Starting phenix.real_space_refine on Fri Oct 10 11:52:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xb2_38208/10_2025/8xb2_38208_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xb2_38208/10_2025/8xb2_38208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xb2_38208/10_2025/8xb2_38208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xb2_38208/10_2025/8xb2_38208.map" model { file = "/net/cci-nas-00/data/ceres_data/8xb2_38208/10_2025/8xb2_38208_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xb2_38208/10_2025/8xb2_38208_trim.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 20 5.16 5 Cl 1 4.86 5 C 2907 2.51 5 N 666 2.21 5 O 730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4324 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4293 Classifications: {'peptide': 536} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 516} Chain breaks: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'NAG': 1, 'YNT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.32, per 1000 atoms: 0.31 Number of scatterers: 4324 At special positions: 0 Unit cell: (68.04, 66.96, 92.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 20 16.00 O 730 8.00 N 666 7.00 C 2907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 184 " Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 148.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 988 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 0 sheets defined 76.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 67 through 74 removed outlier: 3.507A pdb=" N VAL A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 89 removed outlier: 4.153A pdb=" N TYR A 84 " --> pdb=" O TRP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 106 through 121 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.974A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A 129 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 125 through 130' Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 removed outlier: 3.629A pdb=" N GLY A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 156 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 251 Processing helix chain 'A' and resid 264 through 284 Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 286 through 296 Processing helix chain 'A' and resid 305 through 319 removed outlier: 3.524A pdb=" N ILE A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 332 removed outlier: 4.053A pdb=" N TYR A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 372 removed outlier: 3.565A pdb=" N ASP A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.864A pdb=" N VAL A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.535A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 removed outlier: 3.881A pdb=" N HIS A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 458 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.754A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 495 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.571A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 577 Processing helix chain 'A' and resid 583 through 591 removed outlier: 3.532A pdb=" N GLY A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 616 267 hydrogen bonds defined for protein. 786 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.54 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1261 1.34 - 1.46: 1253 1.46 - 1.58: 1919 1.58 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 4465 Sorted by residual: bond pdb=" C05 YNT A 702 " pdb=" N04 YNT A 702 " ideal model delta sigma weight residual 1.467 1.568 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C06 YNT A 702 " pdb=" N04 YNT A 702 " ideal model delta sigma weight residual 1.454 1.553 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" C05 YNT A 702 " pdb=" C08 YNT A 702 " ideal model delta sigma weight residual 1.526 1.455 0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C06 YNT A 702 " pdb=" C11 YNT A 702 " ideal model delta sigma weight residual 1.520 1.451 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C06 YNT A 702 " pdb=" C07 YNT A 702 " ideal model delta sigma weight residual 1.549 1.513 0.036 2.00e-02 2.50e+03 3.26e+00 ... (remaining 4460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 5824 1.21 - 2.42: 212 2.42 - 3.63: 52 3.63 - 4.85: 7 4.85 - 6.06: 2 Bond angle restraints: 6097 Sorted by residual: angle pdb=" N GLY A 582 " pdb=" CA GLY A 582 " pdb=" C GLY A 582 " ideal model delta sigma weight residual 110.96 113.67 -2.71 1.19e+00 7.06e-01 5.18e+00 angle pdb=" N LEU A 67 " pdb=" CA LEU A 67 " pdb=" C LEU A 67 " ideal