Starting phenix.real_space_refine on Wed Mar 5 20:27:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hiz_34830/03_2025/8hiz_34830_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hiz_34830/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hiz_34830/03_2025/8hiz_34830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hiz_34830/03_2025/8hiz_34830.map" model { file = "/net/cci-nas-00/data/ceres_data/8hiz_34830/03_2025/8hiz_34830_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hiz_34830/03_2025/8hiz_34830_neut.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP: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: 2.75, per 1000 atoms: 0.84 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: 0.80 Conformation dependent library (CDL) restraints added in 369.1 milliseconds 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: 0.36 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: 0.95 Time building geometry restraints manager: 0.96 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: 1.080 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.750 Find NCS groups from input model: 0.040 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.110 ------------------------------------------------------------------------------- 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= 0.282 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (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 TRP 0.018 0.001 TRP A 355 HIS 0.001 0.000 HIS A 388 PHE 0.012 0.001 PHE A 381 TYR 0.018 0.001 TYR A 250 ARG 0.007 0.000 ARG A 16 *********************** 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 : 0.344 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: 0.1617 time to fit residues: 13.8231 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 : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4129 r_free = 0.4129 target = 0.162097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.137524 restraints weight = 6102.865| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.51 r_work: 0.3691 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3351 Z= 0.194 Angle : 0.533 8.495 4561 Z= 0.269 Chirality : 0.043 0.129 501 Planarity : 0.004 0.043 579 Dihedral : 11.017 65.150 517 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.43), residues: 414 helix: 2.13 (0.36), residues: 211 sheet: -0.11 (0.67), residues: 72 loop : -0.27 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 355 HIS 0.006 0.001 HIS A 267 PHE 0.009 0.001 PHE A 381 TYR 0.012 0.001 TYR A 160 ARG 0.005 0.000 ARG A 16 *********************** 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 : 0.378 Fit side-chains REVERT: A 218 GLN cc_start: 0.8130 (tm-30) cc_final: 0.7810 (tp40) REVERT: A 251 ASN cc_start: 0.8324 (t0) cc_final: 0.8089 (t0) outliers start: 2 outliers final: 0 residues processed: 64 average time/residue: 0.1612 time to fit residues: 12.7814 Evaluate side-chains 54 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 16 optimal weight: 0.0000 chunk 2 optimal weight: 0.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.162919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.138550 restraints weight = 5985.673| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.48 r_work: 0.3706 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1370 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= 0.174 Angle : 0.494 5.403 4561 Z= 0.252 Chirality : 0.042 0.132 501 Planarity : 0.004 0.047 579 Dihedral : 9.969 67.958 517 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.21 % Allowed : 8.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.43), residues: 414 helix: 2.02 (0.35), residues: 213 sheet: -0.05 (0.68), residues: 68 loop : -0.34 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 355 HIS 0.006 0.001 HIS A 267 PHE 0.013 0.001 PHE A 381 TYR 0.015 0.001 TYR A 160 ARG 0.005 0.000 ARG A 16 *********************** 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 67 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.329 Fit side-chains REVERT: A 145 ASP cc_start: 0.8258 (t0) cc_final: 0.8049 (t0) REVERT: A 251 ASN cc_start: 0.8339 (t0) cc_final: 0.8112 (t0) outliers start: 4 outliers final: 0 residues processed: 65 average time/residue: 0.1616 time to fit residues: 12.8989 Evaluate side-chains 53 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.162640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.138329 restraints weight = 6093.974| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.51 r_work: 0.3697 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1632 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= 0.182 Angle : 0.541 10.137 4561 Z= 0.267 Chirality : 0.043 0.258 501 Planarity : 0.004 0.046 579 Dihedral : 9.045 60.379 517 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.21 % Allowed : 10.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.43), residues: 414 helix: 2.02 (0.35), residues: 213 sheet: -0.02 (0.69), residues: 68 loop : -0.34 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 355 HIS 0.006 0.001 HIS A 267 PHE 0.012 0.001 PHE A 381 TYR 0.021 0.001 TYR A 160 ARG 0.005 0.000 ARG A 16 *********************** 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 67 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.367 Fit side-chains REVERT: A 145 ASP cc_start: 0.8371 (t0) cc_final: 0.8159 (t0) outliers start: 4 outliers final: 3 residues processed: 66 average time/residue: 0.1560 time to fit residues: 12.6773 Evaluate side-chains 56 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.157490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.131981 restraints weight = 6074.544| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.52 r_work: 0.3613 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 3351 Z= 0.300 Angle : 0.581 9.857 4561 Z= 0.293 Chirality : 0.043 0.142 501 Planarity : 0.004 0.045 579 Dihedral : 8.615 56.592 517 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.52 % Allowed : 12.73 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.43), residues: 414 helix: 1.85 (0.36), residues: 211 sheet: -0.17 (0.67), residues: 69 loop : -0.40 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 355 HIS 0.007 0.001 HIS A 267 PHE 0.014 0.001 PHE A 381 TYR 0.014 0.002 TYR A 160 ARG 0.004 0.000 ARG A 16 *********************** 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 55 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.329 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 0.1705 time to fit residues: 11.3073 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 : 0.337 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.0370 chunk 11 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 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 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 = 0.4121 r_free = 0.4121 target = 0.161720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.136389 restraints weight = 6195.932| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.59 r_work: 0.3670 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3351 Z= 0.171 Angle : 0.535 7.555 4561 Z= 0.268 Chirality : 0.042 0.134 501 Planarity : 0.004 0.049 579 Dihedral : 8.096 53.349 517 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.91 % Allowed : 14.55 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.43), residues: 414 helix: 2.01 (0.35), residues: 212 sheet: -0.13 (0.71), residues: 61 loop : -0.47 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 355 HIS 0.007 0.001 HIS A 267 PHE 0.013 0.001 PHE A 381 TYR 0.008 0.001 TYR A 160 ARG 0.005 0.000 ARG A 16 *********************** 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 62 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.345 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 61 average time/residue: 0.1551 time to fit residues: 11.6312 Evaluate side-chains 54 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 215 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS ** 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 = 0.4122 r_free = 0.4122 target = 0.162232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.137181 restraints weight = 5930.702| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.50 r_work: 0.3677 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2016 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= 0.173 Angle : 0.522 6.802 4561 Z= 0.263 Chirality : 0.042 0.135 501 Planarity : 0.004 0.049 579 Dihedral : 7.710 53.357 517 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.61 % Allowed : 16.06 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.43), residues: 414 helix: 2.05 (0.35), residues: 212 sheet: -0.12 (0.71), residues: 61 loop : -0.42 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 355 HIS 0.008 0.001 HIS A 267 PHE 0.011 0.001 PHE A 381 TYR 0.007 0.001 TYR A 160 ARG 0.005 0.000 ARG A 16 *********************** 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 55 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.374 Fit side-chains REVERT: A 299 GLU cc_start: 0.8417 (mp0) cc_final: 0.7597 (mp0) outliers start: 2 outliers final: 2 residues processed: 54 average time/residue: 0.1836 time to fit residues: 12.3421 Evaluate side-chains 56 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 267 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 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 267 HIS ** 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 = 0.4123 r_free = 0.4123 target = 0.162168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.136844 restraints weight = 6067.231| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.52 r_work: 0.3674 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2059 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= 0.185 Angle : 0.531 8.652 4561 Z= 0.263 Chirality : 0.042 0.138 501 Planarity : 0.004 0.049 579 Dihedral : 7.585 55.270 517 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.61 % Allowed : 16.06 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.43), residues: 414 helix: 2.02 (0.35), residues: 212 sheet: -0.09 (0.71), residues: 61 loop : -0.39 (0.55), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 355 HIS 0.010 0.002 HIS A 267 PHE 0.010 0.001 PHE A 381 TYR 0.007 0.001 TYR A 160 ARG 0.005 0.000 ARG A 16 *********************** 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 55 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.374 Fit side-chains REVERT: A 299 GLU cc_start: 0.8427 (mp0) cc_final: 0.7891 (mp0) outliers start: 2 outliers final: 2 residues processed: 54 average time/residue: 0.1710 time to fit residues: 11.6258 Evaluate side-chains 54 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 267 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 7 optimal weight: 0.5980 chunk 24 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.162526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.136831 restraints weight = 6065.986| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.56 r_work: 0.3677 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3351 Z= 0.190 Angle : 0.556 10.633 4561 Z= 0.272 Chirality : 0.042 0.139 501 Planarity : 0.004 0.049 579 Dihedral : 7.544 56.799 517 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.61 % Allowed : 16.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.43), residues: 414 helix: 1.98 (0.35), residues: 212 sheet: -0.08 (0.71), residues: 61 loop : -0.36 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 355 HIS 0.013 0.002 HIS A 267 PHE 0.010 0.001 PHE A 381 TYR 0.010 0.001 TYR A 250 ARG 0.002 0.000 ARG A 16 *********************** 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 54 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.350 Fit side-chains REVERT: A 299 GLU cc_start: 0.8429 (mp0) cc_final: 0.7896 (mp0) outliers start: 2 outliers final: 2 residues processed: 54 average time/residue: 0.1583 time to fit residues: 10.5753 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 : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 128 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN A 234 GLN A 267 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.162908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.137517 restraints weight = 5965.311| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.52 r_work: 0.3688 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2182 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= 0.179 Angle : 0.546 9.965 4561 Z= 0.268 Chirality : 0.042 0.138 501 Planarity : 0.004 0.049 579 Dihedral : 7.407 59.532 517 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.21 % Allowed : 16.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.43), residues: 414 helix: 2.00 (0.36), residues: 213 sheet: 0.10 (0.76), residues: 51 loop : -0.44 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 355 HIS 0.011 0.002 HIS A 267 PHE 0.008 0.001 PHE A 381 TYR 0.007 0.001 TYR A 160 ARG 0.001 0.000 ARG A 331 ********************** 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 58 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.346 Fit side-chains REVERT: A 299 GLU cc_start: 0.8408 (mp0) cc_final: 0.7895 (mp0) outliers start: 4 outliers final: 3 residues processed: 57 average time/residue: 0.1772 time to fit residues: 12.4409 Evaluate side-chains 56 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 128 ILE 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 25 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 2 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 267 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.162280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.136608 restraints weight = 6033.925| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.53 r_work: 0.3668 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2251 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= 0.202 Angle : 0.555 9.722 4561 Z= 0.274 Chirality : 0.042 0.141 501 Planarity : 0.004 0.048 579 Dihedral : 7.330 59.364 517 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.21 % Allowed : 15.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.43), residues: 414 helix: 1.90 (0.35), residues: 213 sheet: 0.10 (0.76), residues: 51 loop : -0.51 (0.53), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 355 HIS 0.004 0.001 HIS A 267 PHE 0.009 0.001 PHE A 381 TYR 0.007 0.001 TYR A 160 ARG 0.003 0.000 ARG A 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2013.14 seconds wall clock time: 35 minutes 27.96 seconds (2127.96 seconds total)