Starting phenix.real_space_refine on Wed Jun 4 19:36:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wn1_32619/06_2025/7wn1_32619.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wn1_32619/06_2025/7wn1_32619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wn1_32619/06_2025/7wn1_32619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wn1_32619/06_2025/7wn1_32619.map" model { file = "/net/cci-nas-00/data/ceres_data/7wn1_32619/06_2025/7wn1_32619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wn1_32619/06_2025/7wn1_32619.cif" } resolution = 3.11 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 2572 2.51 5 N 616 2.21 5 O 687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3901 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2953 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain breaks: 1 Chain: "C" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 929 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'NOS%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 5.61, per 1000 atoms: 1.44 Number of scatterers: 3901 At special positions: 0 Unit cell: (110.39, 60.59, 64.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 687 8.00 N 616 7.00 C 2572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 493.3 milliseconds 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 914 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 64.3% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 31 through 59 removed outlier: 4.331A pdb=" N VAL A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TRP A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 83 removed outlier: 3.547A pdb=" N ASN A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 89 through 111 Processing helix chain 'A' and resid 112 through 144 Processing helix chain 'A' and resid 149 through 175 removed outlier: 3.802A pdb=" N GLN A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 210 Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 239 through 257 removed outlier: 3.734A pdb=" N ILE A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 270 removed outlier: 3.674A pdb=" N GLN A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 290 removed outlier: 3.759A pdb=" N THR A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.967A pdb=" N ASN A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 321 through 332 removed outlier: 3.538A pdb=" N TRP A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 369 removed outlier: 3.804A pdb=" N LEU A 350 " --> pdb=" O CYS A 346 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Proline residue: A 361 - end of helix removed outlier: 5.181A pdb=" N VAL A 366 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 400 removed outlier: 3.655A pdb=" N ILE A 378 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'C' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.193A pdb=" N GLY C 10 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ARG C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.193A pdb=" N GLY C 10 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN C 109 " --> pdb=" O THR C 99 " (cutoff:3.500A) 260 hydrogen bonds defined for protein. 750 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: 1.35 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 823 1.33 - 1.45: 929 1.45 - 1.57: 2205 1.57 - 1.69: 2 1.69 - 1.81: 39 Bond restraints: 3998 Sorted by residual: bond pdb=" C1' NOS A 501 " pdb=" O4' NOS A 501 " ideal model delta sigma weight residual 1.397 1.600 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C1' NOS A 501 " pdb=" C2' NOS A 501 " ideal model delta sigma weight residual 1.528 1.346 0.182 2.00e-02 2.50e+03 8.30e+01 bond pdb=" C2 NOS A 501 " pdb=" N3 NOS A 501 " ideal model delta sigma weight residual 1.293 1.444 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C4 NOS A 501 " pdb=" N3 NOS A 501 " ideal model delta sigma weight residual 1.347 1.497 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" C4' NOS A 501 " pdb=" O4' NOS A 501 " ideal model delta sigma weight residual 1.432 1.309 0.123 2.00e-02 2.50e+03 3.77e+01 ... (remaining 3993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 5331 2.00 - 4.00: 75 4.00 - 6.00: 17 6.00 - 8.00: 4 8.00 - 10.00: 2 Bond angle restraints: 5429 Sorted by residual: angle pdb=" C5 NOS A 501 " pdb=" C6 NOS A 501 " pdb=" O6 NOS A 501 " ideal model delta sigma weight residual 128.65 118.65 10.00 3.00e+00 1.11e-01 1.11e+01 angle pdb=" N SER A 308 " pdb=" CA SER A 308 " pdb=" C SER A 308 " ideal model delta sigma weight residual 107.88 112.42 -4.54 1.41e+00 5.03e-01 1.04e+01 angle pdb=" C3' NOS A 501 " pdb=" C2' NOS A 501 " pdb=" O2' NOS A 501 " ideal model delta sigma weight residual 116.89 107.68 9.21 3.00e+00 1.11e-01 9.42e+00 angle pdb=" C TYR C 37 " pdb=" N ARG C 38 " pdb=" CA ARG C 38 " ideal model delta sigma weight residual 122.65 118.88 3.77 1.49e+00 