 loop : 0.37 (0.61), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 112 HIS 0.011 0.001 HIS D 34 PHE 0.004 0.001 PHE R 130 TYR 0.008 0.001 TYR R 86 ARG 0.017 0.001 ARG D 29 *********************** 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 : 0.324 Fit side-chains revert: symmetry clash REVERT: D 10 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8297 (mm-40) REVERT: R 240 LYS cc_start: 0.8294 (mtpp) cc_final: 0.8047 (mtmm) outliers start: 12 outliers final: 8 residues processed: 74 average time/residue: 0.1296 time to fit residues: 11.9501 Evaluate side-chains 74 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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: 0.5980 chunk 38 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.0770 chunk 3 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.124532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.100912 restraints weight = 6399.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.102281 restraints weight = 3613.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.102734 restraints weight = 2346.896| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3150 Z= 0.207 Angle : 0.546 6.624 4310 Z= 0.272 Chirality : 0.039 0.152 553 Planarity : 0.004 0.042 527 Dihedral : 3.601 15.671 441 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.70 % Allowed : 17.55 % Favored : 77.74 % 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: 2.93 (0.41), residues: 412 helix: 2.78 (0.32), residues: 260 sheet: 1.00 (0.82), residues: 43 loop : 0.25 (0.55), 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 0.007 0.001 PHE R 117 TYR 0.008 0.001 TYR R 86 ARG 0.005 0.001 ARG D 29 *********************** 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 83 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: R 240 LYS cc_start: 0.8307 (mtpp) cc_final: 0.8105 (mtmm) outliers start: 15 outliers final: 11 residues processed: 74 average time/residue: 0.1257 time to fit residues: 11.6883 Evaluate side-chains 73 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 71 LEU Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 227 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.122619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.098544 restraints weight = 6324.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.099842 restraints weight = 3322.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.100212 restraints weight = 2297.800| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 : 0.004 0.041 3150 Z= 0.266 Angle : 0.579 7.684 4310 Z= 0.294 Chirality : 0.041 0.173 553 Planarity : 0.003 0.021 527 Dihedral : 3.718 16.003 441 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 4.39 % Allowed : 20.06 % Favored : 75.55 % 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: 2.80 (0.41), residues: 412 helix: 2.67 (0.32), residues: 260 sheet: 0.91 (0.82), residues: 43 loop : 0.27 (0.55), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 112 HIS 0.009 0.002 HIS D 34 PHE 0.009 0.001 PHE R 117 TYR 0.010 0.001 TYR R 55 ARG 0.006 0.001 ARG R 185 *********************** 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 79 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.360 Fit side-chains REVERT: D 44 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8321 (tp) REVERT: R 240 LYS cc_start: 0.8348 (mtpp) cc_final: 0.8138 (mtmm) outliers start: 14 outliers final: 10 residues processed: 73 average time/residue: 0.0952 time to fit residues: 9.3719 Evaluate side-chains 73 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 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 279 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: 3.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.121410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.097825 restraints weight = 6522.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.096949 restraints weight = 4153.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.098290 restraints weight = 3342.319| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3150 Z= 0.316 Angle : 0.628 7.556 4310 Z= 0.318 Chirality : 0.042 0.151 553 Planarity : 0.004 0.064 527 Dihedral : 3.783 16.962 441 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.70 % Allowed : 20.06 % Favored : 75.24 % 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: 2.51 (0.41), residues: 412 helix: 2.41 (0.32), residues: 260 sheet: 0.91 (0.84), residues: 43 loop : 0.19 (0.55), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 112 HIS 0.004 0.001 HIS D 34 PHE 0.010 0.001 PHE R 117 TYR 0.008 0.001 TYR R 145 ARG 0.006 0.001 ARG D 29 *********************** 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 77 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.348 Fit side-chains REVERT: D 6 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7963 (mt-10) REVERT: D 44 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8334 (tp) outliers start: 15 outliers final: 12 residues processed: 70 average time/residue: 0.1178 time to fit residues: 10.8789 Evaluate side-chains 72 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 25 SER 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 152 THR Chi-restraints excluded: chain R residue 227 MET Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 279 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: 10.0000 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.114582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.089203 restraints weight = 6467.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.089199 restraints weight = 4008.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.090173 restraints weight = 3035.656| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3150 Z= 0.295 Angle : 0.628 7.545 4310 Z= 0.321 Chirality : 0.041 0.163 553 Planarity : 0.003 0.019 527 Dihedral : 3.797 16.292 441 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.76 % Allowed : 21.00 % Favored : 75.24 % 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: 2.41 (0.41), residues: 412 helix: 2.33 (0.32), residues: 260 sheet: 0.75 (0.86), residues: 43 loop : 0.20 (0.56), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 112 HIS 0.004 0.001 HIS D 34 PHE 0.008 0.001 PHE R 117 TYR 0.010 0.001 TYR R 55 ARG 0.011 0.001 ARG D 29 *********************** 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 74 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.420 Fit side-chains REVERT: D 6 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8069 (mt-10) REVERT: D 44 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8313 (tp) outliers start: 12 outliers final: 11 residues processed: 68 average time/residue: 0.0975 time to fit residues: 9.1022 Evaluate side-chains 71 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 25 SER 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 152 THR Chi-restraints excluded: chain R residue 227 MET 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: 0.2980 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 0.0970 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.117679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.090211 restraints weight = 6394.