Starting phenix.real_space_refine on Tue Feb 11 01:36:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xyj_38775/02_2025/8xyj_38775_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xyj_38775/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xyj_38775/02_2025/8xyj_38775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xyj_38775/02_2025/8xyj_38775.map" model { file = "/net/cci-nas-00/data/ceres_data/8xyj_38775/02_2025/8xyj_38775_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xyj_38775/02_2025/8xyj_38775_neut.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 2.83, per 1000 atoms: 0.79 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: 0.87 Conformation dependent library (CDL) restraints added in 416.8 milliseconds 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: 0.29 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: 0.96 Time building geometry restraints manager: 1.03 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: 0.760 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.060 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.970 ------------------------------------------------------------------------------- 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= 0.748 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 : 17.47 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (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 TRP 0.018 0.003 TRP A 390 HIS 0.001 0.001 HIS A 343 PHE 0.015 0.002 PHE A 82 TYR 0.025 0.003 TYR A 385 ARG 0.005 0.001 ARG A 410 *********************** 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 : 0.391 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: 0.1807 time to fit residues: 19.8809 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 : 0.391 ------------------------------------------------------------------------------- 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 37 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 A 278 ASN A 325 ASN A 365 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.144689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.107577 restraints weight = 3968.256| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.80 r_work: 0.2997 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3675 Z= 0.263 Angle : 0.688 6.040 5010 Z= 0.363 Chirality : 0.043 0.136 593 Planarity : 0.005 0.039 612 Dihedral : 9.445 58.305 535 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 5.44 % Allowed : 22.80 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.38), residues: 457 helix: 0.43 (0.28), residues: 317 sheet: None (None), residues: 0 loop : -2.72 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 390 HIS 0.002 0.001 HIS A 466 PHE 0.019 0.002 PHE A 187 TYR 0.016 0.002 TYR A 385 ARG 0.004 0.001 ARG A 119 *********************** 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 80 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.360 Fit side-chains REVERT: A 93 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7860 (tt) REVERT: A 128 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: A 143 MET cc_start: 0.8456 (mmm) cc_final: 0.7891 (tpt) REVERT: A 214 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7169 (m-80) REVERT: A 376 GLU cc_start: 0.7406 (mp0) cc_final: 0.7203 (mp0) REVERT: A 402 TYR cc_start: 0.6453 (t80) cc_final: 0.6146 (t80) REVERT: A 406 LYS cc_start: 0.7162 (tmtt) cc_final: 0.6857 (tmtt) REVERT: A 473 ARG cc_start: 0.8287 (tpt170) cc_final: 0.8076 (tpt170) REVERT: A 481 ARG cc_start: 0.7501 (tmm160) cc_final: 0.7032 (ttp-170) outliers start: 21 outliers final: 14 residues processed: 77 average time/residue: 0.1955 time to fit residues: 18.1697 Evaluate side-chains 74 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 170 THR Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 214 PHE 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 418 VAL 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 4 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 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 = 0.3605 r_free = 0.3605 target = 0.147675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.109947 restraints weight = 3932.287| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.85 r_work: 0.3019 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1972 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= 0.215 Angle : 0.623 5.957 5010 Z= 0.326 Chirality : 0.041 0.129 593 Planarity : 0.004 0.038 612 Dihedral : 8.529 59.230 523 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 5.70 % Allowed : 22.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.40), residues: 457 helix: 1.13 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -2.08 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 390 HIS 0.001 0.000 HIS A 343 PHE 0.014 0.001 PHE A 187 TYR 0.014 0.002 TYR A 385 ARG 0.001 0.000 ARG A 340 *********************** 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 83 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.360 Fit side-chains REVERT: A 108 LEU cc_start: 0.8529 (tp) cc_final: 0.8327 (tt) REVERT: A 128 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: A 214 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7063 (m-80) REVERT: A 376 GLU cc_start: 0.7509 (mp0) cc_final: 0.7303 (mp0) REVERT: A 402 TYR cc_start: 0.6368 (t80) cc_final: 0.6009 (t80) REVERT: A 406 LYS cc_start: 0.7109 (tmtt) cc_final: 0.6819 (tmtt) REVERT: A 437 TYR cc_start: 0.5189 (p90) cc_final: 0.3418 (t80) REVERT: A 481 ARG cc_start: 0.7465 (tmm160) cc_final: 0.6854 (ttp-170) outliers start: 22 outliers final: 15 residues processed: 80 average time/residue: 0.1720 time to fit residues: 16.7899 Evaluate side-chains 75 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 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 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 28 optimal weight: 2.9990 chunk 43 optimal weight: 0.0470 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.148716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.110214 restraints weight = 3974.462| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.90 r_work: 0.3028 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2188 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= 0.203 Angle : 0.624 5.899 5010 Z= 0.324 Chirality : 0.041 0.128 593 Planarity : 0.004 0.037 612 Dihedral : 8.102 59.261 521 