Starting phenix.real_space_refine on Fri Aug 22 13:46:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hiz_34830/08_2025/8hiz_34830_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hiz_34830/08_2025/8hiz_34830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hiz_34830/08_2025/8hiz_34830_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hiz_34830/08_2025/8hiz_34830_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hiz_34830/08_2025/8hiz_34830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hiz_34830/08_2025/8hiz_34830.map" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2083 2.51 5 N 553 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3274 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3226 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.13, per 1000 atoms: 0.35 Number of scatterers: 3274 At special positions: 0 Unit cell: (67.048, 73.95, 71.978, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 3 15.00 O 621 8.00 N 553 7.00 C 2083 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: 0.19 Conformation dependent library (CDL) restraints added in 88.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 758 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 54.1% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 Processing helix chain 'A' and resid 24 through 33 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.701A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.914A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 206 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 302 through 307 removed outlier: 4.410A pdb=" N ASP A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 344 through 361 removed outlier: 4.497A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 394 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.533A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 279 removed outlier: 6.473A pdb=" N ILE A 215 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 243 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 187 hydrogen bonds defined for protein. 546 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: 0.53 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1063 1.35 - 1.46: 766 1.46 - 1.58: 1490 1.58 - 1.70: 5 1.70 - 1.81: 27 Bond restraints: 3351 Sorted by residual: bond pdb=" O2B NAP A 501 " pdb=" P2B NAP A 501 " ideal model delta sigma weight residual 1.736 1.614 0.122 2.00e-02 2.50e+03 3.69e+01 bond pdb=" N LYS A 213 " pdb=" CA LYS A 213 " ideal model delta sigma weight residual 1.453 1.486 -0.032 1.27e-02 6.20e+03 6.40e+00 bond pdb=" C1D NAP A 501 " pdb=" O4D NAP A 501 " ideal model delta sigma weight residual 1.375 1.425 -0.050 2.00e-02 2.50e+03 6.13e+00 bond pdb=" C5D NAP A 501 " pdb=" O5D NAP A 501 " ideal model delta sigma weight residual 1.403 1.449 -0.046 2.00e-02 2.50e+03 5.38e+00 bond pdb=" O5D NAP A 501 " pdb=" PN NAP A 501 " ideal model delta sigma weight residual 1.649 1.604 0.045 2.00e-02 2.50e+03 5.04e+00 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 4376 1.53 - 3.07: 142 3.07 - 4.60: 36 4.60 - 6.14: 3 6.14 - 7.67: 4 Bond angle restraints: 4561 Sorted by residual: angle pdb=" O GLY A 212 " pdb=" C GLY A 212 " pdb=" N LYS A 213 " ideal model delta sigma weight residual 122.41 126.80 -4.39 1.25e+00 6.40e-01 1.23e+01 angle pdb=" CA GLY A 212 " pdb=" C GLY A 212 " pdb=" N LYS A 213 " ideal model delta sigma weight residual 118.42 114.17 4.25 1.26e+00 6.30e-01 1.14e+01 angle pdb=" C VAL A 146 " pdb=" N TYR A 147 " pdb=" CA TYR A 147 " ideal model delta sigma weight residual 123.05 127.62 -4.57 1.57e+00 4.06e-01 8.47e+00 angle pdb=" CA GLY A 254 " pdb=" C GLY A 254 " pdb=" N LEU A 255 " ideal model delta sigma weight residual 114.23 116.53 -2.30 8.80e-01 1.29e+00 6.83e+00 angle pdb=" C2B NAP A 501 " pdb=" O2B NAP A 501 " pdb=" P2B NAP A 501 " ideal model delta sigma weight residual 117.19 109.52 7.67 3.00e+00 1.11e-01 6.54e+00 ... (remaining 4556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 1787 17.73 - 35.45: 180 35.45 - 53.18: 41 53.18 - 70.90: 17 70.90 - 88.63: 7 Dihedral angle restraints: 2032 sinusoidal: 843 harmonic: 1189 Sorted by residual: dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 164.56 15.44 0 5.00e+00 4.00e-02 9.53e+00 dihedral pdb=" CA LYS A 213 " pdb=" CB LYS A 213 " pdb=" CG LYS A 213 " pdb=" CD LYS A 213 " ideal model delta sinusoidal sigma weight residual -60.00 -114.74 54.74 3 1.50e+01 4.44e-03 9.30e+00 dihedral pdb=" CB LYS A 167 " pdb=" CG LYS A 167 " pdb=" CD LYS A 167 " pdb=" CE LYS A 167 " ideal model delta sinusoidal sigma weight residual 60.00 114.59 -54.59 3 1.50e+01 4.44e-03 9.29e+00 ... (remaining 2029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 288 0.026 - 0.053: 120 0.053 - 0.079: 46 0.079 - 0.105: 33 0.105 - 0.131: 14 Chirality restraints: 501 Sorted by residual: chirality pdb=" CA ILE A 37 " pdb=" N ILE A 37 " pdb=" C ILE A 37 " pdb=" CB ILE A 37 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE A 108 " pdb=" N ILE A 108 " pdb=" C ILE A 108 " pdb=" CB ILE A 108 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA PRO A 150 " pdb=" N PRO A 150 " pdb=" C PRO A 150 " pdb=" CB PRO A 150 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.62e-01 ... (remaining 498 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAP A 501 " -0.002 2.00e-02 2.50e+03 3.33e-02 2.22e+01 pdb=" C2N NAP A 501 " 0.023 2.00e-02 2.50e+03 pdb=" C3N NAP A 501 " 0.015 2.00e-02 2.50e+03 pdb=" C4N NAP A 501 " 0.064 2.00e-02 2.50e+03 pdb=" C5N NAP A 501 " -0.043 2.00e-02 2.50e+03 pdb=" C6N NAP A 501 " -0.014 2.00e-02 2.50e+03 pdb=" C7N NAP A 501 " -0.045 2.00e-02 2.50e+03 pdb=" N1N NAP A 501 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO A 142 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 212 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C GLY A 212 " 0.028 2.00e-02 2.50e+03 pdb=" O GLY A 212 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS A 213 " -0.010 2.00e-02 2.50e+03 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1056 2.84 - 3.35: 3369 3.35 - 3.87: 5827 3.87 - 4.38: 6598 4.38 - 4.90: 11179 Nonbonded interactions: 28029 Sorted by model distance: nonbonded pdb=" ND1 HIS A 388 " pdb=" O ILE A 393 " model vdw 2.324 3.120 nonbonded pdb=" OD2 ASP A 244 " pdb=" OG SER A 269 " model vdw 2.329 3.040 nonbonded pdb=" O PHE A 171 " pdb=" NZ LYS A 177 " model vdw 2.356 3.120 nonbonded pdb=" OE1 GLU A 383 " pdb=" NH2 ARG A 406 " model vdw 2.357 3.120 nonbonded pdb=" N ILE A 4 " pdb=" OG SER A 81 " model vdw 2.379 3.120 ... (remaining 28024 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.370 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 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 0.122 3351 Z= 0.220 Angle : 0.703 7.671 4561 Z= 0.393 Chirality : 0.042 0.131 501 Planarity : 0.005 0.048 579 Dihedral : 16.641 88.630 1274 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.30 % Allowed : 0.00 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.44), residues: 414 helix: 2.04 (0.36), residues: 211 sheet: -0.07 (0.66), residues: 70 loop : 0.02 (0.59), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 16 TYR 0.018 0.001 TYR A 250 PHE 0.012 0.001 PHE A 381 TRP 0.018 0.001 TRP A 355 HIS 0.001 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 3351) covalent geometry : angle 0.70280 ( 4561) hydrogen bonds : bond 0.10260 ( 187) hydrogen bonds : angle 4.76878 ( 546) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.130 Fit side-chains REVERT: A 30 TRP cc_start: 0.8868 (t-100) cc_final: 0.8645 (t-100) REVERT: A 218 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7876 (tp40) REVERT: A 332 GLU cc_start: 0.7669 (pp20) cc_final: 0.7407 (pp20) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.0636 time to fit residues: 5.4970 Evaluate side-chains 57 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.162639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.138055 restraints weight = 6151.597| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.53 r_work: 0.3697 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3351 Z= 0.122 Angle : 0.530 8.858 4561 Z= 0.268 Chirality : 0.043 0.131 501 Planarity : 0.004 0.044 579 Dihedral : 11.013 65.568 517 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.61 % Allowed : 6.67 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.43), residues: 