model delta sigma weight residual 113.43 110.67 2.76 1.26e+00 6.30e-01 4.81e+00 angle pdb=" N GLY A 324 " pdb=" CA GLY A 324 " pdb=" C GLY A 324 " ideal model delta sigma weight residual 115.30 112.25 3.05 1.44e+00 4.82e-01 4.48e+00 angle pdb=" C06 YNT A 702 " pdb=" C07 YNT A 702 " pdb=" O03 YNT A 702 " ideal model delta sigma weight residual 107.29 113.35 -6.06 3.00e+00 1.11e-01 4.08e+00 angle pdb=" N GLY A 591 " pdb=" CA GLY A 591 " pdb=" C GLY A 591 " ideal model delta sigma weight residual 115.66 112.54 3.12 1.56e+00 4.11e-01 4.00e+00 ... (remaining 6092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.19: 2364 22.19 - 44.38: 129 44.38 - 66.57: 16 66.57 - 88.75: 4 88.75 - 110.94: 6 Dihedral angle restraints: 2519 sinusoidal: 968 harmonic: 1551 Sorted by residual: dihedral pdb=" C1 NAG A 701 " pdb=" C2 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" O3 NAG A 701 " ideal model delta sinusoidal sigma weight residual -175.09 -64.15 -110.94 1 3.00e+01 1.11e-03 1.45e+01 dihedral pdb=" C1 NAG A 701 " pdb=" C2 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" C4 NAG A 701 " ideal model delta sinusoidal sigma weight residual -52.39 57.20 -109.59 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" N2 NAG A 701 " pdb=" C2 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" O3 NAG A 701 " ideal model delta sinusoidal sigma weight residual 62.25 171.40 -109.15 1 3.00e+01 1.11e-03 1.42e+01 ... (remaining 2516 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 592 0.058 - 0.116: 85 0.116 - 0.175: 5 0.175 - 0.233: 0 0.233 - 0.291: 1 Chirality restraints: 683 Sorted by residual: chirality pdb=" C06 YNT A 702 " pdb=" C07 YNT A 702 " pdb=" C11 YNT A 702 " pdb=" N04 YNT A 702 " both_signs ideal model delta sigma weight residual False 2.39 2.68 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA PRO A 132 " pdb=" N PRO A 132 " pdb=" C PRO A 132 " pdb=" CB PRO A 132 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 680 not shown) Planarity restraints: 738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 391 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO A 392 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 392 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 392 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 253 " 0.011 2.00e-02 2.50e+03 9.58e-03 2.30e+00 pdb=" CG TRP A 253 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 253 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 253 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 253 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 253 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 253 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 253 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 253 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 253 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 550 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO A 551 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 551 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 551 " 0.019 5.00e-02 4.00e+02 ... (remaining 735 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 634 2.75 - 3.28: 4644 3.28 - 3.82: 7436 3.82 - 4.36: 9276 4.36 - 4.90: 15905 Nonbonded interactions: 37895 Sorted by model distance: nonbonded pdb=" OD1 ASP A 75 " pdb=" OG SER A 419 " model vdw 2.208 3.040 nonbonded pdb=" O CYS A 520 " pdb=" OG SER A 525 " model vdw 2.245 3.040 nonbonded pdb=" O GLY A 281 " pdb=" N LEU A 284 " model vdw 2.308 3.120 nonbonded pdb=" O LEU A 252 " pdb=" NH1 ARG A 442 " model vdw 2.335 3.120 nonbonded pdb=" NE2 GLN A 118 " pdb=" O PHE A 335 " model vdw 2.348 3.120 ... (remaining 37890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.790 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 4467 Z= 0.235 Angle : 0.574 6.057 6102 Z= 0.335 Chirality : 0.041 0.291 683 Planarity : 0.004 0.043 737 Dihedral : 15.203 110.943 1528 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 31.