Starting phenix.real_space_refine on Fri Aug 22 13:48:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xyj_38775/08_2025/8xyj_38775_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xyj_38775/08_2025/8xyj_38775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xyj_38775/08_2025/8xyj_38775_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xyj_38775/08_2025/8xyj_38775_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xyj_38775/08_2025/8xyj_38775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xyj_38775/08_2025/8xyj_38775.map" } resolution = 3.33 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= 0.003 sd= 0.074 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 18 5.16 5 C 2390 2.51 5 N 559 2.21 5 O 615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3582 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3572 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 20, 'TRANS': 438} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 1.13, per 1000 atoms: 0.32 Number of scatterers: 3582 At special positions: 0 Unit cell: (63.679, 85.181, 71.949, 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 18 16.00 O 615 8.00 N 559 7.00 C 2390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.30 Conformation dependent library (CDL) restraints added in 146.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 856 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 75.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 39 through 51 Processing helix chain 'A' and resid 58 through 63 removed outlier: 4.130A pdb=" N GLY A 61 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL A 62 " --> pdb=" O PRO A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 98 Processing helix chain 'A' and resid 113 through 126 removed outlier: 4.201A pdb=" N THR A 122 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 145 Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 159 through 176 removed outlier: 3.712A pdb=" N TYR A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 208 Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 254 through 285 Proline residue: A 260 - end of helix Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.776A pdb=" N LEU A 291 " --> pdb=" O MET A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.986A pdb=" N ASP A 302 " --> pdb=" O VAL A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 310 through 341 Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.995A pdb=" N MET A 350 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 372 Processing helix chain 'A' and resid 381 through 407 removed outlier: 4.098A pdb=" N TYR A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 438 Proline residue: A 435 - end of helix Processing helix chain 'A' and resid 439 through 460 removed outlier: 3.962A pdb=" N SER A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 470 through 484 248 hydrogen bonds defined for protein. 726 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: 0.41 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 536 1.30 - 1.43: 1030 1.43 - 1.56: 2085 1.56 - 1.68: 0 1.68 - 1.81: 24 Bond restraints: 3675 Sorted by residual: bond pdb=" CA LEU A 120 " pdb=" C LEU A 120 " ideal model delta sigma weight residual 1.521 1.419 0.102 1.36e-02 5.41e+03 5.63e+01 bond pdb=" CA ARG A 119 " pdb=" C ARG A 119 " ideal model delta sigma weight residual 1.520 1.443 0.077 1.48e-02 4.57e+03 2.69e+01 bond pdb=" C LEU A 120 " pdb=" O LEU A 120 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.31e-02 5.83e+03 2.40e+01 bond pdb=" C ARG A 119 " pdb=" O ARG A 119 " ideal model delta sigma weight residual 1.237 1.178 0.059 1.28e-02 6.10e+03 2.12e+01 bond pdb=" N LEU A 120 " pdb=" CA LEU A 120 " ideal model delta sigma weight residual 1.457 1.400 0.057 1.27e-02 6.20e+03 2.03e+01 ... (remaining 3670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 4898 2.99 - 5.98: 106 5.98 - 8.97: 4 8.97 - 11.96: 1 11.96 - 14.96: 1 Bond angle restraints: 5010 Sorted by residual: angle pdb=" N LEU A 120 " pdb=" CA LEU A 120 " pdb=" C LEU A 120 " ideal model delta sigma weight residual 113.41 98.45 14.96 1.22e+00 6.72e-01 1.50e+02 angle pdb=" N ARG A 119 " pdb=" CA ARG A 119 " pdb=" C ARG A 119 " ideal model delta sigma weight residual 114.56 102.85 11.71 1.27e+00 6.20e-01 8.51e+01 angle pdb=" N ILE A 55 " pdb=" CA ILE A 55 " pdb=" C ILE A 55 " ideal model delta sigma weight residual 112.83 108.23 4.60 9.90e-01 1.02e+00 2.16e+01 angle