4.50e-01 6.40e+00 angle pdb=" C2 NOS A 501 " pdb=" N3 NOS A 501 " pdb=" C4 NOS A 501 " ideal model delta sigma weight residual 112.58 119.70 -7.12 3.00e+00 1.11e-01 5.63e+00 ... (remaining 5424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 2048 15.24 - 30.48: 199 30.48 - 45.71: 56 45.71 - 60.95: 17 60.95 - 76.19: 3 Dihedral angle restraints: 2323 sinusoidal: 899 harmonic: 1424 Sorted by residual: dihedral pdb=" CA LEU A 256 " pdb=" C LEU A 256 " pdb=" N PHE A 257 " pdb=" CA PHE A 257 " ideal model delta harmonic sigma weight residual -180.00 -161.88 -18.12 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA MET A 145 " pdb=" C MET A 145 " pdb=" N GLU A 146 " pdb=" CA GLU A 146 " ideal model delta harmonic sigma weight residual 180.00 162.85 17.15 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA VAL A 332 " pdb=" C VAL A 332 " pdb=" N ASP A 333 " pdb=" CA ASP A 333 " ideal model delta harmonic sigma weight residual -180.00 -164.41 -15.59 0 5.00e+00 4.00e-02 9.72e+00 ... (remaining 2320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 372 0.031 - 0.061: 174 0.061 - 0.092: 56 0.092 - 0.122: 20 0.122 - 0.153: 8 Chirality restraints: 630 Sorted by residual: chirality pdb=" CB ILE A 193 " pdb=" CA ILE A 193 " pdb=" CG1 ILE A 193 " pdb=" CG2 ILE A 193 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" C1' NOS A 501 " pdb=" C2' NOS A 501 " pdb=" N9 NOS A 501 " pdb=" O4' NOS A 501 " both_signs ideal model delta sigma weight residual False 2.36 2.50 -0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA ASP A 147 " pdb=" N ASP A 147 " pdb=" C ASP A 147 " pdb=" CB ASP A 147 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 627 not shown) Planarity restraints: 665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 257 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A 258 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 334 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO A 335 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 335 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 335 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 412 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.51e+00 pdb=" N PRO A 413 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 413 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 413 " -0.017 5.00e-02 4.00e+02 ... (remaining 662 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 835 2.78 - 3.31: 3841 3.31 - 3.84: 6568 3.84 - 4.37: 7875 4.37 - 4.90: 13686 Nonbonded interactions: 32805 Sorted by model distance: nonbonded pdb=" OH TYR A 65 " pdb=" OD1 ASP A 117 " model vdw 2.246 3.040 nonbonded pdb=" OG1 THR A 41 " pdb=" OD1 ASN A 209 " model vdw 2.256 3.040 nonbonded pdb=" O CYS A 395 " pdb=" OG1 THR A 399 " model vdw 2.283 3.040 nonbonded pdb=" O LEU A 256 " pdb=" N GLY A 261 " model vdw 2.320 3.120 nonbonded pdb=" NE2 GLN C 81 " pdb=" OD1 ASN C 83 " model vdw 2.320 3.120 ... (remaining 32800 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 33.420 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 19.020 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 0.203 3999 Z= 0.360 Angle : 0.651 10.003 5431 Z= 0.333 Chirality : 0.042 0.153 630 Planarity : 0.004 0.035 665 Dihedral : 13.871 76.187 1406 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.00 (0.38), residues: 487 helix: 1.09 (0.30), residues: 285 sheet: 0.84 (0.64), residues: 58 loop : -0.10 (0.58), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 251 HIS 0.004 0.001 HIS A 334 PHE 0.016 0.001 PHE C 27 TYR 0.018 0.001 TYR C 102 ARG 0.002 0.000 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.18087 ( 256) hydrogen bonds : angle 6.16735 ( 750) SS BOND : bond 0.00151 ( 1) SS BOND : angle 0.17564 ( 2) covalent geometry : bond 0.00727 ( 3998) covalent geometry : angle 0.65079 ( 5429) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.473 Fit side-chains REVERT: A 175 VAL cc_start: 0.8097 (t) cc_final: 0.7828 (m) REVERT: A 303 LYS cc_start: 0.8628 (tppt) cc_final: 0.8418 (tppt) REVERT: A 407 ASN cc_start: 0.8197 (t0) cc_final: 0.7963 (t0) REVERT: C 94 TYR cc_start: 0.8213 (m-10) cc_final: 0.8003 (m-10) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1778 time to fit residues: 16.2749 Evaluate side-chains 62 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 209 ASN C 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.113197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.099988 restraints weight = 5147.435| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.60 r_work: 0.3055 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3999 Z= 0.156 Angle : 0.570 6.524 5431 Z= 0.308 Chirality : 0.043 0.144 630 Planarity : 0.004 0.033 665 Dihedral : 5.672 35.770 540 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.33 % Allowed : 5.35 % Favored : 92.33 % 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: 