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.70 (0.32), residues: 530 helix: -1.32 (0.23), residues: 368 sheet: None (None), residues: 0 loop : -2.60 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 301 TYR 0.016 0.001 TYR A 205 PHE 0.014 0.001 PHE A 408 TRP 0.026 0.001 TRP A 253 HIS 0.003 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 4465) covalent geometry : angle 0.57087 ( 6097) SS BOND : bond 0.00013 ( 1) SS BOND : angle 1.80166 ( 2) hydrogen bonds : bond 0.12003 ( 267) hydrogen bonds : angle 6.43827 ( 786) link_NAG-ASN : bond 0.00415 ( 1) link_NAG-ASN : angle 2.37876 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.170 Fit side-chains REVERT: A 329 PHE cc_start: 0.8463 (t80) cc_final: 0.7783 (m-10) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.0860 time to fit residues: 10.1381 Evaluate side-chains 68 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 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 89 ASN A 220 HIS A 234 GLN A 372 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.125453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.109751 restraints weight = 5703.964| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.49 r_work: 0.3090 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 4467 Z= 0.172 Angle : 0.597 6.216 6102 Z= 0.301 Chirality : 0.044 0.291 683 Planarity : 0.005 0.044 737 Dihedral : 9.504 79.234 622 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.65 % Allowed : 12.17 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.35), residues: 530 helix: 0.25 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -1.59 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 607 TYR 0.018 0.002 TYR A 84 PHE 0.014 0.002 PHE A 362 TRP 0.014 0.001 TRP A 253 HIS 0.003 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 4465) covalent geometry : angle 0.59347 ( 6097) SS BOND : bond 0.00166 ( 1) SS BOND : angle 2.15049 ( 2) hydrogen bonds : bond 0.04316 ( 267) hydrogen bonds : angle 4.79014 ( 786) link_NAG-ASN : bond 0.01193 ( 1) link_NAG-ASN : angle 2.24990 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.165 Fit side-chains REVERT: A 232 LEU cc_start: 0.8396 (mt) cc_final: 0.8193 (mp) REVERT: A 282 VAL cc_start: 0.8914 (t) cc_final: 0.8538 (m) REVERT: A 329 PHE cc_start: 0.8505 (t80) cc_final: 0.7326 (m-10) REVERT: A 421 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7490 (mtp) REVERT: A 556 TRP cc_start: 0.7011 (m100) cc_final: 0.6523 (m-10) REVERT: A 607 ARG cc_start: 0.7485 (mtm110) cc_final: 0.6794 (ptm-80) outliers start: 12 outliers final: 7 residues processed: 86 average time/residue: 0.0626 time to fit residues: 7.0646 Evaluate side-chains 75 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 601 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 21 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 17 optimal weight: 0.4980 chunk 14 optimal weight: 0.0020 chunk 52 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.132710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.118329 restraints weight = 5610.796| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.36 r_work: 0.3176 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4467 Z= 0.120 Angle : 0.536 7.206 6102 Z= 0.267 Chirality : 0.041 0.260 683 Planarity : 0.004 0.040 737 Dihedral : 8.346 68.363 622 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.33 % Allowed : 15.71 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.36), residues: 530 helix: 0.96 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -1.18 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 341 TYR 0.017 0.001 TYR A 84 PHE 0.016 0.001 PHE A 408 TRP 0.008 0.001 TRP A 553 HIS 0.003 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4465) covalent geometry : angle 0.53407 ( 6097) SS BOND : bond 0.00065 ( 1) SS BOND : angle 1.44824 ( 2) hydrogen bonds : bond 0.03816 ( 267) hydrogen bonds : angle 4.41784 ( 786) link_NAG-ASN : bond 0.01000 ( 1) link_NAG-ASN : angle 2.04824 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.139 Fit side-chains REVERT: A 107 MET cc_start: 0.8549 (ttm) cc_final: 0.8322 (ttm) REVERT: A 232 LEU cc_start: 0.8328 (mt) cc_final: 0.8110 (mp) REVERT: A 329 PHE cc_start: 0.8419 (t80) cc_final: 0.7346 (m-10) REVERT: A 421 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7559 (mtp) REVERT: A 556 TRP cc_start: 0.6992 (m100) cc_final: 0.6586 (m-10) REVERT: A 607 ARG cc_start: 0.7461 (mtm110) cc_final: 0.6960 (ptm-80) outliers start: 6 outliers final: 4 residues processed: 78 average time/residue: 0.0547 time to fit residues: 5.8080 Evaluate side-chains 74 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 50 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.125523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.109544 restraints weight = 5588.796| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.51 r_work: 0.3131 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4467 Z= 0.180 Angle : 0.578 7.292 6102 Z= 0.289 Chirality : 0.044 0.244 683 Planarity : 0.005 0.049 737 Dihedral : 7.899 62.235 622 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.10 % Allowed : 15.93 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.36), residues: 