pdb=" N LEU A 483 " pdb=" CA LEU A 483 " pdb=" C LEU A 483 " ideal model delta sigma weight residual 111.82 106.73 5.09 1.16e+00 7.43e-01 1.93e+01 angle pdb=" N PHE A 56 " pdb=" CA PHE A 56 " pdb=" C PHE A 56 " ideal model delta sigma weight residual 112.45 106.51 5.94 1.39e+00 5.18e-01 1.82e+01 ... (remaining 5005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 1801 16.42 - 32.84: 252 32.84 - 49.26: 58 49.26 - 65.68: 17 65.68 - 82.10: 1 Dihedral angle restraints: 2129 sinusoidal: 792 harmonic: 1337 Sorted by residual: dihedral pdb=" CA ILE A 290 " pdb=" C ILE A 290 " pdb=" N LEU A 291 " pdb=" CA LEU A 291 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA GLY A 112 " pdb=" C GLY A 112 " pdb=" N GLY A 113 " pdb=" CA GLY A 113 " ideal model delta harmonic sigma weight residual 180.00 157.06 22.94 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA GLY A 220 " pdb=" C GLY A 220 " pdb=" N SER A 221 " pdb=" CA SER A 221 " ideal model delta harmonic sigma weight residual -180.00 -159.56 -20.44 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 2126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 365 0.046 - 0.091: 184 0.091 - 0.137: 31 0.137 - 0.183: 10 0.183 - 0.228: 3 Chirality restraints: 593 Sorted by residual: chirality pdb=" CB ILE A 378 " pdb=" CA ILE A 378 " pdb=" CG1 ILE A 378 " pdb=" CG2 ILE A 378 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA SER A 238 " pdb=" N SER A 238 " pdb=" C SER A 238 " pdb=" CB SER A 238 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.98e-01 chirality pdb=" CB VAL A 296 " pdb=" CA VAL A 296 " pdb=" CG1 VAL A 296 " pdb=" CG2 VAL A 296 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.77e-01 ... (remaining 590 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 237 " -0.023 2.00e-02 2.50e+03 4.51e-02 2.03e+01 pdb=" C PHE A 237 " 0.078 2.00e-02 2.50e+03 pdb=" O PHE A 237 " -0.028 2.00e-02 2.50e+03 pdb=" N SER A 238 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 117 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.61e+00 pdb=" C PHE A 117 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE A 117 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE A 118 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 312 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO A 313 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 313 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 313 " -0.026 5.00e-02 4.00e+02 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 572 2.74 - 3.28: 3818 3.28 - 3.82: 6195 3.82 - 4.36: 7379 4.36 - 4.90: 12713 Nonbonded interactions: 30677 Sorted by model distance: nonbonded pdb=" OH TYR A 104 " pdb=" ND1 HIS A 343 " model vdw 2.196 3.120 nonbonded pdb=" O PHE A 214 " pdb=" ND2 ASN A 216 " model vdw 2.219 3.120 nonbonded pdb=" NH2 ARG A 159 " pdb=" O VAL A 375 " model vdw 2.246 3.120 nonbonded pdb=" OE1 GLU A 92 " pdb=" NE2 GLN A 400 " model vdw 2.264 3.120 nonbonded pdb=" O SER A 211 " pdb=" ND2 ASN A 216 " model vdw 2.269 3.120 ... (remaining 30672 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.600 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 : 0.012 0.102 3675 Z= 0.540 Angle : 1.022 14.955 5010 Z= 0.604 Chirality : 0.054 0.228 593 Planarity : 0.006 0.046 612 Dihedral : 15.950 82.103 1273 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.07 % Favored : 89.50 % Rotamer: Outliers : 8.03 % Allowed : 17.88 % Favored : 74.09 % 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 aren not related in a simple way. whole: -3.13 (0.34), residues: 457 helix: -1.29 (0.25), residues: 319 sheet: None (None), residues: 0 loop : -3.79 (0.46), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 410 TYR 0.025 0.003 TYR A 385 PHE 0.015 0.002 PHE A 82 TRP 0.018 0.003 TRP A 390 HIS 0.001 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.01189 ( 3675) covalent geometry : angle 1.02201 ( 5010) hydrogen bonds : bond 0.13238 ( 248) hydrogen bonds : angle 6.84430 ( 726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.085 Fit side-chains REVERT: A 128 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: A 143 MET cc_start: 0.8206 (mmm) cc_final: 0.7578 (tpt) REVERT: A 214 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.6939 (m-80) REVERT: A 402 TYR cc_start: 0.6672 (t80) cc_final: 0.6200 (t80) REVERT: A 406 LYS cc_start: 0.7229 (tmtt) cc_final: 0.6993 (tmtt) outliers start: 31 outliers final: 18 residues processed: 91 average time/residue: 0.0643 time