Starting phenix.real_space_refine on Tue Feb 3 13:15:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l16_62735/02_2026/9l16_62735_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l16_62735/02_2026/9l16_62735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l16_62735/02_2026/9l16_62735_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l16_62735/02_2026/9l16_62735_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l16_62735/02_2026/9l16_62735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l16_62735/02_2026/9l16_62735.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.002 sd= 0.066 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 1958 2.51 5 N 483 2.21 5 O 506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2968 Number of models: 1 Model: "" Number of chains: 2 Chain: "L" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 531 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 65} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "R" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2437 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 6, 'TRANS': 309} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 65 Time building chain proxies: 0.81, per 1000 atoms: 0.27 Number of scatterers: 2968 At special positions: 0 Unit cell: (62.4, 82.16, 97.76, 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 506 8.00 N 483 7.00 C 1958 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 8 " - pdb=" SG CYS L 34 " distance=2.03 Simple disulfide: pdb=" SG CYS L 9 " - pdb=" SG CYS L 52 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 298 " distance=2.03 Simple disulfide: pdb=" SG CYS R 129 " - pdb=" SG CYS R 210 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.19 Conformation dependent library (CDL) restraints added in 69.2 milliseconds 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 2 sheets defined 70.4% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'L' and resid 18 through 20 No H-bonds generated for 'chain 'L' and resid 18 through 20' Processing helix chain 'L' and resid 57 through 67 Processing helix chain 'R' and resid 40 through 44 Processing helix chain 'R' and resid 50 through 87 Proline residue: R 62 - end of helix removed outlier: 3.564A pdb=" N ILE R 67 " --> pdb=" O ILE R 63 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU R 74 " --> pdb=" O PHE R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 120 removed outlier: 3.555A pdb=" N THR R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU R 111 " --> pdb=" O PHE R 107 " (cutoff:3.500A) Proline residue: R 112 - end of helix Processing helix chain 'R' and resid 125 through 159 Processing helix chain 'R' and resid 160 through 165 Processing helix chain 'R' and resid 167 through 190 removed outlier: 3.993A pdb=" N VAL R 180 " --> pdb=" O LYS R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 197 Processing helix chain 'R' and resid 216 through 230 removed outlier: 4.237A pdb=" N PHE R 220 " --> pdb=" O HIS R 216 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE R 221 " --> pdb=" O VAL R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 251 removed outlier: 4.150A pdb=" N LEU R 244 " --> pdb=" O SER R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 292 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 297 through 326 removed outlier: 3.546A pdb=" N SER R 301 " --> pdb=" O THR R 297 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS R 302 " --> pdb=" O CYS R 298 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 343 Processing sheet with id=AA1, first strand: chain 'L' and resid 22 through 25 removed outlier: 4.408A pdb=" N SER L 24 " --> pdb=" O LEU L 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 198 through 202 removed outlier: 4.952A pdb=" N SER R 202 " --> pdb=" O ALA R 207 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ALA R 207 " --> pdb=" O SER R 202 " (cutoff:3.500A) 207 hydrogen bonds defined for protein. 606 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: 0.47 Time building geometry restraints manager: 0.