Starting phenix.real_space_refine on Fri Aug 22 13:46:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hho_34805/08_2025/8hho_34805_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hho_34805/08_2025/8hho_34805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hho_34805/08_2025/8hho_34805_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hho_34805/08_2025/8hho_34805_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hho_34805/08_2025/8hho_34805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hho_34805/08_2025/8hho_34805.map" } resolution = 3.2 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: 1.23, per 1000 atoms: 0.38 Number of scatterers: 3274 At special positions: 0 Unit cell: (67.048, 72.964, 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: 0.27 Conformation dependent library (CDL) restraints added in 88.9 milliseconds Enol-peptide restraints added in 238.4 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: 17 helices and 2 sheets defined 55.0% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 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: 3.730A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.839A 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: 3.928A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 221 through 235 Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.653A pdb=" N VAL A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 339 through 344 removed outlier: 3.536A pdb=" N ASN A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 394 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.451A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA A 143 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY A 70 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 279 removed outlier: 6.213A pdb=" N ILE A 215 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 243 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 182 hydrogen bonds defined for protein. 525 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: 0.60 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1047 1.34 - 1.45: 426 1.45 - 1.57: 1846 1.57 - 1.69: 5 1.69 - 1.80: 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 1.611 0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C4A NAP A 501 " pdb=" C5A NAP A 501 " ideal model delta sigma weight residual 1.385 1.471 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C5A NAP A 501 " pdb=" C6A NAP A 501 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C8A NAP A 501 " pdb=" N7A NAP A 501 " ideal model delta sigma weight residual 1.301 1.359 -0.058 2.00e-02 2.50e+03 8.27e+00 bond pdb=" C1D NAP A 501 " pdb=" O4D NAP A 501 " ideal model delta sigma weight residual 1.375 1.430 -0.055 2.00e-02 2.50e+03 7.61e+00 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 4399 1.81 - 3.61: 131 3.61 - 5.42: 23 5.42 - 7.22: 5 7.22 - 9.03: 3 Bond angle restraints: 4561 Sorted by residual: angle pdb=" C VAL A 146 " pdb=" N TYR A 147 " pdb=" CA TYR A 147 " ideal model delta sigma weight residual 122.40 127.84 -5.44 1.45e+00 4.76e-01 1.41e+01 angle pdb=" N GLY A 70 " pdb=" CA GLY A 70 " pdb=" C GLY A 70 " ideal model delta sigma weight residual 110.87 116.17 -5.30 1.54e+00 4.22e-01 1.19e+01 angle pdb=" C2A NAP A 501 " pdb=" N3A NAP A 501 " pdb=" C4A NAP A 501 " ideal model delta sigma weight residual 111.82 120.85 -9.03 3.00e+00 1.11e-01 9.06e+00 angle pdb=" CA GLU A 233 " pdb=" CB GLU A 233 " pdb=" CG GLU A 233 " ideal model delta sigma weight residual 114.10 119.49 -5.39 2.00e+00 2.50e-01 7.25e+00 angle pdb=" PA NAP A 501 " pdb=" O3 NAP A 501 " pdb=" PN NAP A 501 " ideal model delta sigma weight residual 128.45 120.55 7.90 3.00e+00 1.11e-01 6.93e+00 ... (remaining 4556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1792 17.95 - 35.90: 179 35.90 - 53.84: 53 53.84 - 71.79: 3 71.79 - 89.74: 5 Dihedral angle restraints: 2032 sinusoidal: 843 harmonic: 1189 Sorted by residual: dihedral pdb=" CA MET A 153 " pdb=" C MET A 153 " pdb=" N GLY A 154 " pdb=" CA GLY A 154 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 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 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CB GLU A 316 " pdb=" CG GLU A 316 " pdb=" CD GLU A 316 " pdb=" OE1 GLU A 316 " ideal model delta sinusoidal sigma weight residual 0.00 89.74 -89.74 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 2029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 370 0.044 - 0.088: 89 0.088 - 0.132: 38 0.132 - 0.176: 1 0.176 - 0.220: 3 Chirality