Starting phenix.real_space_refine on Wed Mar 5 16:13:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3l_44144/03_2025/9b3l_44144_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3l_44144/03_2025/9b3l_44144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b3l_44144/03_2025/9b3l_44144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3l_44144/03_2025/9b3l_44144.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3l_44144/03_2025/9b3l_44144_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3l_44144/03_2025/9b3l_44144_neut.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 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 15 5.16 5 C 1768 2.51 5 N 407 2.21 5 O 433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2623 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2623 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 12, 'TRANS': 345} Chain breaks: 3 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 86 Time building chain proxies: 2.77, per 1000 atoms: 1.06 Number of scatterers: 2623 At special positions: 0 Unit cell: (59.4, 70.95, 80.025, 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 15 16.00 O 433 8.00 N 407 7.00 C 1768 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: 0.63 Conformation dependent library (CDL) restraints added in 323.9 milliseconds 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 644 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 89.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 5 through 21 removed outlier: 3.871A pdb=" N ILE A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY A 20 " --> pdb=" O PHE A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 removed outlier: 4.047A pdb=" N LYS A 31 " --> pdb=" O PRO A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 64 removed outlier: 3.887A pdb=" N LEU A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Proline residue: A 56 - end of helix removed outlier: 3.638A pdb=" N LYS A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 88 Processing helix chain 'A' and resid 90 through 120 Proline residue: A 110 - end of helix removed outlier: 3.588A pdb=" N ALA A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 151 removed outlier: 3.630A pdb=" N GLY A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 156 through 175 removed outlier: 3.842A pdb=" N TYR A 160 " --> pdb=" O ARG A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 232 removed outlier: 3.630A pdb=" N PHE A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 261 Processing helix chain 'A' and resid 267 through 288 Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 303 through 321 Proline residue: A 311 - end of helix Processing helix chain 'A' and resid 326 through 354 Proline residue: A 344 - end of helix removed outlier: 3.667A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 390 233 hydrogen bonds defined for protein. 699 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: 0.78 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 776 1.34 - 1.46: 581 1.46 - 1.58: 1301 1.58 - 1.69: 0 1.69 - 1.81: 29 Bond restraints: 2687 Sorted by residual: bond pdb=" CB ASN A 319 " pdb=" CG ASN A 319 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.94e-01 bond pdb=" CB ASP A 385 " pdb=" CG ASP A 385 " ideal model delta sigma weight residual 1.516 1.533 -0.017 2.50e-02 1.60e+03 4.77e-01 bond pdb=" CA ASN A 319 " pdb=" CB ASN A 319 " ideal model delta sigma weight residual 1.528 1.539 -0.011 1.66e-02 3.63e+03 4.30e-01 bond pdb=" CG PRO A 24 " pdb=" CD PRO A 24 " ideal model delta sigma weight residual 1.503 1.481 0.022 3.40e-02 8.65e+02 4.28e-01 bond pdb=" C MET A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.28e-02 6.10e+03 4.06e-01 ... (remaining 2682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 3491 1.12 - 2.23: 127 2.23 - 3.35: 16 3.35 - 4.47: 6 4.47 - 5.58: 8 Bond angle restraints: 3648 Sorted by residual: angle pdb=" N PHE A 259 " pdb=" CA PHE A 259 " pdb=" C PHE A 259 " ideal model delta sigma weight residual 112.90 109.93 2.97 1.31e+00 5.83e-01 5.13e+00 angle pdb=" C TYR A 257 " pdb=" N PHE A 258 " pdb=" CA PHE A 258 " ideal model delta sigma weight residual 122.31 118.74 3.57 2.00e+00 2.50e-01 3.19e+00 angle pdb=" CA ASN A 319 " pdb=" CB ASN A 319 " pdb=" CG ASN A 319 " ideal model delta sigma weight residual 112.60 114.33 -1.73 1.00e+00 1.00e+00 2.98e+00 angle pdb=" N VAL A 302 " pdb=" CA VAL A 302 " pdb=" C VAL A 302 " ideal model delta sigma weight residual 113.16 110.61 2.55 1.49e+00 4.50e-01 2.92e+00 angle pdb=" CA ASP A 385 " pdb=" CB ASP A 385 " pdb=" CG ASP A 385 " ideal model delta sigma weight residual 112.60 114.30 -1.70 1.00e+00 1.00e+00 2.90e+00 ... (remaining 3643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.94: 1219 11.94 - 23.89: 182 23.89 - 35.83: 79 35.83 - 47.77: 35 47.77 - 59.71: 9 Dihedral angle restraints: 1524 sinusoidal: 514 harmonic: 1010 Sorted by residual: dihedral pdb=" CA PHE A 259 " pdb=" C PHE A 259 " pdb=" N ASP A 260 " pdb=" CA ASP A 260 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" N ASN A 137 " pdb=" CA ASN A 137 " pdb=" CB ASN A 137 " pdb=" CG ASN A 137 " ideal model delta sinusoidal sigma weight residual -60.00 -119.71 59.71 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ILE A 346 " pdb=" CB ILE A 346 " pdb=" CG1 ILE A 346 " pdb=" CD1 ILE