to fit residues: 7.0480 Evaluate side-chains 83 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 601 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 49 ASN A 132 GLN ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.147093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.109327 restraints weight = 3991.236| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.90 r_work: 0.3021 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3675 Z= 0.154 Angle : 0.668 6.004 5010 Z= 0.351 Chirality : 0.042 0.125 593 Planarity : 0.005 0.039 612 Dihedral : 9.253 57.066 535 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 5.18 % Allowed : 22.28 % Favored : 72.54 % 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 aren not related in a simple way. whole: -0.64 (0.39), residues: 457 helix: 0.53 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -2.67 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 119 TYR 0.013 0.001 TYR A 385 PHE 0.018 0.001 PHE A 187 TRP 0.015 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 3675) covalent geometry : angle 0.66809 ( 5010) hydrogen bonds : bond 0.04438 ( 248) hydrogen bonds : angle 4.70068 ( 726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.092 Fit side-chains REVERT: A 93 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7701 (tt) REVERT: A 108 LEU cc_start: 0.8504 (tp) cc_final: 0.8304 (tt) REVERT: A 128 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: A 143 MET cc_start: 0.8402 (mmm) cc_final: 0.7846 (tpt) REVERT: A 214 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.7101 (m-80) REVERT: A 376 GLU cc_start: 0.7343 (mp0) cc_final: 0.7135 (mp0) REVERT: A 402 TYR cc_start: 0.6273 (t80) cc_final: 0.6054 (t80) REVERT: A 406 LYS cc_start: 0.7091 (tmtt) cc_final: 0.6806 (tmtt) REVERT: A 473 ARG cc_start: 0.8276 (tpt170) cc_final: 0.8061 (tpt170) REVERT: A 481 ARG cc_start: 0.7459 (tmm160) cc_final: 0.6966 (ttp-170) outliers start: 20 outliers final: 15 residues processed: 76 average time/residue: 0.0565 time to fit residues: 5.2164 Evaluate side-chains 74 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 601 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 13 optimal weight: 0.6980 chunk 44 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.0040 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 325 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.143541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.105716 restraints weight = 4011.414| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.87 r_work: 0.2950 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3675 Z= 0.216 Angle : 0.681 6.046 5010 Z= 0.355 Chirality : 0.044 0.134 593 Planarity : 0.004 0.037 612 Dihedral : 8.900 59.869 523 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 7.25 % Allowed : 21.24 % Favored : 71.50 % 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 aren not related in a simple way. whole: -0.02 (0.40), residues: 457 helix: 0.91 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -2.22 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 410 TYR 0.023 0.002 TYR A 385 PHE 0.016 0.002 PHE A 187 TRP 0.015 0.001 TRP A 390 HIS 0.001 0.000 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 3675) covalent geometry : angle 0.68058 ( 5010) hydrogen bonds : bond 0.04795 ( 248) hydrogen bonds : angle 4.55894 ( 726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.130 Fit side-chains REVERT: A 128 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: A 143 MET cc_start: 0.8515 (mmm) cc_final: 0.8009 (tpt) REVERT: A 214 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.7150 (m-80) REVERT: A 376 GLU cc_start: 0.7518 (mp0) cc_final: 0.7317 (mp0) REVERT: A 402 TYR cc_start: 0.6446 (t80) cc_final: 0.5986 (t80) REVERT: A 406 LYS cc_start: 0.7129 (tmtt) cc_final: 0.6806 (tmtt) REVERT: A 481 ARG cc_start: 0.7499 (tmm160) cc_final: 0.6887 (ttp-170) outliers start: 28 outliers final: 19 residues processed: 82 average time/residue: 0.0583 time to fit residues: 5.8867 Evaluate side-chains 77 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 601 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.146967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.108703 restraints weight = 3944.390| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.88 r_work: 0.3002 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3675 Z= 0.164 Angle : 0.634 5.930 5010 Z= 0.331 Chirality : 0.042 0.127 593 