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 905 1.34 - 1.46: 643 1.46 - 1.58: 1459 1.58 - 1.70: 0 1.70 - 1.82: 27 Bond restraints: 3034 Sorted by residual: bond pdb=" N ASP L 2 " pdb=" CA ASP L 2 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.44e+00 bond pdb=" N GLN L 48 " pdb=" CA GLN L 48 " ideal model delta sigma weight residual 1.453 1.481 -0.028 1.37e-02 5.33e+03 4.03e+00 bond pdb=" C THR L 70 " pdb=" N PRO L 71 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.85e+00 bond pdb=" C SER R 49 " pdb=" N LYS R 50 " ideal model delta sigma weight residual 1.333 1.309 0.025 1.56e-02 4.11e+03 2.47e+00 bond pdb=" N SER L 1 " pdb=" CA SER L 1 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.31e+00 ... (remaining 3029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 4002 1.52 - 3.04: 102 3.04 - 4.56: 23 4.56 - 6.08: 8 6.08 - 7.60: 3 Bond angle restraints: 4138 Sorted by residual: angle pdb=" N GLN R 286 " pdb=" CA GLN R 286 " pdb=" C GLN R 286 " ideal model delta sigma weight residual 111.07 106.86 4.21 1.07e+00 8.73e-01 1.55e+01 angle pdb=" N ASP L 2 " pdb=" CA ASP L 2 " pdb=" C ASP L 2 " ideal model delta sigma weight residual 110.80 103.20 7.60 2.13e+00 2.20e-01 1.27e+01 angle pdb=" C ALA R 157 " pdb=" N ILE R 158 " pdb=" CA ILE R 158 " ideal model delta sigma weight residual 122.97 119.74 3.23 9.80e-01 1.04e+00 1.09e+01 angle pdb=" CA ASP L 2 " pdb=" CB ASP L 2 " pdb=" CG ASP L 2 " ideal model delta sigma weight residual 112.60 115.66 -3.06 1.00e+00 1.00e+00 9.39e+00 angle pdb=" N ILE R 293 " pdb=" CA ILE R 293 " pdb=" C ILE R 293 " ideal model delta sigma weight residual 113.07 108.99 4.08 1.36e+00 5.41e-01 9.02e+00 ... (remaining 4133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.83: 1579 11.83 - 23.65: 148 23.65 - 35.48: 44 35.48 - 47.30: 21 47.30 - 59.13: 10 Dihedral angle restraints: 1802 sinusoidal: 649 harmonic: 1153 Sorted by residual: dihedral pdb=" CB CYS R 48 " pdb=" SG CYS R 48 " pdb=" SG CYS R 298 " pdb=" CB CYS R 298 " ideal model delta sinusoidal sigma weight residual -86.00 -136.00 50.00 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CA ILE R 230 " pdb=" C ILE R 230 " pdb=" N GLY R 231 " pdb=" CA GLY R 231 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA CYS R 48 " pdb=" C CYS R 48 " pdb=" N SER R 49 " pdb=" CA SER R 49 " ideal model delta harmonic sigma weight residual 180.00 163.20 16.80 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 1799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 292 0.027 - 0.055: 130 0.055 - 0.082: 61 0.082 - 0.109: 16 0.109 - 0.137: 9 Chirality restraints: 508 Sorted by residual: chirality pdb=" CB ILE R 223 " pdb=" CA ILE R 223 " pdb=" CG1 ILE R 223 " pdb=" CG2 ILE R 223 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE L 36 " pdb=" N ILE L 36 " pdb=" C ILE L 36 " pdb=" CB ILE L 36 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA CYS R 48 " pdb=" N CYS R 48 " pdb=" C CYS R 48 " pdb=" CB CYS R 48 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 505 not shown) Planarity restraints: 504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 230 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C ILE R 230 " -0.037 2.00e-02 2.50e+03 pdb=" O ILE R 230 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY R 231 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR L 70 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.33e+00 pdb=" N PRO L 71 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO L 71 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 71 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 234 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO R 235 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO R 235 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 235 " -0.025 5.00e-02 4.00e+02 ... (remaining 501 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1055 2.85 - 3.37: 3209 3.37 - 3.88: 4981 3.88 - 4.39: 5522 4.39 - 4.90: 9163 Nonbonded interactions: 23930 Sorted by model distance: nonbonded pdb=" O SER L 1 " pdb=" N GLY L 3 " model vdw 2.343 3.120 nonbonded pdb=" O LYS R 50 " pdb=" N VAL R 53 " model vdw 2.452 3.120 nonbonded pdb=" N ASP L 2 " pdb=" OD1 ASP L 2 " model vdw 2.494 3.120 nonbonded pdb=" O SER R 49 " pdb=" CA LYS R 50 " model vdw 2.579 2.776 nonbonded pdb=" OG SER L 47 " pdb=" NE2 GLN L 48 " model vdw 2.587 3.120 ... (remaining 23925 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: 1.060 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.030 Find NCS groups from input model: 0.010 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5402 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 0.041 3038 Z= 0.227 Angle : 0.654 7.600 4146 Z= 0.369 Chirality : 0.040 0.137 508 Planarity : 0.005 0.052 504 Dihedral : 12.246 59.130 1040 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.27 % Favored : 92.47 % Rotamer: Outliers : 8.01 % Allowed : 7.37 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.43), residues: 385 helix: 0.87 (0.33), residues: 248 sheet: -1.91 (0.98), residues: 26 loop : -2.38 (0.56), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 334 TYR 0.021 0.002 TYR R 136 PHE 0.015 0.001 PHE R 272 TRP 0.006 0.001 TRP R 122 HIS 0.002 0.001 HIS R 127 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 3034) covalent geometry : angle 0.65394 ( 4138) SS BOND : bond 0.00114 ( 4) SS BOND : angle 0.89219 ( 8) hydrogen bonds : bond 0.12914 ( 207) hydrogen bonds : angle 6.28459 ( 606) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.103 Fit side-chains REVERT: L 35 SER cc_start: 0.8076 (p) cc_final: 0.7839 (t) REVERT: R 92 MET cc_start: 0.7014 (ttp) cc_final: 0.6501 (ttt) REVERT: R 199 LEU cc_start: 0.5245 (OUTLIER) cc_final: 0.4999 (pp) REVERT: R 212 LEU cc_start: 0.7506 (mt) cc_final: 0.7278 (mt) REVERT: R 312 TYR cc_start: 0.6116 (OUTLIER) cc_final: 0.4999 (t80) REVERT: R 317 VAL cc_start: 0.5707 (t) cc_final: 0.5122 (t) REVERT: R 332 LYS cc_start: 0.7679 (tttp) cc_final: 0.6864 (mptt) outliers start: 25 outliers final: 3 residues processed: 113 average time/residue: 0.0534 time to fit residues: 7.2193 Evaluate side-chains 73 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 312 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.0570 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 286 GLN R 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.205970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.173224 restraints weight = 3414.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.177987 restraints weight = 1658.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.181070 restraints weight = 1014.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.183091 restraints weight = 741.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.184004 restraints weight = 606.877| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3038 Z= 0.160 Angle : 0.647 6.580 4146 Z= 0.331 Chirality : 0.039 0.193 508 Planarity : 0.004 0.053 504 Dihedral : 5.995 47.070 426 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.13 % Allowed : 13.78 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.42), residues: 385 helix: 1.13 (0.32), residues: 249 sheet: -0.81 (1.18), residues: 16 loop : -2.30 (0.53), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 258 TYR 0.012 0.002 TYR R 136 PHE 0.016 0.002 PHE R 328 TRP 0.008 0.001 TRP R 183 HIS 0.001 0.001 HIS R 167 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 3034) covalent geometry : angle 0.64377 ( 4138) SS BOND : bond 0.00752 ( 4) SS BOND : angle 1.50203 ( 8) hydrogen bonds : bond 0.04731 ( 207) hydrogen bonds : angle 4.82311 ( 606) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.064 Fit side-chains REVERT: L 35 SER cc_start: 0.8252 (p) cc_final: 0.7936 (t) REVERT: R 92 MET cc_start: 0.7424 (ttp) cc_final: 0.7085 (ttt) REVERT: R 237 LEU cc_start: 0.7288 (tp) cc_final: 0.6703 (mm) REVERT: R 312 TYR cc_start: 0.5987 (OUTLIER) cc_final: 0.5605 (t80) REVERT: R 332 LYS cc_start: 0.7458 (tttp) cc_final: 0.6812 (mptt) outliers start: 16 outliers final: 11 residues processed: 80 average time/residue: 0.0429 time to fit residues: 4.3029 Evaluate side-chains 75 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 255 ASN Chi-restraints excluded: chain R residue 297 THR Chi-restraints excluded: chain R residue 312 TYR Chi-restraints excluded: chain R residue 320 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 11 optimal weight: 0.0270 chunk 0 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 0.0980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 286 GLN R 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.201018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.168413 restraints weight = 3430.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.172725 restraints weight = 1763.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.175247 restraints weight = 1104.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.177142 restraints weight = 818.