A 346 " ideal model delta sinusoidal sigma weight residual 60.00 115.94 -55.94 3 1.50e+01 4.44e-03 9.37e+00 ... (remaining 1521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 253 0.027 - 0.054: 95 0.054 - 0.081: 57 0.081 - 0.108: 25 0.108 - 0.134: 4 Chirality restraints: 434 Sorted by residual: chirality pdb=" CA THR A 206 " pdb=" N THR A 206 " pdb=" C THR A 206 " pdb=" CB THR A 206 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CG LEU A 165 " pdb=" CB LEU A 165 " pdb=" CD1 LEU A 165 " pdb=" CD2 LEU A 165 " both_signs ideal model delta sigma weight residual False -2.59 -2.48 -0.11 2.00e-01 2.50e+01 3.28e-01 chirality pdb=" CA PRO A 344 " pdb=" N PRO A 344 " pdb=" C PRO A 344 " pdb=" CB PRO A 344 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.12e-01 ... (remaining 431 not shown) Planarity restraints: 445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 26 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO A 27 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 343 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO A 344 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 256 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C ILE A 256 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE A 256 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR A 257 " 0.008 2.00e-02 2.50e+03 ... (remaining 442 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 734 2.80 - 3.32: 2727 3.32 - 3.85: 4553 3.85 - 4.37: 4861 4.37 - 4.90: 8619 Nonbonded interactions: 21494 Sorted by model distance: nonbonded pdb=" NZ LYS A 232 " pdb=" O ALA A 289 " model vdw 2.274 3.120 nonbonded pdb=" O SER A 241 " pdb=" OG1 THR A 245 " model vdw 2.304 3.040 nonbonded pdb=" O SER A 122 " pdb=" NZ LYS A 125 " model vdw 2.309 3.120 nonbonded pdb=" OD1 ASP A 385 " pdb=" N LEU A 386 " model vdw 2.442 3.120 nonbonded pdb=" OG SER A 133 " pdb=" OG1 THR A 314 " model vdw 2.463 3.040 ... (remaining 21489 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.310 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 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: 0.8204 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 : 0.003 0.022 2687 Z= 0.202 Angle : 0.537 5.582 3648 Z= 0.286 Chirality : 0.040 0.134 434 Planarity : 0.005 0.053 445 Dihedral : 15.962 59.714 880 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.40 % Allowed : 32.41 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.46), residues: 350 helix: 2.04 (0.30), residues: 302 sheet: None (None), residues: 0 loop : -2.80 (0.84), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 PHE 0.012 0.001 PHE A 216 TYR 0.011 0.001 TYR A 228 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.278 Fit side-chains REVERT: A 156 ARG cc_start: 0.6516 (ttm-80) cc_final: 0.6315 (ttm-80) REVERT: A 338 MET cc_start: 0.8799 (ttm) cc_final: 0.8526 (ttp) outliers start: 1 outliers final: 1 residues processed: 72 average time/residue: 0.1245 time to fit residues: 11.0042 Evaluate side-chains 69 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.0050 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.165754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.133462 restraints weight = 3595.235| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.96 r_work: 0.3426 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2687 Z= 0.227 Angle : 0.511 5.590 3648 Z= 0.273 Chirality : 0.041 0.126 434 Planarity : 0.005 0.052 445 Dihedral : 4.143 18.195 372 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 5.53 % Allowed : 29.25 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.45), residues: 350 helix: 2.18 (0.29), residues: 308 sheet: None (None), residues: 0 loop : -2.66 (0.91), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 PHE 0.013 0.001 PHE A 216 TYR 0.010 0.001 TYR A 160 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.319 Fit side-chains REVERT: A 64 LYS cc_start: 0.4965 (OUTLIER) cc_final: 0.4729 (tptm) REVERT: A 128 ASN cc_start: 0.7309 (t0) cc_final: 0.7109 (t0) REVERT: A 338 MET cc_start: 0.8785 (ttm) cc_final: 0.8545 (ttp) outliers start: 14 outliers final: 9 residues processed: 77 average time/residue: 0.1309 time to fit residues: 12.4507 Evaluate side-chains 74 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 320 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.165880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.133659 restraints weight = 3639.437| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.97 r_work: 0.3417 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2687 Z= 0.221 Angle : 0.500 5.492 3648 Z= 0.265 Chirality : 0.041 0.121 434 Planarity : 0.004 0.049 445 Dihedral : 4.114 19.140 370 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 5.93 % Allowed : 27.27 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.45), residues: 350 helix: 2.26 (0.29), residues: 308 sheet: None (None), residues: 0 loop : -2.64 (0.90), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 PHE 0.013 0.001 PHE A 159 TYR 0.012 0.001 TYR A 360 ARG 0.003 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.279 Fit side-chains REVERT: A 64 LYS cc_start: 0.4899 (OUTLIER) cc_final: 0.4672 (tptm) REVERT: A 160 TYR cc_start: 0.7804 (m-80) cc_final: 0.7527 (m-80) REVERT: A 338 MET cc_start: 0.8804 (ttm) cc_final: 0.8594 (ttp) outliers start: 15 