Planarity : 0.004 0.037 612 Dihedral : 8.370 59.056 521 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 7.25 % Allowed : 22.80 % Favored : 69.95 % 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 aren not related in a simple way. whole: 0.44 (0.40), residues: 457 helix: 1.24 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -2.01 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 333 TYR 0.016 0.001 TYR A 385 PHE 0.016 0.001 PHE A 187 TRP 0.014 0.001 TRP A 390 HIS 0.000 0.000 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 3675) covalent geometry : angle 0.63361 ( 5010) hydrogen bonds : bond 0.04351 ( 248) hydrogen bonds : angle 4.35405 ( 726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 0.084 Fit side-chains REVERT: A 108 LEU cc_start: 0.8525 (tp) cc_final: 0.8312 (tt) REVERT: A 128 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: A 214 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.7164 (m-80) REVERT: A 236 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8053 (mp) REVERT: A 341 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8185 (mm-30) REVERT: A 402 TYR cc_start: 0.6309 (t80) cc_final: 0.6071 (t80) REVERT: A 481 ARG cc_start: 0.7450 (tmm160) cc_final: 0.6789 (ttp-170) outliers start: 28 outliers final: 21 residues processed: 83 average time/residue: 0.0621 time to fit residues: 6.3076 Evaluate side-chains 80 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 601 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 0.0370 chunk 20 optimal weight: 0.5980 chunk 43 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.149894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.111390 restraints weight = 3968.240| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.90 r_work: 0.3062 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3675 Z= 0.137 Angle : 0.615 5.875 5010 Z= 0.318 Chirality : 0.040 0.129 593 Planarity : 0.004 0.037 612 Dihedral : 7.914 58.685 520 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 6.22 % Allowed : 22.28 % Favored : 71.50 % 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 aren not related in a simple way. whole: 0.83 (0.41), residues: 457 helix: 1.56 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.92 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 159 TYR 0.014 0.001 TYR A 142 PHE 0.016 0.001 PHE A 187 TRP 0.013 0.001 TRP A 390 HIS 0.000 0.000 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3675) covalent geometry : angle 0.61491 ( 5010) hydrogen bonds : bond 0.04087 ( 248) hydrogen bonds : angle 4.19725 ( 726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.084 Fit side-chains REVERT: A 143 MET cc_start: 0.8526 (mmm) cc_final: 0.8285 (mmt) REVERT: A 214 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.7149 (m-80) REVERT: A 341 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8186 (mm-30) REVERT: A 350 MET cc_start: 0.8768 (mtt) cc_final: 0.8560 (mmm) REVERT: A 402 TYR cc_start: 0.6326 (t80) cc_final: 0.5989 (t80) REVERT: A 437 TYR cc_start: 0.5201 (OUTLIER) cc_final: 0.3295 (t80) REVERT: A 473 ARG cc_start: 0.8266 (tpt170) cc_final: 0.8057 (tpt170) REVERT: A 481 ARG cc_start: 0.7408 (tmm160) cc_final: 0.6899 (ttp-170) outliers start: 24 outliers final: 17 residues processed: 80 average time/residue: 0.0644 time to fit residues: 6.2765 Evaluate side-chains 74 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 601 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 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 = 0.3617 r_free = 0.3617 target = 0.149271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.111055 restraints weight = 3952.188| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.87 r_work: 0.3038 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3675 Z= 0.150 Angle : 0.651 8.614 5010 Z= 0.330 Chirality : 0.041 0.126 593 Planarity : 0.004 0.036 612 Dihedral : 7.215 51.427 517 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 6.22 % Allowed : 23.58 % Favored : 70.21 % 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 aren not related in a simple way. whole: 0.96 (0.41), residues: 457 helix: 1.65 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.86 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 410 TYR 0.017 0.001 TYR A 385 PHE 0.015 0.001 PHE A 187 TRP 0.013 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 3675) covalent geometry : angle 0.65088 ( 5010) hydrogen bonds : bond 0.04113 ( 248) hydrogen