restraints: 501 Sorted by residual: chirality pdb=" C2B NAP A 501 " pdb=" C1B NAP A 501 " pdb=" C3B NAP A 501 " pdb=" O2B NAP A 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.54 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C1B NAP A 501 " pdb=" C2B NAP A 501 " pdb=" N9A NAP A 501 " pdb=" O4B NAP A 501 " both_signs ideal model delta sigma weight residual False 2.31 2.52 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C3D NAP A 501 " pdb=" C2D NAP A 501 " pdb=" C4D NAP A 501 " pdb=" O3D NAP A 501 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.20 2.00e-01 2.50e+01 9.62e-01 ... (remaining 498 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 75 " -0.032 5.00e-02 4.00e+02 4.95e-02 3.91e+00 pdb=" N PRO A 76 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO A 142 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 396 " -0.129 9.50e-02 1.11e+02 5.82e-02 2.33e+00 pdb=" NE ARG A 396 " 0.005 2.00e-02 2.50e+03 pdb=" CZ ARG A 396 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 396 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 396 " -0.008 2.00e-02 2.50e+03 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 133 2.72 - 3.26: 3421 3.26 - 3.81: 5773 3.81 - 4.35: 7046 4.35 - 4.90: 11574 Nonbonded interactions: 27947 Sorted by model distance: nonbonded pdb=" O2N NAP A 501 " pdb=" O3D NAP A 501 " model vdw 2.169 3.040 nonbonded pdb=" NH2 ARG A 65 " pdb=" OD1 ASP A 98 " model vdw 2.268 3.120 nonbonded pdb=" ND2 ASN A 251 " pdb=" O GLY A 275 " model vdw 2.268 3.120 nonbonded pdb=" ND1 HIS A 388 " pdb=" O ILE A 393 " model vdw 2.295 3.120 nonbonded pdb=" NZ LYS A 105 " pdb=" OD2 ASP A 145 " model vdw 2.310 3.120 ... (remaining 27942 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: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.900 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.005 0.125 3351 Z= 0.250 Angle : 0.764 9.028 4561 Z= 0.415 Chirality : 0.045 0.220 501 Planarity : 0.005 0.058 579 Dihedral : 15.654 89.740 1274 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.30 % Allowed : 0.61 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.42), residues: 414 helix: 1.92 (0.37), residues: 210 sheet: 0.99 (0.69), residues: 61 loop : -0.23 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 396 TYR 0.018 0.001 TYR A 385 PHE 0.004 0.001 PHE A 381 TRP 0.008 0.001 TRP A 92 HIS 0.006 0.002 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 3351) covalent geometry : angle 0.76407 ( 4561) hydrogen bonds : bond 0.10375 ( 182) hydrogen bonds : angle 5.21396 ( 525) *********************** 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 74 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.081 Fit side-chains REVERT: A 385 TYR cc_start: 0.7648 (t80) cc_final: 0.7294 (t80) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.0636 time to fit residues: 5.6537 Evaluate side-chains 61 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.073 ------------------------------------------------------------------------------- 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: 0.0670 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN A 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.136536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.116015 restraints weight = 7074.434| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.61 r_work: 0.3459 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3351 Z= 0.195 Angle : 0.612 6.467 4561 Z= 0.322 Chirality : 0.046 0.163 501 Planarity : 0.005 0.042 579 Dihedral : 9.902 87.999 517 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.82 % Allowed : 10.30 % Favored : 87.88 % 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: 1.54 (0.42), residues: 414 helix: 2.05 (0.36), residues: 208 sheet: 0.74 (0.69), residues: 61 loop : -0.32 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 65 TYR 0.022 0.002 TYR A 250 PHE 0.012 0.001 PHE A 381 TRP 0.022 0.002 TRP A 263 HIS 0.005 0.002 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 3351) covalent geometry : angle 0.61155 ( 4561) hydrogen bonds : bond 0.04001 ( 182) hydrogen bonds : angle 4.72877 ( 525) *********************** 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 76 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: A 249 ILE cc_start: 0.7615 (mm) cc_final: 0.7149 (mt) REVERT: A 263 TRP cc_start: 0.7752 (t-100) cc_final: 0.7436 (t-100) REVERT: A 367 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8006 (mm-30) outliers start: 6 outliers final: 1 residues processed: 72 