530 helix: 1.07 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -1.14 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 341 TYR 0.020 0.002 TYR A 84 PHE 0.014 0.002 PHE A 409 TRP 0.009 0.001 TRP A 253 HIS 0.004 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 4465) covalent geometry : angle 0.57476 ( 6097) SS BOND : bond 0.00092 ( 1) SS BOND : angle 1.88623 ( 2) hydrogen bonds : bond 0.04182 ( 267) hydrogen bonds : angle 4.53927 ( 786) link_NAG-ASN : bond 0.00845 ( 1) link_NAG-ASN : angle 2.22850 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.166 Fit side-chains REVERT: A 232 LEU cc_start: 0.8417 (mt) cc_final: 0.8193 (mp) REVERT: A 329 PHE cc_start: 0.8510 (t80) cc_final: 0.7490 (m-10) REVERT: A 421 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7638 (mtp) REVERT: A 556 TRP cc_start: 0.7101 (m100) cc_final: 0.6659 (m-10) REVERT: A 607 ARG cc_start: 0.7458 (mtm110) cc_final: 0.6866 (ptm-80) outliers start: 14 outliers final: 10 residues processed: 78 average time/residue: 0.0567 time to fit residues: 5.9004 Evaluate side-chains 75 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 601 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 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 = 0.3730 r_free = 0.3730 target = 0.147597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.134717 restraints weight = 5462.779| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.27 r_work: 0.3298 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4467 Z= 0.157 Angle : 0.557 7.217 6102 Z= 0.278 Chirality : 0.042 0.225 683 Planarity : 0.004 0.049 737 Dihedral : 7.371 56.564 622 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.54 % Allowed : 17.70 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.36), residues: 530 helix: 1.22 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -1.00 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 341 TYR 0.020 0.002 TYR A 84 PHE 0.018 0.001 PHE A 408 TRP 0.007 0.001 TRP A 553 HIS 0.005 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 4465) covalent geometry : angle 0.55426 ( 6097) SS BOND : bond 0.00087 ( 1) SS BOND : angle 1.76960 ( 2) hydrogen bonds : bond 0.03992 ( 267) hydrogen bonds : angle 4.47781 ( 786) link_NAG-ASN : bond 0.00805 ( 1) link_NAG-ASN : angle 2.31356 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.163 Fit side-chains REVERT: A 107 MET cc_start: 0.8590 (ttm) cc_final: 0.8372 (ttm) REVERT: A 317 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.9012 (t80) REVERT: A 329 PHE cc_start: 0.8511 (t80) cc_final: 0.7544 (m-10) REVERT: A 377 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7718 (pm20) REVERT: A 421 MET cc_start: 0.8107 (ttm) cc_final: 0.7655 (mtp) REVERT: A 434 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8058 (m-30) REVERT: A 556 TRP cc_start: 0.7040 (m100) cc_final: 0.6630 (m-10) REVERT: A 607 ARG cc_start: 0.7268 (mtm110) cc_final: 0.6964 (ptm-80) outliers start: 16 outliers final: 10 residues processed: 80 average time/residue: 0.0688 time to fit residues: 7.2738 Evaluate side-chains 79 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 601 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 52 optimal weight: 0.0470 chunk 20 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.142880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.129212 restraints weight = 5580.841| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.38 r_work: 0.3229 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4467 Z= 0.129 Angle : 0.537 7.595 6102 Z= 0.264 Chirality : 0.041 0.200 683 Planarity : 0.004 0.047 737 Dihedral : 6.560 48.423 622 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.10 % Allowed : 19.69 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.36), residues: 530 helix: 1.46 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -0.79 (0.47), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 341 TYR 0.017 0.001 TYR A 84 PHE 0.016 0.001 PHE A 408 TRP 0.008 0.001 TRP A 553 HIS 0.005 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4465) covalent geometry : angle 0.53421 ( 6097) SS BOND : bond 0.00034 ( 1) SS BOND : angle 1.46134 ( 2) hydrogen bonds : bond 0.03711 ( 267) hydrogen bonds : angle 4.37563 ( 786) link_NAG-ASN : bond 0.00710 ( 1) link_NAG-ASN : angle 2.48598 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.195 Fit side-chains REVERT: A 107 MET cc_start: 0.8562 (ttm) cc_final: 0.8332 (ttm) REVERT: A 329 PHE cc_start: 0.8442 (t80) cc_final: 0.7404 (m-10) REVERT: A 377 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: A 382 