1.38 (0.38), residues: 487 helix: 1.49 (0.29), residues: 289 sheet: 0.96 (0.64), residues: 58 loop : -0.17 (0.57), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 251 HIS 0.003 0.001 HIS A 180 PHE 0.017 0.001 PHE C 27 TYR 0.015 0.001 TYR C 102 ARG 0.003 0.001 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.05767 ( 256) hydrogen bonds : angle 4.66742 ( 750) SS BOND : bond 0.00089 ( 1) SS BOND : angle 0.30316 ( 2) covalent geometry : bond 0.00335 ( 3998) covalent geometry : angle 0.57057 ( 5429) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.402 Fit side-chains REVERT: A 303 LYS cc_start: 0.8772 (tppt) cc_final: 0.8557 (tppt) REVERT: A 407 ASN cc_start: 0.8464 (t0) cc_final: 0.8103 (t0) outliers start: 10 outliers final: 5 residues processed: 64 average time/residue: 0.1732 time to fit residues: 13.9999 Evaluate side-chains 59 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 82 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 46 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3339 r_free = 0.3339 target = 0.112515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.099422 restraints weight = 5113.393| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.59 r_work: 0.3051 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3999 Z= 0.153 Angle : 0.547 6.465 5431 Z= 0.295 Chirality : 0.043 0.147 630 Planarity : 0.004 0.034 665 Dihedral : 5.314 32.098 540 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.56 % Allowed : 9.07 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.67 (0.38), residues: 487 helix: 1.69 (0.29), residues: 289 sheet: 1.12 (0.64), residues: 58 loop : -0.01 (0.59), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 251 HIS 0.003 0.001 HIS A 180 PHE 0.016 0.001 PHE C 27 TYR 0.019 0.001 TYR C 102 ARG 0.002 0.001 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.05183 ( 256) hydrogen bonds : angle 4.38892 ( 750) SS BOND : bond 0.00113 ( 1) SS BOND : angle 0.33589 ( 2) covalent geometry : bond 0.00339 ( 3998) covalent geometry : angle 0.54746 ( 5429) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 303 LYS cc_start: 0.8782 (tppt) cc_final: 0.8557 (tppt) REVERT: C 19 ARG cc_start: 0.8648 (mtp85) cc_final: 0.8233 (mtp-110) outliers start: 11 outliers final: 8 residues processed: 63 average time/residue: 0.1690 time to fit residues: 13.3341 Evaluate side-chains 65 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 34 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.110903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.097272 restraints weight = 5091.722| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.63 r_work: 0.3041 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3999 Z= 0.152 Angle : 0.541 6.376 5431 Z= 0.291 Chirality : 0.043 0.141 630 Planarity : 0.004 0.035 665 Dihedral : 5.139 29.383 540 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.72 % Allowed : 11.16 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.72 (0.38), residues: 487 helix: 1.68 (0.29), residues: 295 sheet: 1.10 (0.64), residues: 58 loop : 0.08 (0.60), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.015 0.001 PHE C 27 TYR 0.019 0.001 TYR C 102 ARG 0.001 0.000 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.04998 ( 256) hydrogen bonds : angle 4.29829 ( 750) SS BOND : bond 0.00114 ( 1) SS BOND : angle 0.33332 ( 2) covalent geometry : bond 0.00338 ( 3998) covalent geometry : angle 0.54104 ( 5429) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8289 (m-30) REVERT: A 303 LYS cc_start: 0.8796 (tppt) cc_final: 0.8569 (tppt) REVERT: A 407 ASN cc_start: 0.8427 (t0) cc_final: 0.8057 (t0) outliers start: 16 outliers final: 11 residues processed: 64 average time/residue: 0.1853 time to fit residues: 15.1322 Evaluate side-chains 68 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 107 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 28 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.0040 chunk 19 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.113583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.100079 restraints weight = 5209.946| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.61 r_work: 0.3075 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3999 Z= 0.130 Angle : 0.522 7.109 5431 Z= 0.279 Chirality : 0.042 0.149 630 Planarity : 0.004 0.035 665 Dihedral : 4.953 26.558 540 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.26 % Allowed : 13.02 % Favored : 83.72 % 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: 1.84 (0.38), residues: 487 helix: 1.84 (0.29), residues: 294 sheet: 1.02 (0.64), residues: 58 loop : 0.03 (0.60), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.014 0.001 PHE C 27 TYR 0.017 0.001 TYR C 102 ARG 0.001 0.000 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.04627 ( 256) hydrogen bonds : angle 4.20644 ( 750) SS BOND : bond 0.00080 ( 1) SS BOND : angle 0.28917 ( 2) covalent geometry : bond 0.00278 ( 3998) covalent geometry : angle 0.52191 ( 5429) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8224 (m-30) REVERT: C 19 ARG cc_start: 0.8649 (mtp85) cc_final: 0.8377 (mtp-110) REVERT: C 88 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6555 (pm20) outliers start: 14 outliers final: 7 residues processed: 64 average time/residue: 0.1627 time to fit residues: 13.2284 Evaluate side-chains 65 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3372 r_free = 0.3372 target = 0.114541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.100706 restraints weight = 5127.106| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.59 r_work: 0.3093 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3999 Z= 0.148 Angle : 0.535 6.326 5431 Z= 0.286 Chirality : 0.042 0.150 630 Planarity : 0.004 0.035 665 Dihedral : 4.956 26.851 540 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.72 % Allowed : 13.49 % Favored : 82.79 % 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: 1.77 (0.38), residues: 487 helix: 1.75 (0.29), residues: 295 sheet: 1.01 (0.64), residues: 58 loop : 0.06 (0.60), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.014 0.001 PHE C 27 TYR 0.017 0.001 TYR C 102 ARG 0.001 0.000 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.04827 ( 256) hydrogen bonds : angle 4.21044 ( 750) SS BOND : bond 0.00191 ( 1) SS BOND : angle 0.38990 ( 2) covalent geometry : bond 0.00332 ( 3998) covalent geometry : angle 0.53458 ( 5429) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.460 Fit side-chains REVERT: A 113 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8247 (m-30) REVERT: C 88 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6638 (pm20) outliers start: 16 outliers final: 9 residues processed: 67 average time/residue: 0.1700 time to fit residues: 15.2195 Evaluate side-chains 67 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.111710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.098031 restraints weight = 5055.625| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.60 r_work: 0.3056 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3999 Z= 0.148 Angle : 0.538 7.436 5431 Z= 0.287 Chirality : 0.042 0.152 630 Planarity : 0.004 0.035 665 Dihedral : 4.925 26.709 540 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.95 % Allowed : 13.95 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.78 (0.38), residues: 487 helix: 1.79 (0.29), residues: 294 sheet: 1.06 (0.64), residues: 59 loop : -0.04 (0.58), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.014 0.001 PHE C 27 TYR 0.019 0.001 TYR C 102 ARG 0.001 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.04820 ( 256) hydrogen bonds : angle 4.19620 ( 750) SS BOND : bond 0.00099 ( 1) SS BOND : angle 0.41008 ( 2) covalent geometry : bond 0.00333 ( 3998) covalent geometry : angle 0.53779 ( 5429) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.446 Fit side-chains REVERT: A 113 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.8246 (m-30) REVERT: A 368 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.6243 (mp0) REVERT: C 64 LYS cc_start: 0.7512 (tppt) cc_final: 0.7140 (mttp) REVERT: C 88 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6617 (pm20) outliers start: 17 outliers final: 12 residues processed: 65 average time/residue: 0.1521 time to fit residues: 12.6024 Evaluate side-chains 71 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 107 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 0.0050 chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 0.0670 chunk 3 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 0.0170 overall best weight: 0.2570 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.118718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.105110 restraints weight = 5073.712| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.61 r_work: 0.3145 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3999 Z= 0.112 Angle : 0.504 7.851 5431 Z= 0.266 Chirality : 0.041 0.162 630 Planarity : 0.004 0.034 665 Dihedral : 4.633 29.219 540 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.72 % Allowed : 15.12 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.38), residues: 487 helix: 2.08 (0.29), residues: 293 sheet: 1.27 (0.65), residues: 58 loop : 0.13 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 251 HIS 0.002 0.001 HIS A 334 PHE 0.011 0.001 PHE C 27 TYR 0.013 0.001 TYR C 102 ARG 0.001 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 256) hydrogen bonds : angle 4.03467 ( 750) SS BOND : bond 0.00023 ( 1) SS BOND : angle 0.39725 ( 2) covalent geometry : bond 0.00223 ( 3998) covalent geometry : angle 0.50428 ( 5429) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.412 Fit side-chains REVERT: A 113 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8210 (m-30) REVERT: A 