average time/residue: 0.0673 time to fit residues: 5.8582 Evaluate side-chains 63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.0670 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.139074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.118637 restraints weight = 6986.571| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.68 r_work: 0.3493 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3351 Z= 0.124 Angle : 0.561 8.254 4561 Z= 0.292 Chirality : 0.044 0.155 501 Planarity : 0.004 0.041 579 Dihedral : 8.943 81.274 517 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.52 % Allowed : 11.52 % Favored : 86.97 % 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: 1.53 (0.42), residues: 414 helix: 1.97 (0.35), residues: 208 sheet: 0.89 (0.70), residues: 61 loop : -0.30 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.019 0.001 TYR A 250 PHE 0.008 0.001 PHE A 381 TRP 0.015 0.001 TRP A 263 HIS 0.004 0.002 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3351) covalent geometry : angle 0.56140 ( 4561) hydrogen bonds : bond 0.03517 ( 182) hydrogen bonds : angle 4.60247 ( 525) *********************** 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 78 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.114 Fit side-chains REVERT: A 263 TRP cc_start: 0.7814 (t-100) cc_final: 0.7428 (t-100) REVERT: A 283 GLU cc_start: 0.8127 (tt0) cc_final: 0.7892 (tp30) REVERT: A 366 GLU cc_start: 0.8597 (pm20) cc_final: 0.8335 (pm20) REVERT: A 367 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7917 (mm-30) outliers start: 5 outliers final: 3 residues processed: 76 average time/residue: 0.0622 time to fit residues: 5.7841 Evaluate side-chains 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 0.0170 chunk 28 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.139351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.119044 restraints weight = 6946.214| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.57 r_work: 0.3502 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3351 Z= 0.129 Angle : 0.547 5.761 4561 Z= 0.288 Chirality : 0.044 0.151 501 Planarity : 0.004 0.041 579 Dihedral : 8.396 81.226 517 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.12 % Allowed : 15.15 % Favored : 82.73 % 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: 1.80 (0.43), residues: 414 helix: 2.14 (0.35), residues: 202 sheet: 1.00 (0.68), residues: 66 loop : 0.01 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 396 TYR 0.017 0.001 TYR A 250 PHE 0.009 0.001 PHE A 57 TRP 0.016 0.001 TRP A 92 HIS 0.005 0.002 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3351) covalent geometry : angle 0.54742 ( 4561) hydrogen bonds : bond 0.03484 ( 182) hydrogen bonds : angle 4.51609 ( 525) *********************** 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 76 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 251 ASN cc_start: 0.8714 (t0) cc_final: 0.8467 (t0) REVERT: A 263 TRP cc_start: 0.7782 (t-100) cc_final: 0.7412 (t-100) REVERT: A 367 GLU cc_start: 0.8254 (mm-30) cc_final: 0.8003 (mm-30) outliers start: 7 outliers final: 4 residues processed: 73 average time/residue: 0.0644 time to fit residues: 5.7124 Evaluate side-chains 68 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 4 optimal weight: 0.0060 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.134561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.113775 restraints weight = 6986.272| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.54 r_work: 0.3419 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3351 Z= 0.211 Angle : 0.640 7.468 4561 Z= 0.330 Chirality : 0.046 0.183 501 Planarity : 0.005 0.043 579 Dihedral : 8.185 83.165 517 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.42 % Allowed : 14.55 % Favored : 83.03 % 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: 1.58 (0.42), residues: 414 helix: 2.03 (0.36), residues: 202 sheet: 0.63 (0.66), residues: 66 loop : -0.07 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 396 TYR 0.014 0.002 TYR A 250 PHE 0.011 0.002 PHE A 381 TRP 0.015 0.002 TRP A 92 HIS 0.005 0.002 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 3351) covalent geometry : angle 0.64027 ( 4561) hydrogen bonds : bond 0.03874 ( 182) hydrogen bonds : angle 4.71628 ( 525) *********************** 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 74 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.8517 (t80) cc_final: 0.8281 (t80) REVERT: A 251 ASN cc_start: 0.8721 (t0) cc_final: 0.8290 (t0) REVERT: A 263 