Starting phenix.real_space_refine on Wed Sep 17 03:41:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8znd_60268/09_2025/8znd_60268.cif Found real_map, /net/cci-nas-00/data/ceres_data/8znd_60268/09_2025/8znd_60268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8znd_60268/09_2025/8znd_60268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8znd_60268/09_2025/8znd_60268.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8znd_60268/09_2025/8znd_60268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8znd_60268/09_2025/8znd_60268.map" } resolution = 2.53 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= 0.002 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 2104 2.51 5 N 563 2.21 5 O 650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3334 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 72 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1, 'water': 24} Link IDs: {None: 24} Time building chain proxies: 0.96, per 1000 atoms: 0.29 Number of scatterers: 3334 At special positions: 0 Unit cell: (66.176, 63.92, 70.688, 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 650 8.00 N 563 7.00 C 2104 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: 0.34 Conformation dependent library (CDL) restraints added in 146.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 758 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 3 sheets defined 56.2% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 19 through 21 No H-bonds generated for 'chain 'A' and resid 19 through 21' Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.681A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 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 170 through 174 removed outlier: 3.551A 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 234 removed outlier: 3.728A pdb=" N TYR A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.556A pdb=" N LEU A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 323 through 334 removed outlier: 4.023A pdb=" N ASP A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 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: 4.643A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.643A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 279 removed outlier: 3.558A pdb=" N VAL A 242 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE A 215 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 194 hydrogen bonds defined for protein. 555 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: 0.57 Time building geometry restraints manager: 0.40 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: 1069 1.34 - 1.46: 465 1.46 - 1.57: 1820 1.57 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3386 Sorted by residual: bond pdb=" O2B NDP A 500 " pdb=" P2B NDP A 500 " ideal model delta sigma weight residual 1.833 1.607 0.226 3.80e-02 6.93e+02 3.53e+01 bond pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.757 1.596 0.161 3.50e-02 8.16e+02 2.13e+01 bond pdb=" N TYR A 250 " pdb=" CA TYR A 250 " ideal model delta sigma weight residual 1.455 1.413 0.042 1.25e-02 6.40e+03 1.15e+01 bond pdb=" C2B NDP A 500 " pdb=" O2B NDP A 500 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.90e-02 1.19e+03 9.52e+00 bond pdb=" CA TYR A 250 " pdb=" C TYR A 250 " ideal model delta sigma weight residual 1.520 1.487 0.034 1.22e-02 6.72e+03 7.60e+00 ... (remaining 3381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 4575 4.44 - 8.88: 19 8.88 - 13.31: 1 13.31 - 17.75: 2 17.75 - 22.19: 1 Bond angle restraints: 4598 Sorted by residual: angle pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 107.74 129.93 -22.19 1.95e+00 2.62e-01 1.29e+02 angle pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " ideal model delta sigma weight residual 103.84 119.43 -15.59 1.91e+00 2.73e-01 6.63e+01 angle pdb=" C5D NDP A 500 " pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 104.93 118.60 -13.67 2.66e+00 1.41e-01 2.64e+01 angle pdb=" O2N NDP A 500 " pdb=" PN NDP A 500 " pdb=" O5D NDP A 500 " ideal model delta sigma weight residual 100.52 109.34 -8.82 1.91e+00 2.74e-01 2.13e+01 angle pdb=" O1X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.46 112.28 5.18 1.17e+00 7.36e-01 1.97e+01 ... (remaining 4593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.43: 1872 23.43 - 46.87: 110 46.87 - 70.30: 17 70.30 - 93.73: 9 93.73 - 117.16: 1 Dihedral angle restraints: 2009 sinusoidal: 820 harmonic: 1189 Sorted by residual: dihedral pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " ideal model delta sinusoidal sigma weight residual 175.04 57.88 117.16 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" CA PHE A 341 " pdb=" C PHE A 341 " pdb=" N LEU A 342 " pdb=" CA