bonds : angle 4.21774 ( 726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.117 Fit side-chains REVERT: A 143 MET cc_start: 0.8553 (mmm) cc_final: 0.8291 (mmt) REVERT: A 214 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7143 (m-80) REVERT: A 254 ASN cc_start: 0.7322 (p0) cc_final: 0.6997 (p0) REVERT: A 341 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8186 (mm-30) REVERT: A 402 TYR cc_start: 0.6370 (t80) cc_final: 0.5997 (t80) REVERT: A 437 TYR cc_start: 0.5324 (OUTLIER) cc_final: 0.3350 (t80) outliers start: 24 outliers final: 20 residues processed: 82 average time/residue: 0.0647 time to fit residues: 6.4423 Evaluate side-chains 80 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 601 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.149661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.111209 restraints weight = 4003.107| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.88 r_work: 0.3044 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3675 Z= 0.156 Angle : 0.660 7.954 5010 Z= 0.336 Chirality : 0.041 0.127 593 Planarity : 0.004 0.036 612 Dihedral : 7.081 51.790 517 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 6.22 % Allowed : 23.58 % Favored : 70.21 % 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 aren not related in a simple way. whole: 1.01 (0.40), residues: 457 helix: 1.68 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.84 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 410 TYR 0.017 0.002 TYR A 385 PHE 0.015 0.001 PHE A 187 TRP 0.013 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 3675) covalent geometry : angle 0.65961 ( 5010) hydrogen bonds : bond 0.04184 ( 248) hydrogen bonds : angle 4.22025 ( 726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.114 Fit side-chains REVERT: A 143 MET cc_start: 0.8571 (mmm) cc_final: 0.8304 (mmt) REVERT: A 214 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7140 (m-80) REVERT: A 254 ASN cc_start: 0.7316 (p0) cc_final: 0.6987 (p0) REVERT: A 341 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8132 (mm-30) REVERT: A 376 GLU cc_start: 0.7494 (mp0) cc_final: 0.7244 (mp0) REVERT: A 402 TYR cc_start: 0.6392 (t80) cc_final: 0.5988 (t80) REVERT: A 437 TYR cc_start: 0.5362 (OUTLIER) cc_final: 0.3386 (t80) outliers start: 24 outliers final: 19 residues processed: 84 average time/residue: 0.0592 time to fit residues: 6.0446 Evaluate side-chains 83 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 601 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 43 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.150724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.112618 restraints weight = 3953.132| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.85 r_work: 0.3064 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3675 Z= 0.146 Angle : 0.656 9.042 5010 Z= 0.333 Chirality : 0.041 0.181 593 Planarity : 0.004 0.035 612 Dihedral : 6.827 52.039 516 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 5.96 % Allowed : 24.09 % Favored : 69.95 % 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 aren not related in a simple way. whole: 1.11 (0.40), residues: 457 helix: 1.77 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.82 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 473 TYR 0.016 0.001 TYR A 189 PHE 0.015 0.001 PHE A 187 TRP 0.012 0.001 TRP A 390 HIS 0.001 0.000 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 3675) covalent geometry : angle 0.65629 ( 5010) hydrogen bonds : bond 0.04061 ( 248) hydrogen bonds : angle 4.21108 ( 726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.132 Fit side-chains REVERT: A 143 MET cc_start: 0.8575 (mmm) cc_final: 0.8306 (mmt) REVERT: A 214 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.7113 (m-80) REVERT: A 254 ASN cc_start: 0.7310 (p0) cc_final: 0.6981 (p0) REVERT: A 341 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8144 (mm-30) REVERT: A 376 GLU cc_start: 0.7483 (mp0) cc_final: 0.7233 (mp0) REVERT: A 402 TYR cc_start: 0.6252 (t80) cc_final: 0.5962 (t80) REVERT: A 437 TYR cc_start: 0.5410 (OUTLIER) cc_final: 0.3398 (t80) outliers start: 23 outliers final: 20 residues processed: 78 average time/residue: 0.0636 time to fit residues: 6.1526 Evaluate side-chains 80 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 601 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 43 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.154867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.117979 