TRP cc_start: 0.7812 (t-100) cc_final: 0.7602 (t-100) REVERT: A 366 GLU cc_start: 0.8611 (pm20) cc_final: 0.8377 (pm20) REVERT: A 367 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7906 (mm-30) outliers start: 8 outliers final: 7 residues processed: 70 average time/residue: 0.0641 time to fit residues: 5.4307 Evaluate side-chains 70 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 314 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: 0.9980 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.135748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.115277 restraints weight = 6995.214| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.54 r_work: 0.3442 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3351 Z= 0.159 Angle : 0.589 7.464 4561 Z= 0.305 Chirality : 0.045 0.184 501 Planarity : 0.005 0.043 579 Dihedral : 7.982 82.921 517 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.82 % Allowed : 15.76 % 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: 1.48 (0.42), residues: 414 helix: 2.02 (0.36), residues: 202 sheet: 0.46 (0.68), residues: 61 loop : -0.16 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 396 TYR 0.016 0.002 TYR A 250 PHE 0.010 0.001 PHE A 381 TRP 0.014 0.001 TRP A 92 HIS 0.006 0.002 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 3351) covalent geometry : angle 0.58925 ( 4561) hydrogen bonds : bond 0.03684 ( 182) hydrogen bonds : angle 4.66460 ( 525) *********************** 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 71 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 ASN cc_start: 0.8709 (t0) cc_final: 0.8311 (t0) REVERT: A 263 TRP cc_start: 0.7947 (t-100) cc_final: 0.7708 (t-100) REVERT: A 367 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7912 (mm-30) outliers start: 6 outliers final: 4 residues processed: 69 average time/residue: 0.0631 time to fit residues: 5.2619 Evaluate side-chains 66 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.136080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.115873 restraints weight = 7038.272| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.65 r_work: 0.3447 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3351 Z= 0.142 Angle : 0.572 6.980 4561 Z= 0.298 Chirality : 0.044 0.174 501 Planarity : 0.005 0.044 579 Dihedral : 7.842 82.804 517 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.52 % Allowed : 16.36 % Favored : 82.12 % 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: 1.49 (0.42), residues: 414 helix: 2.06 (0.36), residues: 202 sheet: 0.49 (0.68), residues: 61 loop : -0.22 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 396 TYR 0.016 0.001 TYR A 250 PHE 0.009 0.001 PHE A 381 TRP 0.012 0.001 TRP A 263 HIS 0.005 0.002 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 3351) covalent geometry : angle 0.57160 ( 4561) hydrogen bonds : bond 0.03587 ( 182) hydrogen bonds : angle 4.62649 ( 525) *********************** 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 70 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: A 251 ASN cc_start: 0.8693 (t0) cc_final: 0.8373 (t0) REVERT: A 263 TRP cc_start: 0.7827 (t-100) cc_final: 0.7593 (t-100) REVERT: A 367 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7988 (mm-30) outliers start: 5 outliers final: 4 residues processed: 69 average time/residue: 0.0631 time to fit residues: 5.2605 Evaluate side-chains 66 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.137439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.117099 restraints weight = 7119.784| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.55 r_work: 0.3469 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3351 Z= 0.134 Angle : 0.584 7.272 4561 Z= 0.304 Chirality : 0.044 0.170 501 Planarity : 0.005 0.043 579 Dihedral : 7.763 82.673 517 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.82 % Allowed : 17.27 % 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: 1.48 (0.42), residues: 414 helix: 2.04 (0.36), residues: 202 sheet: 0.53 (0.67), residues: 61 loop : -0.24 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 396 TYR 0.016 0.001 TYR A 250 PHE 0.009 0.001 PHE A 381 TRP 0.044 0.002 TRP A 92 HIS 0.006 0.002 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 3351) covalent geometry : angle 0.58379 ( 4561) hydrogen bonds : bond 0.03546 ( 182) hydrogen bonds : angle 4.64321 ( 525) *********************** 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 73 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: A 251 ASN cc_start: 0.8679 (t0) cc_final: 