414 helix: 2.14 (0.36), residues: 211 sheet: -0.10 (0.67), residues: 72 loop : -0.27 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 16 TYR 0.012 0.001 TYR A 160 PHE 0.009 0.001 PHE A 381 TRP 0.015 0.001 TRP A 355 HIS 0.006 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 3351) covalent geometry : angle 0.53042 ( 4561) hydrogen bonds : bond 0.03500 ( 187) hydrogen bonds : angle 4.14266 ( 546) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.128 Fit side-chains REVERT: A 218 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7802 (tp40) REVERT: A 251 ASN cc_start: 0.8316 (t0) cc_final: 0.8078 (t0) outliers start: 2 outliers final: 0 residues processed: 64 average time/residue: 0.0670 time to fit residues: 5.2610 Evaluate side-chains 56 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.158111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.133093 restraints weight = 6097.045| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.52 r_work: 0.3627 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3351 Z= 0.175 Angle : 0.540 5.494 4561 Z= 0.277 Chirality : 0.043 0.131 501 Planarity : 0.004 0.044 579 Dihedral : 9.791 67.725 517 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.82 % Allowed : 7.58 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.43), residues: 414 helix: 1.87 (0.36), residues: 211 sheet: -0.39 (0.66), residues: 71 loop : -0.27 (0.57), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 16 TYR 0.013 0.001 TYR A 160 PHE 0.011 0.001 PHE A 381 TRP 0.014 0.002 TRP A 355 HIS 0.006 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 3351) covalent geometry : angle 0.54026 ( 4561) hydrogen bonds : bond 0.03772 ( 187) hydrogen bonds : angle 4.22283 ( 546) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.127 Fit side-chains REVERT: A 145 ASP cc_start: 0.8359 (t0) cc_final: 0.8158 (t0) outliers start: 6 outliers final: 3 residues processed: 61 average time/residue: 0.0703 time to fit residues: 5.2232 Evaluate side-chains 51 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.157274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.131698 restraints weight = 6065.899| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.51 r_work: 0.3610 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3351 Z= 0.190 Angle : 0.590 10.378 4561 Z= 0.297 Chirality : 0.044 0.239 501 Planarity : 0.004 0.046 579 Dihedral : 8.992 54.565 517 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.52 % Allowed : 12.42 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.43), residues: 414 helix: 1.76 (0.36), residues: 211 sheet: -0.19 (0.67), residues: 69 loop : -0.32 (0.57), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 16 TYR 0.010 0.001 TYR A 363 PHE 0.014 0.001 PHE A 381 TRP 0.016 0.002 TRP A 355 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 3351) covalent geometry : angle 0.59003 ( 4561) hydrogen bonds : bond 0.03821 ( 187) hydrogen bonds : angle 4.28759 ( 546) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.080 Fit side-chains REVERT: A 337 GLN cc_start: 0.8238 (pt0) cc_final: 0.7934 (pt0) outliers start: 5 outliers final: 2 residues processed: 60 average time/residue: 0.0680 time to fit residues: 5.0057 Evaluate side-chains 55 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.0570 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 30.0000 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.157988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.132716 restraints weight = 6055.040| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.52 r_work: 0.3625 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3351 Z= 0.154 Angle : 0.558 10.642 4561 Z= 0.280 Chirality : 0.043 0.234 501 Planarity : 0.004 0.048 579 Dihedral : 8.405 56.047 517 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.21 % Allowed : 14.85 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.43), residues: 414 helix: 1.84 (0.36), residues: 211 sheet: -0.09 (0.68), residues: 69 loop : -0.31 (0.57), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 16 TYR 0.008 0.001 TYR A 363 PHE 0.014 0.001 PHE A 381 TRP 0.016 0.001 TRP