outliers final: 9 residues processed: 80 average time/residue: 0.1200 time to fit residues: 11.8124 Evaluate side-chains 73 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 331 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 17 optimal weight: 0.0670 chunk 30 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.165808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.133316 restraints weight = 3639.470| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.99 r_work: 0.3408 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2687 Z= 0.217 Angle : 0.520 7.132 3648 Z= 0.269 Chirality : 0.041 0.128 434 Planarity : 0.004 0.047 445 Dihedral : 4.136 19.585 370 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 6.32 % Allowed : 28.46 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.45), residues: 350 helix: 2.26 (0.29), residues: 308 sheet: None (None), residues: 0 loop : -2.54 (0.92), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 PHE 0.013 0.001 PHE A 159 TYR 0.023 0.002 TYR A 225 ARG 0.001 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.285 Fit side-chains REVERT: A 64 LYS cc_start: 0.4777 (OUTLIER) cc_final: 0.4507 (tptm) REVERT: A 128 ASN cc_start: 0.7408 (t0) cc_final: 0.7207 (t0) outliers start: 16 outliers final: 13 residues processed: 79 average time/residue: 0.1218 time to fit residues: 11.9554 Evaluate side-chains 79 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 356 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 2 optimal weight: 0.0050 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.0020 chunk 1 optimal weight: 0.0970 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.3400 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.167644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.135322 restraints weight = 3612.727| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.96 r_work: 0.3439 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2687 Z= 0.181 Angle : 0.521 6.378 3648 Z= 0.264 Chirality : 0.041 0.142 434 Planarity : 0.004 0.046 445 Dihedral : 4.085 20.526 370 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 5.53 % Allowed : 30.04 % Favored : 64.43 % 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: 2.74 (0.46), residues: 350 helix: 2.35 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -2.41 (0.92), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 293 HIS 0.002 0.000 HIS A 155 PHE 0.011 0.001 PHE A 159 TYR 0.017 0.001 TYR A 225 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.255 Fit side-chains REVERT: A 64 LYS cc_start: 0.4918 (OUTLIER) cc_final: 0.4620 (tptm) REVERT: A 156 ARG cc_start: 0.6618 (ttm-80) cc_final: 0.6224 (ttm-80) REVERT: A 160 TYR cc_start: 0.7712 (m-80) cc_final: 0.7161 (m-80) REVERT: A 341 PHE cc_start: 0.7621 (t80) cc_final: 0.7393 (t80) outliers start: 14 outliers final: 11 residues processed: 81 average time/residue: 0.1107 time to fit residues: 11.1441 Evaluate side-chains 80 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 356 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 1 optimal weight: 0.1980 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.165789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.133547 restraints weight = 3648.759| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.95 r_work: 0.3420 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2687 Z= 0.229 Angle : 0.545 5.486 3648 Z= 0.277 Chirality : 0.043 0.265 434 Planarity : 0.004 0.044 445 Dihedral : 4.096 20.446 370 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 7.51 % Allowed : 27.67 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.45), residues: 350 helix: 2.30 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -2.42 (0.89), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 293 HIS 0.002 0.000 HIS A 155 PHE 0.015 0.002 PHE A 335 TYR 0.013 0.001 TYR A 225 ARG 0.001 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.253 Fit side-chains REVERT: A 64 LYS cc_start: 0.4897 (OUTLIER) cc_final: 0.4590 (tptm) REVERT: A 128 ASN cc_start: 0.7428 (t0) cc_final: 0.7215 (t0) outliers start: 19 outliers final: 15 residues processed: 75 average time/residue: 0.1119 time to fit residues: 10.4240 Evaluate side-chains 77 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 356 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 0.0870 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.0770 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 0.2980 overall best weight: 0.3516 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.167501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.135375 restraints weight = 3742.548| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.98 r_work: 0.3440 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2687 Z= 0.181 Angle : 0.531 6.070 3648 Z= 0.269 Chirality : 0.042 0.224 434 Planarity : 0.004 0.043 445 Dihedral : 4.051 20.581 370 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 6.32 % Allowed : 29.25 % Favored : 64.43 % 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: 2.71 (0.46), residues: 350 helix: 2.32 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -2.30 (0.89), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 PHE 0.011 0.001 PHE A 335 TYR 0.014 0.001 TYR A 225 ARG 0.003 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.304 Fit side-chains