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.177994 restraints weight = 679.612| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3038 Z= 0.150 Angle : 0.655 7.889 4146 Z= 0.320 Chirality : 0.042 0.279 508 Planarity : 0.004 0.053 504 Dihedral : 5.862 43.939 426 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 5.77 % Allowed : 16.03 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.41), residues: 385 helix: 1.26 (0.31), residues: 249 sheet: -0.49 (1.24), residues: 16 loop : -2.27 (0.52), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 26 TYR 0.011 0.001 TYR R 243 PHE 0.022 0.002 PHE R 328 TRP 0.008 0.001 TRP R 183 HIS 0.003 0.001 HIS L 66 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 3034) covalent geometry : angle 0.65429 ( 4138) SS BOND : bond 0.00828 ( 4) SS BOND : angle 0.93461 ( 8) hydrogen bonds : bond 0.04433 ( 207) hydrogen bonds : angle 4.56479 ( 606) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.106 Fit side-chains REVERT: L 35 SER cc_start: 0.8359 (p) cc_final: 0.8003 (t) REVERT: R 137 LYS cc_start: 0.6797 (mmtp) cc_final: 0.6399 (mmtt) REVERT: R 176 LYS cc_start: 0.5827 (mttt) cc_final: 0.5404 (mmmt) REVERT: R 332 LYS cc_start: 0.7535 (tttp) cc_final: 0.7009 (mptt) outliers start: 18 outliers final: 14 residues processed: 82 average time/residue: 0.0512 time to fit residues: 5.1394 Evaluate side-chains 82 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 210 CYS Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 255 ASN Chi-restraints excluded: chain R residue 297 THR Chi-restraints excluded: chain R residue 320 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 24 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.195679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.158771 restraints weight = 3366.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.163014 restraints weight = 1743.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.165840 restraints weight = 1136.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.167321 restraints weight = 869.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.168315 restraints weight = 749.281| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 3038 Z= 0.220 Angle : 0.764 10.545 4146 Z= 0.376 Chirality : 0.042 0.194 508 Planarity : 0.005 0.053 504 Dihedral : 5.778 41.880 424 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.13 % Allowed : 18.91 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.39), residues: 385 helix: 0.66 (0.30), residues: 251 sheet: -0.10 (1.18), residues: 10 loop : -2.26 (0.49), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 170 TYR 0.015 0.002 TYR R 136 PHE 0.017 0.002 PHE R 272 TRP 0.010 0.001 TRP R 114 HIS 0.004 0.001 HIS R 167 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 3034) covalent geometry : angle 0.76341 ( 4138) SS BOND : bond 0.00295 ( 4) SS BOND : angle 0.81533 ( 8) hydrogen bonds : bond 0.05148 ( 207) hydrogen bonds : angle 4.92363 ( 606) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.108 Fit side-chains REVERT: R 92 MET cc_start: 0.8205 (ttp) cc_final: 0.7936 (ttt) REVERT: R 137 LYS cc_start: 0.7224 (mmtp) cc_final: 0.6950 (mmtt) REVERT: R 176 LYS cc_start: 0.6256 (mttt) cc_final: 0.5833 (mmmt) REVERT: R 223 ILE cc_start: 0.6438 (OUTLIER) cc_final: 0.6175 (tp) REVERT: R 237 LEU cc_start: 0.7831 (tp) cc_final: 0.7584 (mm) REVERT: R 276 GLN cc_start: 0.6574 (OUTLIER) cc_final: 0.5944 (tp40) REVERT: R 332 LYS cc_start: 0.7696 (tttp) cc_final: 0.7050 (mptt) outliers start: 16 outliers final: 10 residues processed: 80 average time/residue: 0.0345 time to fit residues: 3.4960 Evaluate side-chains 75 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 255 ASN Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 297 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 33 optimal weight: 0.0570 chunk 10 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.203142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.166057 restraints weight = 3179.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.170919 restraints weight = 1527.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.174028 restraints weight = 957.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.175761 restraints weight = 718.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.176735 restraints weight = 606.053| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 moved from start: 0.6388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3038 Z= 0.143 Angle : 0.685 11.015 4146 Z= 0.323 Chirality : 0.041 0.189 508 Planarity : 0.004 0.053 504 Dihedral : 5.389 43.481 424 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.53 % Allowed : 22.44 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.41), residues: 385 helix: 1.14 (0.32), residues: 245 sheet: -0.27 (1.20), residues: 10 loop : -1.98 (0.50), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 26 TYR 0.013 0.001 TYR R 136 PHE 0.012 0.002 PHE R 86 TRP 0.009 0.001 TRP R 183 HIS 0.001 0.000 HIS R 167 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 3034) covalent geometry : angle 0.68553 ( 4138) SS BOND : bond 0.00162 ( 4) SS BOND : angle 0.65502 ( 8) hydrogen bonds : bond 0.04399 ( 207) hydrogen bonds : angle 4.61680 ( 606) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.104 Fit side-chains REVERT: R 92 MET cc_start: 0.8117 (ttp) cc_final: 0.7897 (ttt) REVERT: R 176 LYS cc_start: 0.5955 (mttt) cc_final: 0.5725 (mmmt) REVERT: R 208 MET cc_start: 0.6823 (mmm) cc_final: 0.6429 (mmm) REVERT: R 223 ILE cc_start: 0.6265 (OUTLIER) cc_final: 0.6030 (tp) REVERT: R 276 GLN cc_start: 0.6500 (OUTLIER) cc_final: 0.5802 (tp40) REVERT: R 329 ILE cc_start: 0.8080 (tp) cc_final: 0.7783 (tt) REVERT: R 332 LYS cc_start: 0.7926 (tttp) cc_final: 0.7218 (mptt) outliers start: 11 outliers final: 8 residues processed: 70 average time/residue: 0.0415 time to fit residues: 3.6187 Evaluate side-chains 68 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 210 CYS Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 255 ASN Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 297 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 0.0270 chunk 3 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.202920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.165470 restraints weight = 3183.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.170207 restraints weight = 1535.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.173097 restraints weight = 965.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.174913 restraints weight = 740.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.175830 restraints weight = 622.974| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.6695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3038 Z= 0.154 Angle : 0.725 9.481 4146 Z= 0.342 Chirality : 0.042 0.176 508 Planarity : 0.004 0.053 504 Dihedral : 5.229 44.327 422 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.49 % Allowed : 21.15 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.41), residues: 385 helix: 1.06 (0.32), residues: 245 sheet: -0.45 (1.20), residues: 16 loop : -1.95 (0.53), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 26 TYR 0.015 0.001 TYR R 83 PHE 0.012 0.002 PHE R 86 TRP 0.020 0.002 TRP R 114 HIS 0.002 0.000 HIS R 127 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3034) covalent geometry : angle 0.72553 ( 4138) SS BOND : bond 0.00169 ( 4) SS BOND : angle 0.57678 ( 8) hydrogen bonds : bond 0.04446 ( 207) hydrogen bonds : angle 4.75007 ( 606) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.067 Fit side-chains REVERT: R 92 MET cc_start: 0.8127 (ttp) cc_final: 0.7919 (ttt) REVERT: R 176 LYS cc_start: 0.6064 (mttt) cc_final: 0.5848 (mmmt) REVERT: R 208 MET cc_start: 0.6640 (mmm) cc_final: 0.6376 (mmm) REVERT: R 276 GLN cc_start: 0.6736 (OUTLIER) cc_final: 0.6019 (tp40) REVERT: R 329 ILE cc_start: 0.8128 (tp) cc_final: 0.7816 (tt) REVERT: R 332 LYS cc_start: 0.7992 (tttp) cc_final: 0.7256 (mptt) outliers start: 14 outliers final: 9 residues processed: 71 average time/residue: 0.0352 time to fit residues: 3.2136 Evaluate side-chains 70 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 210 CYS Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 255 ASN Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 297 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.201755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.166174 restraints weight = 3243.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.170593 restraints weight = 1602.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.173187 restraints weight = 1010.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.175190 restraints weight = 769.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.176228 restraints weight = 643.925| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.7095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3038 Z= 0.165 Angle : 0.710 9.173 4146 Z= 0.336 Chirality : 0.043 0.263 508 Planarity : 0.005 0.053 504 Dihedral : 5.611 46.616 422 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 5.45 % Allowed : 20.51 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.41), residues: 385 helix: 0.97 (0.32), residues: 250 sheet: -0.42 (1.16), residues: 10 loop : -1.79 (0.54), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 170 TYR 0.023 0.002 TYR R 243 PHE 0.013 0.002 PHE R 70 TRP 0.017 0.002 TRP R 114 HIS 0.002 0.001 HIS R 127 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 3034) covalent geometry : angle 0.71012 ( 4138) SS BOND : bond 0.00182 ( 4) SS BOND : angle 0.57181 ( 8) hydrogen bonds : bond 0.04496 ( 207) hydrogen bonds : angle 4.72812 ( 606) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.118 Fit side-chains REVERT: R 176 LYS cc_start: 0.5988 (mttt) cc_final: 0.5773 (mmmt) REVERT: R 208 MET cc_start: 0.6630 (mmm) cc_final: 0.6337 (mmm) REVERT: R 276 GLN cc_start: 0.6845 (OUTLIER) cc_final: 0.6146 (tp40) REVERT: R 329 ILE cc_start: 0.8237 (tp) cc_final: 0.7955 (tt) REVERT: R 332 LYS cc_start: 0.8008 (tttp) cc_final: 0.7267 (mptt) outliers start: 17 outliers final: 13 residues processed: 72 average time/residue: 0.0495 time to fit residues: 4.4711 Evaluate side-chains 77 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 25 TYR Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 210 CYS Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 255 ASN Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 273 ILE Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 297 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.198707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.162473 restraints weight = 3290.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.167058 restraints weight = 1594.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.170124 restraints weight = 995.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.171892 restraints weight = 740.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.172816 restraints weight = 619.608| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.7435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3038 Z= 0.170 Angle : 0.724 9.315 4146 Z= 0.346 Chirality : 0.041 0.156 508 Planarity : 0.005 0.056 504 Dihedral : 5.526 45.249 422 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.13 % Allowed : 20.83 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.42), residues: 385 helix: 0.99 (0.31), residues: 253 sheet: -0.35 (1.16), residues: 10 loop : -1.71 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 154 TYR 0.026 0.002 TYR R 243 PHE 0.013 0.002 PHE R 328 TRP 0.015 0.002 TRP L 59 HIS 0.002 0.001 HIS R 127 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 3034) covalent geometry : angle 0.72393 ( 4138) SS BOND : bond 0.00171 ( 4) SS BOND : angle 0.57079 ( 8) hydrogen bonds : bond 0.04551 ( 207) hydrogen bonds : angle 4.74222 ( 606) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.066 Fit side-chains REVERT: R 138 MET cc_start: 0.4729 (ttm) cc_final: 0.4484 (ttm) REVERT: R 174 ILE cc_start: 0.7751 (mm) cc_final: 0.7509 (mm) REVERT: R 208 MET cc_start: 0.6563 (mmm) cc_final: 0.6339 (mmm) REVERT: R 239 MET cc_start: 0.4927 (mmp) cc_final: 0.4248 (mmp) REVERT: R 276 GLN cc_start: 0.6851 (OUTLIER) cc_final: 0.6265 (tp40) REVERT: R 329 ILE cc_start: 0.8204 (tp) cc_final: 0.7938 (tt) REVERT: R 332 LYS cc_start: 0.7982 (tttp) cc_final: 0.7292 (mptt) outliers start: 16 outliers final: 13 residues processed: 72 average time/residue: 0.0488 time to fit residues: 4.4075 Evaluate side-chains 73 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 25 TYR Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 210 CYS Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 255 ASN Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 297 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.0970 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 11 optimal weight: 0.3980 chunk 2 optimal weight: 0.0470 chunk 29 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 12 optimal weight: 0.4980 overall best weight: 0.1876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.205917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.169832 restraints weight = 3202.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.174601 restraints weight = 1492.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.177798 restraints weight = 905.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.179370 restraints weight = 660.