LEU A 342 " ideal model delta harmonic sigma weight residual 180.00 162.32 17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CB GLU A 288 " pdb=" CG GLU A 288 " pdb=" CD GLU A 288 " pdb=" OE1 GLU A 288 " ideal model delta sinusoidal sigma weight residual 0.00 -89.63 89.63 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 2006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 381 0.047 - 0.093: 79 0.093 - 0.140: 36 0.140 - 0.186: 2 0.186 - 0.233: 3 Chirality restraints: 501 Sorted by residual: chirality pdb=" C4D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" C5D NDP A 500 " pdb=" O4D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.48 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA TYR A 250 " pdb=" N TYR A 250 " pdb=" C TYR A 250 " pdb=" CB TYR A 250 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C1B NDP A 500 " pdb=" C2B NDP A 500 " pdb=" N9A NDP A 500 " pdb=" O4B NDP A 500 " both_signs ideal model delta sigma weight residual False 2.59 2.40 0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 498 not shown) Planarity restraints: 586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 500 " 0.018 2.00e-02 2.50e+03 3.11e-02 9.68e+00 pdb=" C5N NDP A 500 " -0.039 2.00e-02 2.50e+03 pdb=" C6N NDP A 500 " 0.040 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 500 " 0.031 2.00e-02 2.50e+03 1.92e-02 4.62e+00 pdb=" C3N NDP A 500 " 0.004 2.00e-02 2.50e+03 pdb=" C4N NDP A 500 " 0.005 2.00e-02 2.50e+03 pdb=" C7N NDP A 500 " -0.016 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.031 5.00e-02 4.00e+02 4.62e-02 3.42e+00 pdb=" N PRO A 142 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.025 5.00e-02 4.00e+02 ... (remaining 583 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1217 2.89 - 3.39: 3334 3.39 - 3.90: 6075 3.90 - 4.40: 6964 4.40 - 4.90: 11339 Nonbonded interactions: 28929 Sorted by model distance: nonbonded pdb=" NE ARG A 73 " pdb=" OE1 GLU A 78 " model vdw 2.392 3.120 nonbonded pdb=" O VAL A 401 " pdb=" OG SER A 405 " model vdw 2.402 3.040 nonbonded pdb=" OD1 ASP A 5 " pdb=" OG SER A 81 " model vdw 2.440 3.040 nonbonded pdb=" N ASP A 145 " pdb=" OG1 THR A 148 " model vdw 2.495 3.120 nonbonded pdb=" NZ LYS A 177 " pdb=" OD1 ASN A 358 " model vdw 2.504 3.120 ... (remaining 28924 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.540 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 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 : 0.007 0.226 3386 Z= 0.275 Angle : 0.927 22.188 4598 Z= 0.525 Chirality : 0.048 0.233 501 Planarity : 0.005 0.047 586 Dihedral : 15.596 117.160 1251 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.88 % Allowed : 0.59 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.42), residues: 414 helix: 2.03 (0.35), residues: 202 sheet: -0.23 (0.63), residues: 72 loop : -0.97 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 58 TYR 0.015 0.002 TYR A 363 PHE 0.015 0.002 PHE A 341 TRP 0.008 0.001 TRP A 382 HIS 0.002 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00700 ( 3386) covalent geometry : angle 0.92740 ( 4598) hydrogen bonds : bond 0.14487 ( 178) hydrogen bonds : angle 6.49672 ( 555) *********************** 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 86 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.118 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 84 average time/residue: 0.6655 time to fit residues: 57.0508 Evaluate side-chains 59 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.122 ------------------------------------------------------------------------------- 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: 5.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.114276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.089351 restraints weight = 4149.964| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 1.53 r_work: 0.2729 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3386 Z= 0.118 Angle : 0.476 4.412 4598 Z= 0.254 Chirality : 0.042 0.131 501 Planarity : 0.005 0.044 586 Dihedral : 6.560 99.393 462 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.47 % Allowed : 10.91 % Favored : 87.61 % 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: 1.10 (0.42), residues: 414 helix: 2.00 (0.35), residues: 209 sheet: 0.07 (0.65), residues: 72 loop : -0.93 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 370 TYR 0.011 0.001 TYR A 363 PHE 0.013 0.001 PHE A 341 TRP 0.010 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 3386) covalent geometry : angle 0.47588 ( 4598) hydrogen bonds : bond 0.04278 ( 178) hydrogen bonds : angle 4.40066 ( 555) *********************** 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 72 