Starting phenix.real_space_refine on Wed Mar 5 22:57:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wn1_32619/03_2025/7wn1_32619.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wn1_32619/03_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_32619/03_2025/7wn1_32619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wn1_32619/03_2025/7wn1_32619.map" model { file = "/net/cci-nas-00/data/ceres_data/7wn1_32619/03_2025/7wn1_32619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wn1_32619/03_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.12, per 1000 atoms: 0.80 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: 0.93 Conformation dependent library (CDL) restraints added in 452.8 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: 0.35 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: 1.03 Time building geometry restraints manager: 1.10 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 1.415 1.600 -0.185 1.50e-02 4.44e+03 1.53e+02 bond pdb=" C1' NOS A 501 " pdb=" C2' NOS A 501 " ideal model delta sigma weight residual 1.526 1.346 0.180 1.50e-02 4.44e+03 1.44e+02 bond pdb=" C4' NOS A 501 " pdb=" O4' NOS A 501 " ideal model delta sigma weight residual 1.454 1.309 0.145 1.50e-02 4.44e+03 9.32e+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 ... (remaining 3993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 5332 2.00 - 4.00: 75 4.00 - 6.00: 16 6.00 - 8.00: 5 8.00 - 10.00: 1 Bond angle restraints: 5429 Sorted by residual: angle pdb=" C3' NOS A 501 " pdb=" C2' NOS A 501 " pdb=" O2' NOS A 501 " ideal model delta sigma weight residual 114.60 107.68 6.92 1.50e+00 4.44e-01 2.13e+01 angle pdb=" C3' NOS A 501 " pdb=" C4' NOS A 501 " pdb=" C5' NOS A 501 " ideal model delta sigma weight residual 115.20 109.44 5.76 1.50e+00 4.44e-01 1.47e+01 angle pdb=" C1' NOS A 501 " pdb=" O4' NOS A 501 " pdb=" C4' NOS A 501 " ideal model delta sigma weight residual 109.70 106.15 3.55 1.00e+00 1.00e+00 1.26e+01 angle pdb=" C2' NOS A 501 " pdb=" C1' NOS A 501 " pdb=" N9 NOS A 501 " ideal model delta sigma weight residual 114.00 108.75 5.25 1.50e+00 4.44e-01 1.23e+01 angle pdb=" C1' NOS A 501 " pdb=" C2' NOS A 501 " pdb=" C3' NOS A 501 " ideal model delta sigma weight residual 101.50 104.96 -3.46 1.00e+00 1.00e+00 1.20e+01 ... (remaining 5424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 2049 15.24 - 30.48: 201 30.48 - 45.71: 53 45.71 - 60.95: 17 60.95 - 76.19: 3 Dihedral angle restraints: 2323 sinusoidal: 899 harmonic: 1424 Sorted by residual: dihedral pdb=" C2' NOS A 501 " pdb=" C3' NOS A 501 " pdb=" C4' NOS A 501 " pdb=" O4' NOS A 501 " ideal model delta sinusoidal sigma weight residual 24.00 -2.88 26.88 1 8.00e+00 1.56e-02 1.62e+01 dihedral pdb=" C1' NOS A 501 " pdb=" C4' NOS A 501 " pdb=" O4' NOS A 501 " pdb=" C3' NOS A 501 " ideal model delta sinusoidal sigma weight residual 2.00 -22.80 24.80 1 8.00e+00 1.56e-02 1.38e+01 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 ... (remaining 2320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 372 0.031 - 0.061: 173 0.061 - 0.092: 57 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=" 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 chirality pdb=" CA PHE A 307 " pdb=" N PHE A 307 " pdb=" C PHE A 307 " pdb=" CB PHE A 307 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.59e-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: 1.530 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.960 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.670 ------------------------------------------------------------------------------- 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 0.185 3998 Z= 0.429 Angle : 0.648 10.003 5429 Z= 0.352 Chirality : 0.042 0.153 630 Planarity : 0.004 0.035 665 Dihedral : 13.827 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 *********************** 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 : 0.388 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: 0.1449 time to fit residues: 13.4733 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 : 0.422 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.113378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.100166 restraints weight = 5145.666| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.61 r_work: 0.3057 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3998 Z= 0.220 Angle : 0.574 6.538 5429 Z= 0.310 Chirality : 0.043 0.144 630 Planarity : 0.004 0.033 665 Dihedral : 5.598 37.655 540 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.33 % Allowed : 5.58 % Favored : 92.09 % 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: 1.39 (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 0.004 0.001 HIS A 180 PHE 0.017 0.001 PHE C 27 TYR 0.016 0.001 TYR C 102 ARG 0.002 0.001 ARG A 319 *********************** 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 73 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.459 Fit side-chains REVERT: A 303 LYS cc_start: 0.8775 (tppt) cc_final: 0.8560 (tppt) REVERT: A 407 ASN cc_start: 0.8460 (t0) cc_final: 0.8100 (t0) outliers start: 10 outliers final: 6 residues processed: 66 average time/residue: 0.1567 time to fit residues: 13.0826 Evaluate side-chains 61 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 233 MET 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: 0.9980 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.0770 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 overall best weight: 0.5696 ------------------------------------------------------------------------------- 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 = 0.3353 r_free = 0.3353 target = 0.113179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.099493 restraints weight = 5079.359| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.63 r_work: 0.3078 