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.22 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.40), residues: 457 helix: 1.43 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -2.03 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 PHE 0.016 0.001 PHE A 187 TYR 0.015 0.001 TYR A 385 ARG 0.001 0.000 ARG A 333 *********************** 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 81 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 0.365 Fit side-chains REVERT: A 143 MET cc_start: 0.8464 (mmm) cc_final: 0.8234 (mmt) REVERT: A 214 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.7026 (m-80) REVERT: A 402 TYR cc_start: 0.6215 (t80) cc_final: 0.5982 (t80) REVERT: A 437 TYR cc_start: 0.5026 (p90) cc_final: 0.3298 (t80) REVERT: A 481 ARG cc_start: 0.7408 (tmm160) cc_final: 0.6761 (ttp-170) outliers start: 24 outliers final: 16 residues processed: 79 average time/residue: 0.1822 time to fit residues: 17.3320 Evaluate side-chains 72 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 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 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 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 18 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 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 = 0.3624 r_free = 0.3624 target = 0.149740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.111496 restraints weight = 3980.174| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.88 r_work: 0.3045 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2379 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= 0.203 Angle : 0.624 5.900 5010 Z= 0.320 Chirality : 0.041 0.128 593 Planarity : 0.004 0.036 612 Dihedral : 7.184 57.337 517 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 5.18 % Allowed : 23.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.40), residues: 457 helix: 1.58 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.93 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 PHE 0.015 0.001 PHE A 187 TYR 0.016 0.001 TYR A 385 ARG 0.001 0.000 ARG A 410 *********************** 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 77 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.353 Fit side-chains REVERT: A 143 MET cc_start: 0.8531 (mmm) cc_final: 0.8267 (mmt) REVERT: A 214 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.7090 (m-80) REVERT: A 402 TYR cc_start: 0.6350 (t80) cc_final: 0.6030 (t80) REVERT: A 437 TYR cc_start: 0.5015 (p90) cc_final: 0.3271 (t80) REVERT: A 473 ARG cc_start: 0.8259 (tpt170) cc_final: 0.8040 (tpt170) REVERT: A 481 ARG cc_start: 0.7425 (tmm160) cc_final: 0.6910 (ttp-170) outliers start: 20 outliers final: 18 residues processed: 75 average time/residue: 0.1750 time to fit residues: 15.9079 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 : 0.385 ------------------------------------------------------------------------------- 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 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 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 4 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 0.0370 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 31 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 26 optimal weight: 0.1980 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 overall best weight: 0.3658 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.152091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.114604 restraints weight = 3998.790| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.83 r_work: 0.3089 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3675 Z= 0.173 Angle : 0.628 8.843 5010 Z= 0.317 Chirality : 0.040 0.126 593 Planarity : 0.004 0.036 612 Dihedral : 6.838 53.542 516 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.66 % Allowed : 24.87 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.41), residues: 457 helix: 1.80 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.84 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 390 HIS 0.000 0.000 HIS A 352 PHE 0.015 0.001 PHE A 187 TYR 0.018 0.001 TYR A 189 ARG 0.001 0.000 ARG A 159 *********************** 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 78 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.327 Fit side-chains REVERT: A 143 MET cc_start: 0.8576 (mmm) cc_final: 0.8301 (mmt) REVERT: A 402 TYR cc_start: 0.6401 (t80) cc_final: 0.6048 (t80) REVERT: A 437 TYR cc_start: 0.5064 (p90) cc_final: 0.3350 (t80) REVERT: A 473 ARG cc_start: 0.8250 (tpt170) cc_final: 0.8043 (tpt170) REVERT: A 481 ARG cc_start: 0.7422 (tmm160) cc_final: 0.6900 (ttp-170) REVERT: A 601 LYS cc_start: 0.5121 (OUTLIER) cc_final: 0.4530 (mptm) outliers start: 18 outliers final: 16 residues processed: 75 average time/residue: 0.1805 time to fit residues: 16.3235 Evaluate side-chains 70 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 212 THR Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 296 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 27 optimal weight: 0.0570 chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.151884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.113249 restraints weight = 3972.151| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.91 r_work: 0.3067 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2737 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= 0.189 Angle : 0.614 8.377 5010 Z= 0.313 Chirality : 0.040 0.170 593 Planarity : 0.004 0.035 612 Dihedral : 6.364 49.936 514 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.41), residues: 457 helix: 1.84 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.78 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 390 HIS 0.000 0.000 HIS A 343 PHE 0.014 0.001 PHE A 187 TYR 0.015 0.001 TYR A 385 ARG 0.001 0.000 ARG A 410 *********************** 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 77 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.316 Fit side-chains REVERT: A 93 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7666 (tt) REVERT: A 143 MET cc_start: 0.8572 (mmm) cc_final: 0.8296 (mmt) REVERT: A 214 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.7124 (m-80) REVERT: A 402 TYR cc_start: 0.6305 (t80) cc_final: 0.5991 (t80) REVERT: A 437 TYR cc_start: 0.5155 (p90) cc_final: 0.3389 (t80) REVERT: A 481 ARG cc_start: 0.7375 (tmm160) cc_final: 0.6863 (ttp-170) REVERT: A 601 LYS cc_start: 0.5003 (OUTLIER) cc_final: 0.4691 (mptm) outliers start: 21 outliers final: 15 residues processed: 75 average time/residue: 0.1758 time to fit residues: 15.9807 Evaluate side-chains 73 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 93 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 158 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.150704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.112593 restraints weight = 3916.721| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.85 r_work: 0.3048 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3675 Z= 0.229 Angle : 0.655 9.092 5010 Z= 0.332 Chirality : 0.041 0.180 593 Planarity : 0.004 0.034 612 Dihedral : 6.378 47.292 514 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 5.44 % Allowed : 25.39 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.40), residues: 457 helix: 1.81 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.79 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 PHE 0.014 0.001 PHE A 187 TYR 0.020 0.002 TYR A 189 ARG 0.001 0.000 ARG A 410 *********************** 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 79 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.414 Fit side-chains REVERT: A 93 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7683 (tt) REVERT: A 143 MET cc_start: 0.8582 (mmm) cc_final: 0.8300 (mmt) REVERT: A 214 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.7181 (m-80) REVERT: A 254 ASN cc_start: 0.7230 (p0) cc_final: 0.6909 (p0) REVERT: A 402 TYR cc_start: 0.6331 (t80) cc_final: 0.5991 (t80) REVERT: A 437 TYR cc_start: 0.5255 (p90) cc_final: 0.3400 (t80) outliers start: 21 outliers final: 17 residues processed: 77 average time/residue: 0.1809 time to fit residues: 17.0982 Evaluate side-chains 75 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 93 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 296 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 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 = 0.3635 r_free = 0.3635 target = 0.150621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.112190 restraints weight = 3876.957| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.88 r_work: 0.3047 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3675 Z= 0.221 Angle : 0.665 10.157 5010 Z= 0.337 Chirality : 0.041 0.177 593 Planarity : 0.004 0.034 612 Dihedral : 6.338 44.656 514 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 5.44 % Allowed : 25.39 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.40), residues: 457 helix: 1.81 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.80 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 390 HIS 0.001 0.000 HIS A 213 PHE 0.013 0.001 PHE A 187 TYR 0.017 0.002 TYR A 385 ARG 0.001 0.000 ARG A 473 *********************** 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 : 0.413 Fit side-chains REVERT: A 93 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7669 (tt) REVERT: A 143 MET cc_start: 0.8579 (mmm) cc_final: 0.8302 (mmt) REVERT: A 214 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.7204 (m-80) REVERT: A 254 ASN cc_start: 0.7248 (p0) cc_final: 0.6919 (p0) REVERT: A 402 TYR cc_start: 0.6342 (t80) cc_final: 0.5942 (t80) REVERT: A 437 TYR cc_start: 0.5230 (p90) cc_final: 0.3395 (t80) outliers start: 21 outliers final: 18 residues processed: 75 average time/residue: 0.1827 time to fit residues: 16.6129 Evaluate side-chains 77 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 93 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 296 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 0.0270 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 0.5636 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.155106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.118164 restraints weight = 3878.868| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.76 r_work: 0.3092 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3675 Z= 0.201 Angle : 0.657 9.589 5010 Z= 0.334 Chirality : 0.041 0.192 593 Planarity : 0.004 0.035 612 Dihedral : 6.200 41.091 514 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 5.18 % Allowed : 25.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.40), residues: 457 helix: 1.88 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.73 (0.52), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 390 HIS 0.001 0.000 HIS A 352 PHE 0.014 0.001 PHE A 187 TYR 0.022 0.001 TYR A 189 ARG 0.001 0.000 ARG A 159 ********************** 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 78 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.358 Fit side-chains REVERT: A 93 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7723 (tt) REVERT: A 143 MET cc_start: 0.8583 (mmm) cc_final: 0.8300 (mmt) REVERT: A 214 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.7273 (m-80) REVERT: A 254 ASN cc_start: 0.7362 (p0) cc_final: 0.7034 (p0) REVERT: A 402 TYR cc_start: 0.6235 (t80) cc_final: 0.5989 (t80) REVERT: A 437 TYR cc_start: 0.5344 (p90) cc_final: 0.3423 (t80) REVERT: A 601 LYS cc_start: 0.5098 (OUTLIER) cc_final: 0.4695 (mptm) outliers start: 20 outliers final: 16 residues processed: 75 average time/residue: 0.1805 time to fit residues: 16.5614 Evaluate side-chains 75 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 93 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 296 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 0.0770 chunk 32 optimal weight: 0.0070 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.151597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.116431 restraints weight = 3938.480| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.67 r_work: 0.3105 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2955 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= 0.201 Angle : 0.657 9.215 5010 Z= 0.335 Chirality : 0.041 0.190 593 Planarity : 0.004 0.034 612 Dihedral : 6.137 37.460 514 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.66 % Allowed : 25.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.40), residues: 457 helix: 1.90 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.74 (0.52), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 390 HIS 0.001 0.000 HIS A 343 PHE 0.013 0.001 PHE A 187 TYR 0.016 0.001 TYR A 385 ARG 0.001 0.000 ARG A 410 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2119.33 seconds wall clock time: 38 minutes 11.95 seconds (2291.95 seconds total)