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.144 Fit side-chains REVERT: A 271 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8946 (ttmt) outliers start: 5 outliers final: 1 residues processed: 70 average time/residue: 0.6982 time to fit residues: 49.9468 Evaluate side-chains 61 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 280 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.114323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.089481 restraints weight = 4159.276| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.56 r_work: 0.2755 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3386 Z= 0.104 Angle : 0.441 4.413 4598 Z= 0.235 Chirality : 0.041 0.127 501 Planarity : 0.005 0.046 586 Dihedral : 6.249 90.071 462 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.47 % Allowed : 13.57 % Favored : 84.96 % 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: 1.26 (0.43), residues: 414 helix: 2.17 (0.35), residues: 208 sheet: 0.13 (0.65), residues: 73 loop : -0.90 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 265 TYR 0.010 0.001 TYR A 363 PHE 0.012 0.001 PHE A 341 TRP 0.008 0.001 TRP A 382 HIS 0.002 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 3386) covalent geometry : angle 0.44116 ( 4598) hydrogen bonds : bond 0.04041 ( 178) hydrogen bonds : angle 4.18566 ( 555) *********************** 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: 5 poor density : 62 time to evaluate : 0.136 Fit side-chains REVERT: A 21 MET cc_start: 0.8787 (ptm) cc_final: 0.8571 (ptt) REVERT: A 246 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8073 (mpt180) REVERT: A 265 ARG cc_start: 0.8387 (mmt90) cc_final: 0.8120 (mpp80) outliers start: 5 outliers final: 1 residues processed: 63 average time/residue: 0.7493 time to fit residues: 48.1763 Evaluate side-chains 61 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 277 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 32 optimal weight: 0.0070 chunk 15 optimal weight: 0.8980 overall best weight: 0.9600 ------------------------------------------------------------------------------- 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 = 0.3259 r_free = 0.3259 target = 0.114853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.090127 restraints weight = 4134.351| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.57 r_work: 0.2756 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3386 Z= 0.097 Angle : 0.430 4.394 4598 Z= 0.227 Chirality : 0.041 0.128 501 Planarity : 0.005 0.046 586 Dihedral : 5.986 83.407 462 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.77 % Allowed : 13.86 % Favored : 84.37 % 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: 1.38 (0.43), residues: 414 helix: 2.27 (0.35), residues: 208 sheet: 0.28 (0.66), residues: 73 loop : -0.92 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 370 TYR 0.009 0.001 TYR A 363 PHE 0.011 0.001 PHE A 341 TRP 0.007 0.001 TRP A 382 HIS 0.003 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 3386) covalent geometry : angle 0.42991 ( 4598) hydrogen bonds : bond 0.03761 ( 178) hydrogen bonds : angle 4.03256 ( 555) *********************** 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 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.117 Fit side-chains REVERT: A 21 MET cc_start: 0.8822 (ptm) cc_final: 0.8604 (ptt) REVERT: A 265 ARG cc_start: 0.8412 (mmt90) cc_final: 0.8156 (mpp80) outliers start: 6 outliers final: 3 residues processed: 61 average time/residue: 0.7002 time to fit residues: 43.6900 Evaluate side-chains 61 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 304 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3214 r_free = 0.3214 target = 0.111103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.086436 restraints weight = 4089.893| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 1.51 r_work: 0.2706 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3386 Z= 0.139 Angle : 0.474 4.529 4598 Z= 0.252 Chirality : 0.043 0.133 501 Planarity : 0.005 0.047 586 Dihedral : 5.965 79.481 462 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.65 % Allowed : 13.27 % Favored : 84.07 % 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: 1.27 (0.42), residues: 414 helix: 2.15 (0.35), residues: 209 sheet: 0.35 (0.65), residues: 72 loop : -1.00 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 370 TYR 0.013 0.001 TYR A 363 PHE 0.013 0.001 PHE A 341 TRP 0.008 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3386) covalent geometry : angle 0.47373 ( 4598) hydrogen bonds : bond 0.04504 ( 178) hydrogen bonds : angle 4.17484 ( 555) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.132 Fit side-chains REVERT: A 21 MET cc_start: 0.8906 (ptm) cc_final: 0.8561 (ptt) REVERT: A 265 ARG cc_start: 0.8399 (mmt90) cc_final: 0.8136 (mpp80) REVERT: A 332 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8373 (tm-30) outliers start: 9 outliers final: 4 residues processed: 61 average time/residue: 0.7631 time to fit residues: 47.5952 Evaluate side-chains 59 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 332 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.0570 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 = 0.3244 r_free = 0.3244 target = 0.113556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.088804 restraints weight = 4169.305| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.57 r_work: 0.2767 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3386 Z= 0.090 Angle : 0.422 4.414 4598 Z= 0.222 Chirality : 0.041 0.127 501 Planarity : 0.004 0.046 586 Dihedral : 5.551 72.594 462 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.47 % Allowed : 15.34 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.50 (0.43), residues: 414 helix: 2.36 (0.35), residues: 208 sheet: 0.39 (0.66), residues: 73 loop : -0.89 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 370 TYR 0.008 0.001 TYR A 363 PHE 0.010 0.001 PHE A 341 TRP 0.007 0.001 TRP A 63 HIS 0.001 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 3386) covalent geometry : angle 0.42215 ( 4598) hydrogen bonds : bond 0.03568 ( 178) hydrogen bonds : angle 3.91188 ( 555) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.167 Fit side-chains REVERT: A 29 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8615 (mm-30) REVERT: A 282 GLU cc_start: 0.8460 (mp0) cc_final: 0.8101 (mp0) REVERT: A 332 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8386 (tm-30) outliers start: 5 outliers final: 1 residues processed: 63 average time/residue: 0.7596 time to fit residues: 48.9430 Evaluate side-chains 63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 332 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3242 r_free = 0.3242 target = 0.113114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.088272 restraints weight = 4169.308| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.55 r_work: 0.2723 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3386 Z= 0.108 Angle : 0.447 4.462 4598 Z= 0.236 Chirality : 0.041 0.130 501 Planarity : 0.005 0.047 586 Dihedral : 5.445 68.157 462 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.77 % Allowed : 16.22 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.43), residues: 414 helix: 2.31 (0.35), residues: 209 sheet: 0.42 (0.66), residues: 73 loop : -0.81 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 265 TYR 0.010 0.001 TYR A 363 PHE 0.011 0.001 PHE A 341 TRP 0.007 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 3386) covalent geometry : angle 0.44696 ( 4598) hydrogen bonds : bond 0.03941 ( 178) hydrogen bonds : angle 3.96584 ( 555) *********************** 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 67 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.136 Fit side-chains REVERT: A 29 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8717 (mm-30) REVERT: A 282 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8199 (mp0) REVERT: A 332 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8421 (tm-30) outliers start: 6 outliers final: 2 residues processed: 65 average time/residue: 0.7209 time to fit residues: 47.9155 Evaluate side-chains 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 332 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 7 optimal weight: 0.1980 chunk 21 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3241 r_free = 0.3241 target = 0.112952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.088048 restraints weight = 4200.005| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 1.56 r_work: 0.2733 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3386 Z= 0.108 Angle : 0.446 4.621 4598 Z= 0.235 Chirality : 0.041 0.130 501 Planarity : 0.004 0.047 586 Dihedral : 5.188 60.256 462 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.06 % Allowed : 15.93 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.43), residues: 414 helix: 2.31 (0.35), residues: 209 sheet: 0.40 (0.66), residues: 73 loop : -0.79 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 370 TYR 0.010 0.001 TYR A 363 PHE 0.011 0.001 PHE A 341 TRP 0.007 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 3386) covalent geometry : angle 0.44645 ( 4598) hydrogen bonds : bond 0.03949 ( 178) hydrogen bonds : angle 3.96216 ( 555) *********************** 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 67 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.138 Fit side-chains