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3998 Z= 0.186 Angle : 0.528 6.539 5429 Z= 0.285 Chirality : 0.042 0.144 630 Planarity : 0.004 0.034 665 Dihedral : 5.166 32.332 540 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.33 % Allowed : 9.30 % 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: 1.76 (0.38), residues: 487 helix: 1.79 (0.29), residues: 288 sheet: 1.14 (0.64), residues: 58 loop : -0.03 (0.59), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.016 0.001 PHE C 27 TYR 0.020 0.001 TYR C 102 ARG 0.002 0.000 ARG A 319 *********************** 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 70 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 303 LYS cc_start: 0.8777 (tppt) cc_final: 0.8554 (tppt) outliers start: 10 outliers final: 7 residues processed: 63 average time/residue: 0.1423 time to fit residues: 11.8254 Evaluate side-chains 64 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 30 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.114098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.100620 restraints weight = 5098.043| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.58 r_work: 0.3089 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3998 Z= 0.217 Angle : 0.539 6.935 5429 Z= 0.290 Chirality : 0.043 0.144 630 Planarity : 0.004 0.035 665 Dihedral : 5.042 29.420 540 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.02 % Allowed : 12.09 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.38), residues: 487 helix: 1.82 (0.29), residues: 289 sheet: 1.12 (0.65), residues: 58 loop : 0.04 (0.59), residues: 140 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 0.016 0.001 TYR C 102 ARG 0.002 0.000 ARG A 319 *********************** 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 69 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8252 (m-30) REVERT: A 303 LYS cc_start: 0.8810 (tppt) cc_final: 0.8587 (tppt) outliers start: 13 outliers final: 7 residues processed: 61 average time/residue: 0.1436 time to fit residues: 11.3662 Evaluate side-chains 63 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 0.0670 chunk 31 optimal weight: 0.0870 chunk 19 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 = 0.3373 r_free = 0.3373 target = 0.114653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.100706 restraints weight = 5183.436| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.67 r_work: 0.3084 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3998 Z= 0.167 Angle : 0.512 7.359 5429 Z= 0.273 Chirality : 0.041 0.148 630 Planarity : 0.004 0.034 665 Dihedral : 4.826 26.757 540 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.56 % Allowed : 13.95 % Favored : 83.49 % 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: 1.93 (0.38), residues: 487 helix: 1.89 (0.29), residues: 294 sheet: 1.13 (0.65), residues: 58 loop : 0.07 (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 0.013 0.001 PHE C 27 TYR 0.015 0.001 TYR C 102 ARG 0.001 0.000 ARG A 319 *********************** 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 69 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8235 (m-30) REVERT: C 88 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6473 (pm20) outliers start: 11 outliers final: 5 residues processed: 63 average time/residue: 0.1429 time to fit residues: 11.6614 Evaluate side-chains 62 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 43 optimal weight: 0.0170 chunk 4 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.114868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.100892 restraints weight = 5121.020| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.65 r_work: 0.3072 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3998 Z= 0.180 Angle : 0.516 6.477 5429 Z= 0.275 Chirality : 0.041 0.151 630 Planarity : 0.004 0.035 665 Dihedral : 4.763 27.361 540 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.26 % Allowed : 13.49 % Favored : 83.26 % 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: 2.02 (0.38), residues: 487 helix: 1.95 (0.29), residues: 293 sheet: 1.17 (0.65), residues: 58 loop : 0.14 (0.59), residues: 136 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 0.013 0.001 PHE C 27 TYR 0.016 0.001 TYR C 102 ARG 0.001 0.000 ARG A 291 *********************** 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 71 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8227 (m-30) REVERT: C 88 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6544 (pm20) outliers start: 14 outliers final: 8 residues processed: 65 average time/residue: 0.1354 time to fit residues: 11.5990 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 : 0.441 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 27 optimal weight: 0.0970 chunk 10 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.0050 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.115920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.102082 restraints weight = 5049.232| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.64 r_work: 0.3098 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3998 Z= 0.163 Angle : 0.508 6.482 5429 Z= 0.271 Chirality : 0.041 0.155 630 Planarity : 0.004 0.035 665 Dihedral : 4.641 27.763 540 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.79 % Allowed : 14.42 % 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: 2.13 (0.38), residues: 487 helix: 2.03 (0.29), residues: 293 sheet: 1.27 (0.66), residues: 58 loop : 0.19 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 251 HIS 0.002 0.001 HIS A 334 PHE 0.012 0.001 PHE C 27 TYR 0.015 0.001 TYR C 102 ARG 0.001 0.000 ARG A 291 *********************** 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 68 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8251 (m-30) REVERT: C 88 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6587 (pm20) outliers start: 12 outliers final: 7 residues processed: 61 average time/residue: 0.1384 time to fit residues: 11.0685 Evaluate side-chains 64 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 0.2980 chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3349 r_free = 0.3349 target = 0.112933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.099084 restraints weight = 5102.331| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.64 r_work: 0.3068 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3998 Z= 0.200 Angle : 0.525 7.187 5429 Z= 0.280 Chirality : 0.042 0.158 630 Planarity : 0.004 0.035 665 Dihedral : 4.665 27.736 540 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.02 % Allowed : 15.12 % Favored : 81.86 % 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: 2.09 (0.38), residues: 487 helix: 2.00 (0.29), residues: 293 sheet: 1.23 (0.66), residues: 58 loop : 0.19 (0.60), residues: 136 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 0.013 0.001 PHE C 27 TYR 0.016 0.001 TYR C 102 ARG 0.001 0.000 ARG C 19 *********************** 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 72 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.505 Fit side-chains REVERT: A 113 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8239 (m-30) REVERT: C 64 LYS cc_start: 0.7858 (tppp) cc_final: 0.7647 (tppt) outliers start: 13 outliers final: 8 residues processed: 65 average time/residue: 0.1386 time to fit residues: 11.8137 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 : 0.395 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 32 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 43 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3363 r_free = 0.3363 target = 0.114331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.100733 restraints weight = 5095.545| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.61 r_work: 0.3066 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3998 Z= 0.198 Angle : 0.522 6.906 5429 Z= 0.279 Chirality : 0.042 0.161 630 Planarity : 0.004 0.035 665 Dihedral : 4.671 27.145 540 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.79 % Allowed : 15.35 % Favored : 81.86 % 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: 2.14 (0.38), residues: 487 helix: 2.01 (0.29), residues: 294 sheet: 1.26 (0.67), residues: 58 loop : 0.27 (0.61), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 112 HIS 0.002 0.001 HIS A 180 PHE 0.013 0.001 PHE C 27 TYR 0.017 0.001 TYR C 102 ARG 0.001 0.000 ARG C 19 *********************** 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 66 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.385 Fit side-chains REVERT: A 113 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8241 (m-30) REVERT: C 88 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6580 (pm20) outliers start: 12 outliers final: 9 residues processed: 61 average time/residue: 0.1507 time to fit residues: 11.7788 Evaluate side-chains 65 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 297 THR Chi-restraints excluded: chain A residue 307 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.112537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.098547 restraints weight = 5144.335| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.66 r_work: 0.3059 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3998 Z= 0.202 Angle : 0.525 6.835 5429 Z= 0.282 Chirality : 0.042 0.163 630 Planarity : 0.004 0.035 665 Dihedral : 4.665 27.266 540 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.49 % Allowed : 14.42 % 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: 2.10 (0.38), residues: 487 helix: 2.01 (0.29), residues: 294 sheet: 1.23 (0.65), residues: 59 loop : 0.18 (0.60), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 112 HIS 0.002 0.001 HIS A 180 PHE 0.013 0.001 PHE C 27 TYR 0.017 0.001 TYR C 102 ARG 0.001 0.000 ARG C 45 ********************** 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 70 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.403 Fit side-chains REVERT: A 113 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8255 (m-30) REVERT: A 375 LYS cc_start: 0.8473 (ttmm) cc_final: 0.8155 (mmtm) REVERT: C 64 LYS cc_start: 0.7498 (tppt) cc_final: 0.7163 (mttp) REVERT: C 88 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6685 (pm20) outliers start: 15 outliers final: 10 residues processed: 64 average time/residue: 0.1607 time to fit residues: 13.2686 Evaluate side-chains 67 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 297 THR Chi-restraints excluded: chain A residue 307 PHE 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 Chi-restraints excluded: chain C residue 107 VAL 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: 0.6980 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 38 optimal weight: 0.0770 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3358 r_free = 0.3358 target = 0.113746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.100142 restraints weight = 5027.428| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.62 r_work: 0.3081 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3998 Z= 0.177 Angle : 0.513 6.893 5429 Z= 0.275 Chirality : 0.042 0.166 630 Planarity : 0.004 0.035 665 Dihedral : 4.600 28.034 540 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.26 % Allowed : 14.88 % Favored : 81.86 % 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: 2.24 (0.39), residues: 487 helix: 2.11 (0.29), residues: 293 sheet: 1.30 (0.66), residues: 58 loop : 0.26 (0.61), residues: 136 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 0.012 0.001 PHE C 27 TYR 0.016 0.001 TYR C 102 ARG 0.001 0.000 ARG C 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2218.61 seconds wall clock time: 39 minutes 4.76 seconds (2344.76 seconds total)