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.092660 restraints weight = 3288.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.094320 restraints weight = 2181.121| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 0.040 3150 Z= 0.175 Angle : 0.560 6.524 4310 Z= 0.291 Chirality : 0.040 0.159 553 Planarity : 0.003 0.022 527 Dihedral : 3.634 16.659 441 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.19 % Allowed : 23.20 % Favored : 74.61 % 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: 2.44 (0.42), residues: 412 helix: 2.49 (0.32), residues: 255 sheet: 0.41 (0.86), residues: 45 loop : 0.13 (0.54), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 112 HIS 0.004 0.001 HIS R 306 PHE 0.004 0.001 PHE R 130 TYR 0.006 0.001 TYR R 55 ARG 0.005 0.001 ARG D 29 *********************** 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 70 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.383 Fit side-chains REVERT: D 6 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8138 (mt-10) outliers start: 7 outliers final: 6 residues processed: 65 average time/residue: 0.0817 time to fit residues: 7.5283 Evaluate side-chains 68 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 SER 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 D residue 62 ILE Chi-restraints excluded: chain R residue 61 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 0.0570 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 0.0970 chunk 4 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 overall best weight: 0.3296 ------------------------------------------------------------------------------- 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** D 13 GLN ** R 191 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 = 0.3676 r_free = 0.3676 target = 0.118385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.091335 restraints weight = 6413.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.093719 restraints weight = 3417.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.095110 restraints weight = 2294.251| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3150 Z= 0.169 Angle : 0.596 10.288 4310 Z= 0.297 Chirality : 0.040 0.154 553 Planarity : 0.003 0.021 527 Dihedral : 3.561 15.879 441 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.57 % Allowed : 24.45 % Favored : 73.98 % 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: 2.46 (0.42), residues: 412 helix: 2.58 (0.32), residues: 251 sheet: 0.44 (0.87), residues: 45 loop : 0.00 (0.53), 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 0.004 0.001 PHE R 130 TYR 0.009 0.001 TYR R 55 ARG 0.007 0.001 ARG D 29 *********************** 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 69 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.328 Fit side-chains REVERT: D 6 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8071 (mt-10) outliers start: 5 outliers final: 5 residues processed: 65 average time/residue: 0.0749 time to fit residues: 6.9567 Evaluate side-chains 68 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 2.9990 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: 0.0970 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.115632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.090583 restraints weight = 6502.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.090554 restraints weight = 4094.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.091539 restraints weight = 3027.843| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3150 Z= 0.248 Angle : 0.634 9.691 4310 Z= 0.316 Chirality : 0.041 0.153 553 Planarity : 0.003 0.022 527 Dihedral : 3.582 15.481 441 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.19 % Allowed : 23.82 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.41), residues: 412 helix: 2.46 (0.32), residues: 260 sheet: 0.73 (0.89), residues: 43 loop : 0.07 (0.56), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 112 HIS 0.003 0.001 HIS D 34 PHE 0.008 0.001 PHE R 117 TYR 0.008 0.001 TYR R 86 ARG 0.006 0.000 ARG D 29 ********************** 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 69 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.372 Fit side-chains REVERT: E 22 ASN cc_start: 0.8921 (t0) cc_final: 0.8504 (t0) REVERT: D 6 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8065 (mt-10) REVERT: R 274 ASP cc_start: 0.8930 (t0) cc_final: 0.8710 (t0) outliers start: 7 outliers final: 6 residues processed: 65 average time/residue: 0.0802 time to fit residues: 7.5002 Evaluate side-chains 67 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 SER 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 62 ILE Chi-restraints excluded: chain R residue 61 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.116388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.088940 restraints weight = 6468.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.091371 restraints weight = 3400.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.092772 restraints weight = 2280.197| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3150 Z= 0.209 Angle : 0.609 9.539 4310 Z= 0.306 Chirality : 0.040 0.152 553 Planarity : 0.003 0.018 527 Dihedral : 3.580 16.147 441 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.57 % Allowed : 24.45 % Favored : 73.98 % 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: 2.41 (0.42), residues: 412 helix: 2.38 (0.32), residues: 260 sheet: 0.79 (0.89), residues: 43 loop : 0.03 (0.56), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 112 HIS 0.003 0.001 HIS R 242 PHE 0.006 0.001 PHE R 130 TYR 0.007 0.001 TYR R 55 ARG 0.007 0.000 ARG D 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1271.98 seconds wall clock time: 22 minutes 38.88 seconds (1358.88 seconds total)