REVERT: A 29 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8714 (mm-30) REVERT: A 282 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: A 332 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8419 (tm-30) REVERT: A 388 HIS cc_start: 0.8887 (OUTLIER) cc_final: 0.8663 (t-90) outliers start: 7 outliers final: 2 residues processed: 64 average time/residue: 0.7425 time to fit residues: 48.5502 Evaluate side-chains 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.3230 r_free = 0.3230 target = 0.112135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.087285 restraints weight = 4175.952| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.55 r_work: 0.2733 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3386 Z= 0.111 Angle : 0.455 4.685 4598 Z= 0.240 Chirality : 0.042 0.130 501 Planarity : 0.005 0.047 586 Dihedral : 4.923 51.002 462 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.47 % Allowed : 16.22 % Favored : 82.30 % 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: 1.52 (0.43), residues: 414 helix: 2.29 (0.35), residues: 209 sheet: 0.40 (0.66), residues: 73 loop : -0.75 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 265 TYR 0.010 0.001 TYR A 363 PHE 0.011 0.001 PHE A 341 TRP 0.007 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 3386) covalent geometry : angle 0.45489 ( 4598) hydrogen bonds : bond 0.04011 ( 178) hydrogen bonds : angle 3.97513 ( 555) *********************** 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 68 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.137 Fit side-chains REVERT: A 29 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8732 (mm-30) REVERT: A 282 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: A 332 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8429 (tm-30) outliers start: 5 outliers final: 2 residues processed: 67 average time/residue: 0.7031 time to fit residues: 48.2097 Evaluate side-chains 64 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 332 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.110849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.085855 restraints weight = 4180.373| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 1.55 r_work: 0.2712 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3386 Z= 0.123 Angle : 0.468 5.268 4598 Z= 0.247 Chirality : 0.042 0.131 501 Planarity : 0.005 0.047 586 Dihedral : 4.720 41.637 462 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.18 % Allowed : 16.52 % Favored : 82.30 % 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 (0.43), residues: 414 helix: 2.25 (0.35), residues: 209 sheet: 0.37 (0.66), residues: 73 loop : -0.72 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 370 TYR 0.012 0.001 TYR A 363 PHE 0.012 0.001 PHE A 341 TRP 0.007 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3386) covalent geometry : angle 0.46827 ( 4598) hydrogen bonds : bond 0.04232 ( 178) hydrogen bonds : angle 4.03457 ( 555) ********************** 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 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.136 Fit side-chains REVERT: A 29 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8742 (mm-30) REVERT: A 282 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: A 332 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8416 (tm-30) outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 0.6560 time to fit residues: 42.8974 Evaluate side-chains 62 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 332 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 16 optimal weight: 0.3980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.112421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.087494 restraints weight = 4194.934| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.56 r_work: 0.2741 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3386 Z= 0.107 Angle : 0.457 5.726 4598 Z= 0.240 Chirality : 0.041 0.129 501 Planarity : 0.004 0.047 586 Dihedral : 4.488 39.267 462 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.77 % Allowed : 15.63 % Favored : 82.60 % 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: 1.57 (0.43), residues: 414 helix: 2.33 (0.35), residues: 208 sheet: 0.42 (0.66), residues: 73 loop : -0.69 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 370 TYR 0.010 0.001 TYR A 363 PHE 0.011 0.001 PHE A 341 TRP 0.007 0.001 TRP A 382 HIS 0.006 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 3386) covalent geometry : angle 0.45676 ( 4598) hydrogen bonds : bond 0.03951 ( 178) hydrogen bonds : angle 3.97907 ( 555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1585.49 seconds wall clock time: 28 minutes 4.95 seconds (1684.95 seconds total)