Starting phenix.real_space_refine on Mon Feb 10 21:38:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ul5_26592/02_2025/7ul5_26592.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ul5_26592/02_2025/7ul5_26592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ul5_26592/02_2025/7ul5_26592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ul5_26592/02_2025/7ul5_26592.map" model { file = "/net/cci-nas-00/data/ceres_data/7ul5_26592/02_2025/7ul5_26592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ul5_26592/02_2025/7ul5_26592.cif" } resolution = 3.1 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= -0.001 sd= 0.088 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 24 5.16 5 C 1834 2.51 5 N 449 2.21 5 O 466 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-5592/modules/chem_data/mon_lib" Total number of atoms: 2773 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2169 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 2 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 604 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 85} Chain breaks: 4 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 3.00, per 1000 atoms: 1.08 Number of scatterers: 2773 At special positions: 0 Unit cell: (67.3159, 57.9428, 109.069, 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 24 16.00 O 466 8.00 N 449 7.00 C 1834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 374.3 milliseconds 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 694 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 4 sheets defined 65.5% alpha, 12.1% 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 40 through 71 removed outlier: 3.985A pdb=" N ALA A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 105 removed outlier: 4.245A pdb=" N TYR A 81 " --> pdb=" O ILE A 77 " (cutoff:3.500A) Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 112 through 146 removed outlier: 3.649A pdb=" N VAL A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE A 130 " --> pdb=" O GLN A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.940A pdb=" N ALA A 151 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS A 152 " --> pdb=" O LYS A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 152' Processing helix chain 'A' and resid 155 through 180 removed outlier: 3.515A pdb=" N ALA A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS A 160 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N MET A 161 " --> pdb=" O ARG A 157 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 203 through 217 removed outlier: 3.532A pdb=" N ILE A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 238 removed outlier: 3.627A pdb=" N ILE A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 282 removed outlier: 3.531A pdb=" N ARG A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 288 through 315 removed outlier: 4.273A pdb=" N GLY A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) Proline residue: A 309 - end of helix removed outlier: 3.732A pdb=" N TYR A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 314 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 185 Processing sheet with id=AA2, first strand: chain 'D' and resid 5 through 9 removed outlier: 3.687A pdb=" N SER D 23 " --> pdb=" O SER D 9 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 32 through 33 removed outlier: 3.630A pdb=" N ARG D 32 " --> pdb=" O ARG D 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 32 through 33 removed outlier: 3.630A pdb=" N ARG D 32 " --> pdb=" O ARG D 102 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 576 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: 0.77 Time building geometry restraints manager: 0.84 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: 842 1.34 - 1.46: 637 1.46 - 1.58: 1320 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 2835 Sorted by residual: bond pdb=" CB CYS A 306 " pdb=" SG CYS A 306 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.39e+00 bond pdb=" CG LEU D 33 " pdb=" CD1 LEU D 33 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.11e+00 bond pdb=" CA LEU A 96 " pdb=" C LEU A 96 " ideal model delta sigma weight residual 1.525 1.537 -0.012 1.19e-02 7.06e+03 1.10e+00 bond pdb=" CB VAL D 80 " pdb=" CG2 VAL D 80 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.01e+00 bond pdb=" CA ASP D 111 " pdb=" CB ASP D 111 " ideal model delta sigma weight residual 1.535 1.555 -0.020 2.02e-02 2.45e+03 9.73e-01 ... (remaining 2830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 3740 1.59 - 3.18: 106 3.18 - 4.77: 20 4.77 - 6.36: 0 6.36 - 7.95: 1 Bond angle restraints: 3867 Sorted by residual: angle pdb=" N PHE A 127 " pdb=" CA PHE A 127 " pdb=" C PHE A 127 " ideal model delta sigma weight residual 112.68 116.13 -3.45 1.33e+00 5.65e-01 6.71e+00 angle pdb=" N ASN A 308 " pdb=" CA ASN A 308 " pdb=" C ASN A 308 " ideal model delta sigma weight residual 113.16 116.80 -3.64 1.42e+00 4.96e-01 6.57e+00 angle pdb=" CA LEU A 105 " pdb=" CB LEU A 105 " pdb=" CG LEU A 105 " ideal model delta sigma weight residual 116.30 124.25 -7.95 3.50e+00 8.16e-02 5.17e+00 