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.180815 restraints weight = 559.166| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.7649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3038 Z= 0.132 Angle : 0.693 9.375 4146 Z= 0.325 Chirality : 0.040 0.167 508 Planarity : 0.005 0.057 504 Dihedral : 5.631 57.165 422 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.88 % Allowed : 25.32 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.42), residues: 385 helix: 1.27 (0.31), residues: 253 sheet: -0.11 (1.16), residues: 10 loop : -1.67 (0.57), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 26 TYR 0.017 0.002 TYR R 136 PHE 0.010 0.001 PHE R 328 TRP 0.015 0.001 TRP L 59 HIS 0.001 0.000 HIS R 216 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3034) covalent geometry : angle 0.69305 ( 4138) SS BOND : bond 0.00173 ( 4) SS BOND : angle 0.49860 ( 8) hydrogen bonds : bond 0.04136 ( 207) hydrogen bonds : angle 4.51519 ( 606) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.064 Fit side-chains REVERT: R 239 MET cc_start: 0.5284 (mmp) cc_final: 0.4925 (mmp) REVERT: R 276 GLN cc_start: 0.6791 (OUTLIER) cc_final: 0.6134 (tp40) REVERT: R 329 ILE cc_start: 0.8137 (tp) cc_final: 0.7919 (tt) REVERT: R 332 LYS cc_start: 0.7999 (tttp) cc_final: 0.7291 (mptt) outliers start: 9 outliers final: 6 residues processed: 67 average time/residue: 0.0338 time to fit residues: 2.8600 Evaluate side-chains 65 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 25 TYR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 255 ASN Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 297 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 35 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.197884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.161179 restraints weight = 3260.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.165751 restraints weight = 1560.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.168544 restraints weight = 969.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.170280 restraints weight = 730.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.171643 restraints weight = 614.611| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.7911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3038 Z= 0.185 Angle : 0.778 10.441 4146 Z= 0.365 Chirality : 0.042 0.156 508 Planarity : 0.005 0.056 504 Dihedral : 5.342 48.324 421 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.92 % Allowed : 26.60 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.42), residues: 385 helix: 1.04 (0.31), residues: 253 sheet: -0.38 (1.08), residues: 10 loop : -1.75 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 154 TYR 0.022 0.002 TYR R 243 PHE 0.014 0.002 PHE R 328 TRP 0.014 0.001 TRP L 59 HIS 0.003 0.001 HIS R 127 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 3034) covalent geometry : angle 0.77815 ( 4138) SS BOND : bond 0.00179 ( 4) SS BOND : angle 0.38058 ( 8) hydrogen bonds : bond 0.04591 ( 207) hydrogen bonds : angle 4.77155 ( 606) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.065 Fit side-chains REVERT: R 276 GLN cc_start: 0.7018 (OUTLIER) cc_final: 0.6582 (tp40) REVERT: R 329 ILE cc_start: 0.8258 (tp) cc_final: 0.8022 (tt) REVERT: R 332 LYS cc_start: 0.7959 (tttp) cc_final: 0.7285 (mptt) outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 0.0325 time to fit residues: 2.5310 Evaluate side-chains 61 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 255 ASN Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 297 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 27 optimal weight: 0.9990 chunk 7 optimal weight: 0.0570 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.0370 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.201842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.165902 restraints weight = 3208.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.170636 restraints weight = 1495.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.173350 restraints weight = 921.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.175379 restraints weight = 690.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.176287 restraints weight = 574.916| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.8081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3038 Z= 0.150 Angle : 0.776 11.240 4146 Z= 0.356 Chirality : 0.041 0.169 508 Planarity : 0.005 0.056 504 Dihedral : 5.306 48.776 421 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.56 % Allowed : 25.96 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.42), residues: 385 helix: 1.19 (0.32), residues: 253 sheet: -0.21 (1.05), residues: 10 loop : -1.74 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 26 TYR 0.025 0.002 TYR R 136 PHE 0.011 0.001 PHE R 328 TRP 0.022 0.002 TRP L 59 HIS 0.002 0.000 HIS R 127 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 3034) covalent geometry : angle 0.77612 ( 4138) SS BOND : bond 0.00170 ( 4) SS BOND : angle 0.40296 ( 8) hydrogen bonds : bond 0.04303 ( 207) hydrogen bonds : angle 4.59851 ( 606) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 615.60 seconds wall clock time: 11 minutes 14.23 seconds (674.23 seconds total)