A 355 HIS 0.007 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 3351) covalent geometry : angle 0.55815 ( 4561) hydrogen bonds : bond 0.03620 ( 187) hydrogen bonds : angle 4.25239 ( 546) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.129 Fit side-chains REVERT: A 145 ASP cc_start: 0.8374 (t0) cc_final: 0.8115 (t0) outliers start: 4 outliers final: 4 residues processed: 63 average time/residue: 0.0677 time to fit residues: 5.2188 Evaluate side-chains 60 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 22 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN A 267 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.157704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.132130 restraints weight = 6081.614| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.54 r_work: 0.3618 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 3351 Z= 0.162 Angle : 0.572 10.464 4561 Z= 0.284 Chirality : 0.043 0.189 501 Planarity : 0.004 0.047 579 Dihedral : 7.934 52.017 517 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.82 % Allowed : 16.36 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.43), residues: 414 helix: 1.81 (0.36), residues: 211 sheet: -0.40 (0.68), residues: 64 loop : -0.32 (0.57), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 331 TYR 0.009 0.001 TYR A 363 PHE 0.015 0.001 PHE A 381 TRP 0.016 0.001 TRP A 355 HIS 0.007 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 3351) covalent geometry : angle 0.57153 ( 4561) hydrogen bonds : bond 0.03669 ( 187) hydrogen bonds : angle 4.27433 ( 546) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.084 Fit side-chains REVERT: A 145 ASP cc_start: 0.8378 (t0) cc_final: 0.8136 (t0) outliers start: 6 outliers final: 5 residues processed: 62 average time/residue: 0.0688 time to fit residues: 5.2301 Evaluate side-chains 61 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.159708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.134219 restraints weight = 6144.196| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.55 r_work: 0.3650 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3351 Z= 0.128 Angle : 0.552 8.674 4561 Z= 0.275 Chirality : 0.043 0.180 501 Planarity : 0.004 0.048 579 Dihedral : 7.689 49.116 517 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.91 % Allowed : 16.67 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.43), residues: 414 helix: 1.84 (0.36), residues: 212 sheet: -0.41 (0.68), residues: 64 loop : -0.32 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 16 TYR 0.007 0.001 TYR A 363 PHE 0.014 0.001 PHE A 381 TRP 0.016 0.001 TRP A 355 HIS 0.008 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3351) covalent geometry : angle 0.55228 ( 4561) hydrogen bonds : bond 0.03503 ( 187) hydrogen bonds : angle 4.25462 ( 546) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.117 Fit side-chains REVERT: A 145 ASP cc_start: 0.8348 (t0) cc_final: 0.8075 (t0) outliers start: 3 outliers final: 3 residues processed: 61 average time/residue: 0.0689 time to fit residues: 5.1975 Evaluate side-chains 59 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 206 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.158230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.132905 restraints weight = 6185.402| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.55 r_work: 0.3631 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3351 Z= 0.152 Angle : 0.581 11.253 4561 Z= 0.286 Chirality : 0.043 0.160 501 Planarity : 0.004 0.048 579 Dihedral : 7.537 53.793 517 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.52 % Allowed : 17.58 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.43), residues: 414 helix: 1.77 (0.36), residues: 211 sheet: -0.17 (0.70), residues: 59 loop : -0.39 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 331 TYR 0.008 0.001 TYR A 363 PHE 0.012 0.001 PHE A 381 TRP 0.015 0.001 TRP A 355 HIS 0.007 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 3351) covalent geometry : angle 0.58054 ( 4561) hydrogen bonds : bond 0.03620 ( 187) hydrogen bonds : angle 4.28633 ( 546) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.133 Fit side-chains