angle pdb=" CA ASP D 111 " pdb=" CB ASP D 111 " pdb=" CG ASP D 111 " ideal model delta sigma weight residual 112.60 114.70 -2.10 1.00e+00 1.00e+00 4.39e+00 angle pdb=" N GLN A 126 " pdb=" CA GLN A 126 " pdb=" C GLN A 126 " ideal model delta sigma weight residual 111.36 113.62 -2.26 1.09e+00 8.42e-01 4.30e+00 ... (remaining 3862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.03: 1455 14.03 - 28.05: 134 28.05 - 42.08: 33 42.08 - 56.10: 4 56.10 - 70.13: 1 Dihedral angle restraints: 1627 sinusoidal: 551 harmonic: 1076 Sorted by residual: dihedral pdb=" CG ARG A 249 " pdb=" CD ARG A 249 " pdb=" NE ARG A 249 " pdb=" CZ ARG A 249 " ideal model delta sinusoidal sigma weight residual 180.00 136.43 43.57 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CB MET A 119 " pdb=" CG MET A 119 " pdb=" SD MET A 119 " pdb=" CE MET A 119 " ideal model delta sinusoidal sigma weight residual 60.00 111.66 -51.66 3 1.50e+01 4.44e-03 9.04e+00 dihedral pdb=" CA LEU A 105 " pdb=" C LEU A 105 " pdb=" N VAL A 106 " pdb=" CA VAL A 106 " ideal model delta harmonic sigma weight residual -180.00 -164.97 -15.03 0 5.00e+00 4.00e-02 9.03e+00 ... (remaining 1624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 280 0.032 - 0.063: 126 0.063 - 0.095: 41 0.095 - 0.126: 15 0.126 - 0.158: 3 Chirality restraints: 465 Sorted by residual: chirality pdb=" CA PHE A 127 " pdb=" N PHE A 127 " pdb=" C PHE A 127 " pdb=" CB PHE A 127 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA ILE D 30 " pdb=" N ILE D 30 " pdb=" C ILE D 30 " pdb=" CB ILE D 30 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA PRO A 309 " pdb=" N PRO A 309 " pdb=" C PRO A 309 " pdb=" CB PRO A 309 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 462 not shown) Planarity restraints: 470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 46 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C LEU A 46 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU A 46 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 47 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 211 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.10e+00 pdb=" C TYR A 211 " 0.046 2.00e-02 2.50e+03 pdb=" O TYR A 211 " -0.017 2.00e-02 2.50e+03 pdb=" N THR A 212 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 219 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO A 220 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " -0.028 5.00e-02 4.00e+02 ... (remaining 467 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1094 2.90 - 3.40: 2578 3.40 - 3.90: 4120 3.90 - 4.40: 4429 4.40 - 4.90: 8105 Nonbonded interactions: 20326 Sorted by model distance: nonbonded pdb=" O ASN A 43 " pdb=" OG1 THR A 47 " model vdw 2.404 3.040 nonbonded pdb=" O GLY A 57 " pdb=" ND2 ASN A 61 " model vdw 2.439 3.120 nonbonded pdb=" O VAL A 298 " pdb=" OG1 THR A 301 " model vdw 2.458 3.040 nonbonded pdb=" OH TYR A 71 " pdb=" OD1 ASN A 325 " model vdw 2.463 3.040 nonbonded pdb=" O ASP D 111 " pdb=" OD1 ASP D 111 " model vdw 2.521 3.040 ... (remaining 20321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.550 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2835 Z= 0.251 Angle : 0.639 7.955 3867 Z= 0.363 Chirality : 0.042 0.158 465 Planarity : 0.006 0.050 470 Dihedral : 11.756 70.125 927 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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: -1.07 (0.41), residues: 355 helix: 0.01 (0.31), residues: 225 sheet: -0.48 (0.64), residues: 64 loop : -3.07 (0.57), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 38 HIS 0.003 0.002 HIS A 146 PHE 0.013 0.001 PHE A 217 TYR 0.014 0.002 TYR A 228 ARG 0.003 0.001 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.282 Fit side-chains REVERT: A 281 SER cc_start: 0.8448 (t) cc_final: 0.8085 (m) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1108 time to fit residues: 4.8855 Evaluate side-chains 30 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.137981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.110353 restraints weight = 3240.454| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.84 r_work: 0.3011 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2835 Z= 0.238 Angle : 0.553 6.295 3867 Z= 0.307 Chirality : 0.040 0.125 465 Planarity : 0.005 0.041 470 Dihedral : 3.744 15.326 396 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.37 % Allowed : 6.72 % Favored : 92.91 % 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: 0.97 (0.44), residues: 355 helix: 1.57 (0.33), residues: 224 sheet: -0.08 (0.67), residues: 64 loop : -1.68 (0.73), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 106 HIS 0.003 0.002 HIS A 146 PHE 0.014 0.001 PHE A 213 TYR 0.014 0.001 TYR A 228 ARG 0.004 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.435 Fit side-chains REVERT: A 281 SER cc_start: 0.8310 (t) cc_final: 0.7891 (m) outliers start: 1 outliers final: 1 residues processed: 32 average time/residue: 0.1217 time to fit residues: 5.2801 Evaluate side-chains 33 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.139083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.111611 