REVERT: A 64 LYS cc_start: 0.4832 (OUTLIER) cc_final: 0.4488 (tptm) REVERT: A 128 ASN cc_start: 0.7419 (t0) cc_final: 0.7208 (t0) REVERT: A 341 PHE cc_start: 0.7577 (t80) cc_final: 0.7220 (t80) REVERT: A 346 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7350 (mt) outliers start: 16 outliers final: 11 residues processed: 76 average time/residue: 0.1149 time to fit residues: 10.8964 Evaluate side-chains 77 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 356 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.163869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131664 restraints weight = 3625.253| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.94 r_work: 0.3406 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2687 Z= 0.298 Angle : 0.595 6.470 3648 Z= 0.304 Chirality : 0.044 0.218 434 Planarity : 0.004 0.042 445 Dihedral : 4.250 20.309 370 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 7.11 % Allowed : 29.64 % Favored : 63.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.45), residues: 350 helix: 2.04 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -2.31 (0.84), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 201 HIS 0.001 0.001 HIS A 155 PHE 0.019 0.002 PHE A 159 TYR 0.010 0.002 TYR A 225 ARG 0.002 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.281 Fit side-chains REVERT: A 64 LYS cc_start: 0.4819 (OUTLIER) cc_final: 0.4501 (tptm) REVERT: A 71 ILE cc_start: 0.8284 (mp) cc_final: 0.7706 (mt) REVERT: A 376 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8292 (tm-30) outliers start: 18 outliers final: 12 residues processed: 76 average time/residue: 0.1213 time to fit residues: 11.3392 Evaluate side-chains 76 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 346 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 1 optimal weight: 0.0770 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.165154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.132533 restraints weight = 3620.448| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.99 r_work: 0.3395 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2687 Z= 0.236 Angle : 0.586 6.362 3648 Z= 0.295 Chirality : 0.043 0.206 434 Planarity : 0.004 0.042 445 Dihedral : 4.226 20.857 370 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 6.32 % Allowed : 30.43 % Favored : 63.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.45), residues: 350 helix: 2.04 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -2.26 (0.84), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 PHE 0.014 0.001 PHE A 159 TYR 0.011 0.001 TYR A 225 ARG 0.002 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.259 Fit side-chains REVERT: A 64 LYS cc_start: 0.4793 (OUTLIER) cc_final: 0.4464 (tptm) REVERT: A 71 ILE cc_start: 0.8314 (mp) cc_final: 0.7726 (mt) outliers start: 16 outliers final: 12 residues processed: 75 average time/residue: 0.1174 time to fit residues: 10.8480 Evaluate side-chains 77 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 346 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 25 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.165012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.133153 restraints weight = 3625.910| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.96 r_work: 0.3407 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2687 Z= 0.229 Angle : 0.598 6.936 3648 Z= 0.299 Chirality : 0.043 0.199 434 Planarity : 0.004 0.042 445 Dihedral : 4.262 20.641 370 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.93 % Allowed : 30.83 % Favored : 63.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.45), residues: 350 helix: 2.06 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -2.19 (0.86), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 PHE 0.014 0.001 PHE A 159 TYR 0.011 0.001 TYR A 225 ARG 0.002 0.001 ARG A 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.275 Fit side-chains REVERT: A 64 LYS cc_start: 0.4819 (OUTLIER) cc_final: 0.4480 (tptm) REVERT: A 71 ILE cc_start: 0.8295 (mp) cc_final: 0.7814 (mt) REVERT: A 341 PHE cc_start: 0.7232 (t80) cc_final: 0.6943 (t80) REVERT: A 376 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8402 (tm-30) outliers start: 15 outliers final: 11 residues processed: 77 average time/residue: 0.1172 time to fit residues: 11.0948 Evaluate side-chains 76 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 331 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.165364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132896 restraints weight = 3633.988| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.01 r_work: 0.3398 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2687 Z= 0.240 Angle : 0.599 6.839 3648 Z= 0.300 Chirality : 0.043 0.197 434 Planarity : 0.004 0.042 445 Dihedral : 4.261 20.432 370 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 6.72 % Allowed : 30.43 % Favored : 62.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.45), residues: 350 helix: 2.00 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -2.16 (0.86), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 293 HIS 0.001 0.000 HIS A 155 PHE 0.014 0.002 PHE A 159 TYR 0.010 0.001 TYR A 160 ARG 0.002 0.001 ARG A 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1576.82 seconds wall clock time: 27 minutes 48.08 seconds (1668.08 seconds total)