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8160 (mt-10) REVERT: A 421 MET cc_start: 0.8067 (ttm) cc_final: 0.7611 (mtp) REVERT: A 556 TRP cc_start: 0.7008 (m100) cc_final: 0.6611 (m-10) outliers start: 14 outliers final: 6 residues processed: 85 average time/residue: 0.0619 time to fit residues: 7.0189 Evaluate side-chains 83 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.148965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.136105 restraints weight = 5475.814| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.27 r_work: 0.3272 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4467 Z= 0.139 Angle : 0.545 7.038 6102 Z= 0.272 Chirality : 0.042 0.180 683 Planarity : 0.004 0.047 737 Dihedral : 6.233 43.216 622 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.54 % Allowed : 20.13 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.36), residues: 530 helix: 1.33 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -0.82 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 341 TYR 0.021 0.001 TYR A 590 PHE 0.016 0.001 PHE A 408 TRP 0.007 0.001 TRP A 553 HIS 0.005 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4465) covalent geometry : angle 0.54135 ( 6097) SS BOND : bond 0.00076 ( 1) SS BOND : angle 1.59546 ( 2) hydrogen bonds : bond 0.03818 ( 267) hydrogen bonds : angle 4.41329 ( 786) link_NAG-ASN : bond 0.00654 ( 1) link_NAG-ASN : angle 2.59334 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.173 Fit side-chains REVERT: A 107 MET cc_start: 0.8600 (ttm) cc_final: 0.8363 (ttm) REVERT: A 329 PHE cc_start: 0.8443 (t80) cc_final: 0.7414 (m-10) REVERT: A 377 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7736 (pm20) REVERT: A 382 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8124 (mt-10) REVERT: A 421 MET cc_start: 0.8085 (ttm) cc_final: 0.7601 (mtp) REVERT: A 434 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8052 (m-30) REVERT: A 556 TRP cc_start: 0.6988 (m100) cc_final: 0.6575 (m-10) outliers start: 16 outliers final: 11 residues processed: 84 average time/residue: 0.0608 time to fit residues: 6.8001 Evaluate side-chains 86 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 16 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.149213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.136320 restraints weight = 5481.717| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.27 r_work: 0.3317 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4467 Z= 0.135 Angle : 0.540 7.391 6102 Z= 0.269 Chirality : 0.041 0.167 683 Planarity : 0.005 0.088 737 Dihedral : 5.937 38.153 622 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.42 % Allowed : 19.91 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.36), residues: 530 helix: 1.36 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.74 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 607 TYR 0.016 0.001 TYR A 590 PHE 0.016 0.001 PHE A 408 TRP 0.007 0.001 TRP A 553 HIS 0.005 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4465) covalent geometry : angle 0.53673 ( 6097) SS BOND : bond 0.00024 ( 1) SS BOND : angle 1.57160 ( 2) hydrogen bonds : bond 0.03766 ( 267) hydrogen bonds : angle 4.39206 ( 786) link_NAG-ASN : bond 0.00642 ( 1) link_NAG-ASN : angle 2.54697 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.189 Fit side-chains REVERT: A 107 MET cc_start: 0.8578 (ttm) cc_final: 0.8333 (ttm) REVERT: A 329 PHE cc_start: 0.8454 (t80) cc_final: 0.7474 (m-10) REVERT: A 377 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7707 (pm20) REVERT: A 382 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: A 421 MET cc_start: 0.8053 (ttm) cc_final: 0.7553 (mtp) REVERT: A 434 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8036 (m-30) REVERT: A 556 TRP cc_start: 0.7038 (m100) cc_final: 0.6677 (m-10) outliers start: 20 outliers final: 14 residues processed: 86 average time/residue: 0.0644 time to fit residues: 7.3737 Evaluate side-chains 86 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 601 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.148089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.135175 restraints weight = 5531.310| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.26 r_work: 0.3306 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4467 Z= 0.149 Angle : 0.549 7.112 6102 Z= 0.276 Chirality : 0.042 0.162 683 Planarity : 0.005 0.085 737 Dihedral : 5.740 36.082 622 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.42 % Allowed : 20.13 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.36), residues: 530 helix: 1.31 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.77 