0.8301 (t0) REVERT: A 263 TRP cc_start: 0.7913 (t-100) cc_final: 0.7704 (t-100) REVERT: A 367 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7951 (mm-30) REVERT: A 396 ARG cc_start: 0.7618 (mtm180) cc_final: 0.7064 (mtm180) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.0568 time to fit residues: 4.9526 Evaluate side-chains 69 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.137841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.117576 restraints weight = 6987.912| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.65 r_work: 0.3478 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3351 Z= 0.129 Angle : 0.565 6.934 4561 Z= 0.295 Chirality : 0.044 0.166 501 Planarity : 0.005 0.043 579 Dihedral : 7.632 82.343 517 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % 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: 1.47 (0.42), residues: 414 helix: 2.04 (0.36), residues: 202 sheet: 0.61 (0.68), residues: 61 loop : -0.29 (0.52), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 396 TYR 0.017 0.001 TYR A 250 PHE 0.012 0.001 PHE A 381 TRP 0.041 0.002 TRP A 92 HIS 0.006 0.002 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3351) covalent geometry : angle 0.56459 ( 4561) hydrogen bonds : bond 0.03476 ( 182) hydrogen bonds : angle 4.59200 ( 525) *********************** 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 71 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: A 251 ASN cc_start: 0.8657 (t0) cc_final: 0.8365 (t0) REVERT: A 263 TRP cc_start: 0.7919 (t-100) cc_final: 0.7694 (t-100) REVERT: A 367 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7982 (mm-30) REVERT: A 396 ARG cc_start: 0.7544 (mtm180) cc_final: 0.7266 (mtm180) outliers start: 5 outliers final: 4 residues processed: 70 average time/residue: 0.0488 time to fit residues: 4.2162 Evaluate side-chains 72 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 0.0070 chunk 27 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.138281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.118095 restraints weight = 6895.255| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.62 r_work: 0.3491 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3351 Z= 0.129 Angle : 0.575 7.273 4561 Z= 0.300 Chirality : 0.044 0.162 501 Planarity : 0.005 0.043 579 Dihedral : 7.570 82.023 517 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.21 % Allowed : 17.88 % 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: 1.48 (0.42), residues: 414 helix: 2.05 (0.36), residues: 202 sheet: 0.65 (0.69), residues: 61 loop : -0.31 (0.52), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 396 TYR 0.017 0.001 TYR A 250 PHE 0.014 0.001 PHE A 381 TRP 0.039 0.002 TRP A 92 HIS 0.007 0.002 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 3351) covalent geometry : angle 0.57473 ( 4561) hydrogen bonds : bond 0.03479 ( 182) hydrogen bonds : angle 4.57376 ( 525) ********************** 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 74 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: A 251 ASN cc_start: 0.8679 (t0) cc_final: 0.8346 (t0) REVERT: A 263 TRP cc_start: 0.7877 (t-100) cc_final: 0.7671 (t-100) outliers start: 4 outliers final: 4 residues processed: 73 average time/residue: 0.0664 time to fit residues: 5.8894 Evaluate side-chains 72 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 314 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 28 optimal weight: 7.9990 chunk 13 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.140930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.120513 restraints weight = 7051.089| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.73 r_work: 0.3516 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3351 Z= 0.117 Angle : 0.561 6.936 4561 Z= 0.293 Chirality : 0.044 0.146 501 Planarity : 0.005 0.043 579 Dihedral : 7.408 80.715 517 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % 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: 1.37 (0.42), residues: 414 helix: 1.92 (0.36), residues: 209 sheet: 0.91 (0.73), residues: 56 loop : -0.54 (0.52), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 396 TYR 0.017 0.001 TYR A 250 PHE 0.011 0.001 PHE A 381 TRP 0.036 0.001 TRP A 92 HIS 0.006 0.002 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 3351) covalent geometry : angle 0.56066 ( 4561) hydrogen bonds : bond 0.03307 ( 182) hydrogen bonds : angle 4.52302 ( 525) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 797.14 seconds wall clock time: 14 minutes 20.00 seconds (860.00 seconds total)