303 LYS cc_start: 0.8752 (tppt) cc_final: 0.8141 (pttt) REVERT: A 368 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.6513 (mp0) REVERT: C 64 LYS cc_start: 0.7410 (tppt) cc_final: 0.7102 (mttp) REVERT: C 88 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6538 (pm20) outliers start: 16 outliers final: 7 residues processed: 74 average time/residue: 0.1372 time to fit residues: 13.1365 Evaluate side-chains 67 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 32 optimal weight: 0.0020 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 = 0.3386 r_free = 0.3386 target = 0.115634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.101679 restraints weight = 5071.119| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.66 r_work: 0.3112 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3999 Z= 0.121 Angle : 0.516 7.405 5431 Z= 0.273 Chirality : 0.041 0.163 630 Planarity : 0.004 0.035 665 Dihedral : 4.597 29.322 540 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.33 % Allowed : 16.98 % Favored : 80.70 % 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: 2.08 (0.38), residues: 487 helix: 2.01 (0.29), residues: 297 sheet: 1.17 (0.66), residues: 58 loop : 0.09 (0.61), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 251 HIS 0.002 0.001 HIS A 334 PHE 0.013 0.001 PHE C 27 TYR 0.016 0.001 TYR C 94 ARG 0.004 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 256) hydrogen bonds : angle 4.01644 ( 750) SS BOND : bond 0.00117 ( 1) SS BOND : angle 0.40372 ( 2) covalent geometry : bond 0.00256 ( 3998) covalent geometry : angle 0.51648 ( 5429) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.540 Fit side-chains REVERT: A 113 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8229 (m-30) REVERT: A 303 LYS cc_start: 0.8753 (tppt) cc_final: 0.8146 (pttt) REVERT: A 368 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7971 (mp0) REVERT: C 64 LYS cc_start: 0.7452 (tppt) cc_final: 0.7130 (mttp) REVERT: C 88 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6620 (pm20) outliers start: 10 outliers final: 7 residues processed: 58 average time/residue: 0.1783 time to fit residues: 13.5259 Evaluate side-chains 63 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 358 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.109908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.095905 restraints weight = 5172.018| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.65 r_work: 0.3011 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3999 Z= 0.201 Angle : 0.577 6.479 5431 Z= 0.309 Chirality : 0.044 0.161 630 Planarity : 0.004 0.036 665 Dihedral : 4.987 27.036 540 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.79 % Allowed : 16.98 % Favored : 80.23 % 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: 1.78 (0.38), residues: 487 helix: 1.79 (0.28), residues: 294 sheet: 0.91 (0.65), residues: 59 loop : 0.06 (0.60), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 398 HIS 0.003 0.001 HIS A 180 PHE 0.014 0.001 PHE A 163 TYR 0.023 0.002 TYR C 102 ARG 0.004 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.05268 ( 256) hydrogen bonds : angle 4.19495 ( 750) SS BOND : bond 0.00231 ( 1) SS BOND : angle 0.53213 ( 2) covalent geometry : bond 0.00471 ( 3998) covalent geometry : angle 0.57704 ( 5429) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8296 (m-30) REVERT: A 368 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.6168 (mp0) REVERT: A 407 ASN cc_start: 0.8425 (t0) cc_final: 0.8042 (t0) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.1313 time to fit residues: 11.4222 Evaluate side-chains 69 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 14 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 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.110868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.097115 restraints weight = 5045.693| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.62 r_work: 0.3018 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3999 Z= 0.151 Angle : 0.549 6.923 5431 Z= 0.292 Chirality : 0.044 0.316 630 Planarity : 0.004 0.035 665 Dihedral : 4.913 26.129 540 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.26 % Allowed : 16.28 % Favored : 80.47 % 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: 1.81 (0.38), residues: 487 helix: 1.81 (0.29), residues: 294 sheet: 0.92 (0.66), residues: 59 loop : 0.05 (0.60), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.013 0.001 PHE C 27 TYR 0.018 0.001 TYR C 102 ARG 0.004 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.04874 ( 256) hydrogen bonds : angle 4.14356 ( 750) SS BOND : bond 0.00153 ( 1) SS BOND : angle 0.43097 ( 2) covalent geometry : bond 0.00340 ( 3998) covalent geometry : angle 0.54924 ( 5429) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2663.90 seconds wall clock time: 47 minutes 33.69 seconds (2853.69 seconds total)