restraints weight = 3856.288| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.76 r_work: 0.3087 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3675 Z= 0.143 Angle : 0.650 9.544 5010 Z= 0.330 Chirality : 0.041 0.178 593 Planarity : 0.004 0.035 612 Dihedral : 6.701 52.405 516 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 5.44 % Allowed : 24.61 % Favored : 69.95 % 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 aren not related in a simple way. whole: 1.22 (0.40), residues: 457 helix: 1.85 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.76 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 474 TYR 0.016 0.001 TYR A 385 PHE 0.015 0.001 PHE A 187 TRP 0.012 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 3675) covalent geometry : angle 0.64984 ( 5010) hydrogen bonds : bond 0.04025 ( 248) hydrogen bonds : angle 4.16603 ( 726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.125 Fit side-chains REVERT: A 143 MET cc_start: 0.8581 (mmm) cc_final: 0.8309 (mmt) REVERT: A 214 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.7179 (m-80) REVERT: A 254 ASN cc_start: 0.7363 (p0) cc_final: 0.7038 (p0) REVERT: A 341 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8112 (mm-30) REVERT: A 376 GLU cc_start: 0.7520 (mp0) cc_final: 0.7284 (mp0) REVERT: A 402 TYR cc_start: 0.6195 (t80) cc_final: 0.5927 (t80) REVERT: A 437 TYR cc_start: 0.5527 (OUTLIER) cc_final: 0.3410 (t80) outliers start: 21 outliers final: 16 residues processed: 74 average time/residue: 0.0639 time to fit residues: 5.8598 Evaluate side-chains 74 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 601 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.153845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.116741 restraints weight = 3936.928| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.80 r_work: 0.3082 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3675 Z= 0.146 Angle : 0.664 9.492 5010 Z= 0.336 Chirality : 0.041 0.174 593 Planarity : 0.004 0.034 612 Dihedral : 6.670 53.085 516 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 4.92 % Allowed : 25.39 % Favored : 69.69 % 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 aren not related in a simple way. whole: 1.23 (0.40), residues: 457 helix: 1.85 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.79 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 473 TYR 0.018 0.001 TYR A 189 PHE 0.015 0.001 PHE A 187 TRP 0.013 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 3675) covalent geometry : angle 0.66419 ( 5010) hydrogen bonds : bond 0.04038 ( 248) hydrogen bonds : angle 4.17356 ( 726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.084 Fit side-chains REVERT: A 143 MET cc_start: 0.8574 (mmm) cc_final: 0.8301 (mmt) REVERT: A 214 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7190 (m-80) REVERT: A 254 ASN cc_start: 0.7368 (p0) cc_final: 0.7045 (p0) REVERT: A 376 GLU cc_start: 0.7511 (mp0) cc_final: 0.7279 (mp0) REVERT: A 402 TYR cc_start: 0.6227 (t80) cc_final: 0.5931 (t80) REVERT: A 437 TYR cc_start: 0.5558 (OUTLIER) cc_final: 0.3419 (t80) REVERT: A 601 LYS cc_start: 0.4920 (OUTLIER) cc_final: 0.4540 (mptm) outliers start: 19 outliers final: 15 residues processed: 71 average time/residue: 0.0668 time to fit residues: 5.7690 Evaluate side-chains 72 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 601 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.149799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.114399 restraints weight = 3982.785| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.68 r_work: 0.3076 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3675 Z= 0.154 Angle : 0.669 9.880 5010 Z= 0.340 Chirality : 0.041 0.171 593 Planarity : 0.004 0.035 612 Dihedral : 6.687 53.486 516 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 5.44 % Allowed : 25.13 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.40), residues: 457 helix: 1.86 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.77 (0.52), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 410 TYR 0.018 0.002 TYR A 385 PHE 0.014 0.001 PHE A 187 TRP 0.013 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 3675) covalent geometry : angle 0.66869 ( 5010) hydrogen bonds : bond 0.04041 ( 248) hydrogen bonds : angle 4.20641 ( 726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 934.26 seconds wall clock time: 16 minutes 40.44 seconds (1000.44 seconds total)