REVERT: A 145 ASP cc_start: 0.8441 (t0) cc_final: 0.8170 (t0) outliers start: 5 outliers final: 5 residues processed: 59 average time/residue: 0.0550 time to fit residues: 4.0325 Evaluate side-chains 58 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.160629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.135193 restraints weight = 6091.506| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.55 r_work: 0.3656 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3351 Z= 0.122 Angle : 0.567 10.138 4561 Z= 0.281 Chirality : 0.043 0.167 501 Planarity : 0.004 0.049 579 Dihedral : 7.413 55.739 517 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.52 % Allowed : 17.88 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.43), residues: 414 helix: 1.67 (0.36), residues: 212 sheet: -0.43 (0.68), residues: 64 loop : -0.36 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 331 TYR 0.006 0.001 TYR A 363 PHE 0.012 0.001 PHE A 381 TRP 0.018 0.001 TRP A 355 HIS 0.008 0.002 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3351) covalent geometry : angle 0.56728 ( 4561) hydrogen bonds : bond 0.03424 ( 187) hydrogen bonds : angle 4.29883 ( 546) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.082 Fit side-chains REVERT: A 145 ASP cc_start: 0.8432 (t0) cc_final: 0.8209 (t0) outliers start: 5 outliers final: 4 residues processed: 59 average time/residue: 0.0628 time to fit residues: 4.5796 Evaluate side-chains 58 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 33 optimal weight: 0.4980 chunk 27 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.161413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.136345 restraints weight = 6013.010| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.52 r_work: 0.3669 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3351 Z= 0.119 Angle : 0.568 9.776 4561 Z= 0.281 Chirality : 0.043 0.160 501 Planarity : 0.004 0.049 579 Dihedral : 7.307 57.585 517 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.91 % Allowed : 19.09 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.43), residues: 414 helix: 1.70 (0.36), residues: 212 sheet: -0.42 (0.69), residues: 64 loop : -0.40 (0.55), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 16 TYR 0.006 0.001 TYR A 363 PHE 0.012 0.001 PHE A 381 TRP 0.018 0.001 TRP A 355 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3351) covalent geometry : angle 0.56836 ( 4561) hydrogen bonds : bond 0.03400 ( 187) hydrogen bonds : angle 4.26540 ( 546) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.130 Fit side-chains REVERT: A 145 ASP cc_start: 0.8428 (t0) cc_final: 0.8219 (t0) REVERT: A 299 GLU cc_start: 0.8427 (mp0) cc_final: 0.7653 (mp0) outliers start: 3 outliers final: 3 residues processed: 57 average time/residue: 0.0693 time to fit residues: 4.9031 Evaluate side-chains 59 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 267 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 0.0370 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 28 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN A 193 GLN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.162093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.136991 restraints weight = 6126.486| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.55 r_work: 0.3676 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3351 Z= 0.114 Angle : 0.584 9.379 4561 Z= 0.285 Chirality : 0.043 0.160 501 Planarity : 0.004 0.050 579 Dihedral : 7.273 59.168 517 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.91 % Allowed : 19.70 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.43), residues: 414 helix: 1.65 (0.36), residues: 212 sheet: -0.21 (0.70), residues: 61 loop : -0.47 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 16 TYR 0.005 0.001 TYR A 363 PHE 0.011 0.001 PHE A 381 TRP 0.019 0.001 TRP A 355 HIS 0.014 0.002 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 3351) covalent geometry : angle 0.58357 ( 4561) hydrogen bonds : bond 0.03290 ( 187) hydrogen bonds : angle 4.26217 ( 546) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 952.04 seconds wall clock time: 17 minutes 5.38 seconds (1025.38 seconds total)