restraints weight = 3241.166| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.84 r_work: 0.2995 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2835 Z= 0.235 Angle : 0.529 5.217 3867 Z= 0.295 Chirality : 0.040 0.129 465 Planarity : 0.005 0.038 470 Dihedral : 3.675 14.615 396 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.12 % Allowed : 7.46 % Favored : 91.42 % 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: 1.60 (0.46), residues: 355 helix: 1.98 (0.33), residues: 225 sheet: 0.22 (0.68), residues: 64 loop : -1.26 (0.83), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 106 HIS 0.003 0.002 HIS A 146 PHE 0.014 0.001 PHE A 213 TYR 0.015 0.001 TYR A 228 ARG 0.004 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.307 Fit side-chains REVERT: A 281 SER cc_start: 0.8349 (t) cc_final: 0.7933 (m) outliers start: 3 outliers final: 3 residues processed: 34 average time/residue: 0.0992 time to fit residues: 4.6754 Evaluate side-chains 35 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain D residue 105 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.139405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.111906 restraints weight = 3262.253| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.83 r_work: 0.3012 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2835 Z= 0.217 Angle : 0.506 4.897 3867 Z= 0.283 Chirality : 0.039 0.127 465 Planarity : 0.004 0.037 470 Dihedral : 3.618 14.803 396 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.12 % Allowed : 10.07 % Favored : 88.81 % 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: 1.92 (0.46), residues: 355 helix: 2.14 (0.34), residues: 228 sheet: 0.32 (0.67), residues: 64 loop : -0.92 (0.87), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 106 HIS 0.003 0.002 HIS A 146 PHE 0.012 0.001 PHE A 213 TYR 0.014 0.001 TYR A 211 ARG 0.004 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.255 Fit side-chains REVERT: A 281 SER cc_start: 0.8318 (t) cc_final: 0.7913 (m) outliers start: 3 outliers final: 3 residues processed: 33 average time/residue: 0.1015 time to fit residues: 4.6662 Evaluate side-chains 35 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain D residue 105 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.0070 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.148964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.122292 restraints weight = 3168.111| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.92 r_work: 0.3239 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2835 Z= 0.161 Angle : 0.464 4.993 3867 Z= 0.259 Chirality : 0.038 0.118 465 Planarity : 0.004 0.036 470 Dihedral : 3.482 14.315 396 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.24 % Allowed : 10.07 % Favored : 87.69 % 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: 2.30 (0.47), residues: 355 helix: 2.43 (0.34), residues: 227 sheet: 0.39 (0.66), residues: 66 loop : -0.64 (0.91), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 106 HIS 0.002 0.001 HIS A 146 PHE 0.009 0.001 PHE A 213 TYR 0.012 0.001 TYR A 211 ARG 0.002 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.301 Fit side-chains REVERT: A 281 SER cc_start: 0.8001 (t) cc_final: 0.7617 (m) outliers start: 6 outliers final: 4 residues processed: 34 average time/residue: 0.1005 time to fit residues: 4.7275 Evaluate side-chains 34 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 299 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.0870 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.146760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.120405 restraints weight = 3160.749| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.87 r_work: 0.3232 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2835 Z= 0.199 Angle : 0.485 4.979 3867 Z= 0.270 Chirality : 0.039 0.121 465 Planarity : 0.004 0.037 470 Dihedral : 3.528 14.501 396 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.49 % Allowed : 11.57 % Favored : 86.94 % 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 (0.47), residues: 355 helix: 2.39 (0.34), residues: 228 sheet: 0.52 (0.67), residues: 66 loop : -0.61 (0.93), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 106 HIS 0.002 0.001 HIS A 146 PHE 0.011 0.001 PHE A 213 TYR 0.014 0.001 TYR A 228 ARG 0.003 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.308 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 31 average time/residue: 0.1082 time to fit residues: 4.5852 Evaluate side-chains 32 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 299 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 0.0970 chunk 6 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.147741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.120849 restraints weight = 3256.298| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.94 r_work: 0.3221 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2835 Z= 0.181 Angle : 0.472 4.963 3867 Z= 0.263 Chirality : 0.038 0.119 465 Planarity : 0.004 0.038 470 Dihedral : 3.491 14.232 396 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.49 % Allowed : 11.94 % Favored : 86.57 % 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 (0.47), residues: 355 helix: 2.48 (0.34), residues: 228 sheet: 0.69 (0.67), residues: 66 loop : -0.52 (0.94), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 106 HIS 0.002 0.001 HIS A 146 PHE 0.009 0.001 PHE A 213 TYR 0.013 0.001 TYR A 211 ARG 0.003 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.295 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 31 average time/residue: 0.1026 time to fit residues: 4.3741 Evaluate side-chains 32 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 299 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.0030 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.140816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.113542 restraints weight = 3227.384| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.82 r_work: 0.3041 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2835 Z= 0.172 Angle : 0.465 4.951 3867 Z= 0.259 Chirality : 0.038 0.117 465 Planarity : 0.004 0.037 470 Dihedral : 3.449 14.182 396 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.87 % Allowed : 12.31 % Favored : 85.82 % 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: 2.59 (0.47), residues: 355 helix: 2.54 (0.34), residues: 228 sheet: 0.79 (0.68), residues: 66 loop : -0.45 (0.94), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 106 HIS 0.002 0.001 HIS A 146 PHE 0.009 0.001 PHE A 213 TYR 0.013 0.001 TYR A 211 ARG 0.002 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.323 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 32 average time/residue: 0.1068 time to fit residues: 4.7269 Evaluate side-chains 32 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 299 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.135041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.106919 restraints weight = 3246.996| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.89 r_work: 0.3069 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2835 Z= 0.217 Angle : 0.497 4.964 3867 Z= 0.277 Chirality : 0.039 0.121 465 Planarity : 0.004 0.038 470 Dihedral : 3.533 14.429 396 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.49 % Allowed : 12.69 % Favored : 85.82 % 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: 2.47 (0.47), residues: 355 helix: 2.40 (0.34), residues: 228 sheet: 0.82 (0.68), residues: 66 loop : -0.43 (0.94), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 106 HIS 0.003 0.002 HIS A 146 PHE 0.011 0.001 PHE A 272 TYR 0.015 0.001 TYR A 228 ARG 0.004 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.312 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 32 average time/residue: 0.1039 time to fit residues: 4.6027 Evaluate side-chains 33 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 299 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 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 = 0.3659 r_free = 0.3659 target = 0.145873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.119084 restraints weight = 3215.237| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.91 r_work: 0.3196 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2835 Z= 0.211 Angle : 0.493 4.970 3867 Z= 0.275 Chirality : 0.039 0.121 465 Planarity : 0.004 0.038 470 Dihedral : 3.556 14.219 396 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.49 % Allowed : 12.69 % Favored : 85.82 % 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: 2.50 (0.47), residues: 355 helix: 2.42 (0.34), residues: 228 sheet: 0.91 (0.68), residues: 66 loop : -0.48 (0.92), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 106 HIS 0.003 0.001 HIS A 146 PHE 0.011 0.001 PHE A 272 TYR 0.014 0.001 TYR A 228 ARG 0.004 0.000 ARG A 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.323 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 32 average time/residue: 0.1164 time to fit residues: 5.0338 Evaluate side-chains 33 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 299 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.0770 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 15 optimal weight: 0.0070 chunk 7 optimal weight: 0.6980 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.150586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124101 restraints weight = 3138.559| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.90 r_work: 0.3288 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2835 Z= 0.146 Angle : 0.445 4.943 3867 Z= 0.248 Chirality : 0.038 0.115 465 Planarity : 0.004 0.035 470 Dihedral : 3.397 13.886 396 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.49 % Allowed : 12.69 % Favored : 85.82 % 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: 2.81 (0.47), residues: 355 helix: 2.68 (0.34), residues: 228 sheet: 0.95 (0.69), residues: 66 loop : -0.34 (0.93), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 106 HIS 0.001 0.001 HIS A 146 PHE 0.008 0.001 PHE A 213 TYR 0.012 0.001 TYR A 211 ARG 0.001 0.000 ARG A 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1778.09 seconds wall clock time: 32 minutes 26.38 seconds (1946.38 seconds total)