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 607 TYR 0.016 0.001 TYR A 84 PHE 0.017 0.001 PHE A 408 TRP 0.008 0.001 TRP A 128 HIS 0.005 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 4465) covalent geometry : angle 0.54590 ( 6097) SS BOND : bond 0.00024 ( 1) SS BOND : angle 1.71617 ( 2) hydrogen bonds : bond 0.03892 ( 267) hydrogen bonds : angle 4.43688 ( 786) link_NAG-ASN : bond 0.00619 ( 1) link_NAG-ASN : angle 2.40283 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.164 Fit side-chains REVERT: A 101 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7743 (t80) REVERT: A 107 MET cc_start: 0.8628 (ttm) cc_final: 0.8385 (ttm) REVERT: A 329 PHE cc_start: 0.8466 (t80) cc_final: 0.7528 (m-10) REVERT: A 377 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7693 (pm20) REVERT: A 382 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8125 (mt-10) REVERT: A 421 MET cc_start: 0.8104 (ttm) cc_final: 0.7571 (mtp) REVERT: A 434 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8059 (m-30) REVERT: A 556 TRP cc_start: 0.7024 (m100) cc_final: 0.6606 (m-10) outliers start: 20 outliers final: 15 residues processed: 84 average time/residue: 0.0574 time to fit residues: 6.4983 Evaluate side-chains 89 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.141595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.127967 restraints weight = 5515.305| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.35 r_work: 0.3214 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4467 Z= 0.149 Angle : 0.546 7.150 6102 Z= 0.275 Chirality : 0.042 0.158 683 Planarity : 0.005 0.090 737 Dihedral : 5.454 32.814 622 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.98 % Allowed : 20.35 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.36), residues: 530 helix: 1.33 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.78 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 607 TYR 0.016 0.001 TYR A 84 PHE 0.016 0.001 PHE A 408 TRP 0.007 0.001 TRP A 553 HIS 0.005 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 4465) covalent geometry : angle 0.54336 ( 6097) SS BOND : bond 0.00013 ( 1) SS BOND : angle 1.67484 ( 2) hydrogen bonds : bond 0.03869 ( 267) hydrogen bonds : angle 4.43301 ( 786) link_NAG-ASN : bond 0.00599 ( 1) link_NAG-ASN : angle 2.23633 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.151 Fit side-chains REVERT: A 101 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7729 (t80) REVERT: A 107 MET cc_start: 0.8604 (ttm) cc_final: 0.8360 (ttm) REVERT: A 329 PHE cc_start: 0.8485 (t80) cc_final: 0.7463 (m-10) REVERT: A 377 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7713 (pm20) REVERT: A 382 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8205 (mt-10) REVERT: A 421 MET cc_start: 0.8066 (ttm) cc_final: 0.7529 (mtp) REVERT: A 434 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8080 (m-30) REVERT: A 556 TRP cc_start: 0.7024 (m100) cc_final: 0.6575 (m-10) outliers start: 18 outliers final: 13 residues processed: 81 average time/residue: 0.0605 time to fit residues: 6.5530 Evaluate side-chains 86 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.0980 chunk 48 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.0000 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 0.0060 chunk 50 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 overall best weight: 0.2600 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.141141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.126471 restraints weight = 5548.253| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.45 r_work: 0.3258 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4467 Z= 0.106 Angle : 0.503 6.952 6102 Z= 0.254 Chirality : 0.039 0.144 683 Planarity : 0.005 0.087 737 Dihedral : 4.961 28.495 622 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.65 % Allowed : 21.46 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.37), residues: 530 helix: 1.49 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -0.61 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 607 TYR 0.014 0.001 TYR A 84 PHE 0.013 0.001 PHE A 408 TRP 0.008 0.001 TRP A 553 HIS 0.005 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 4465) covalent geometry : angle 0.50098 ( 6097) SS BOND : bond 0.00013 ( 1) SS BOND : angle 1.02916 ( 2) hydrogen bonds : bond 0.03473 ( 267) hydrogen bonds : angle 4.26114 ( 786) link_NAG-ASN : bond 0.00600 ( 1) link_NAG-ASN : angle 1.99644 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1154.67 seconds wall clock time: 20 minutes 28.94 seconds (1228.94 seconds total)