Starting phenix.real_space_refine on Wed Jul 23 21:17:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xb2_38208/07_2025/8xb2_38208_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xb2_38208/07_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_38208/07_2025/8xb2_38208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xb2_38208/07_2025/8xb2_38208.map" model { file = "/net/cci-nas-00/data/ceres_data/8xb2_38208/07_2025/8xb2_38208_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xb2_38208/07_2025/8xb2_38208_trim.cif" } resolution = 3.04 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= -0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.18, per 1000 atoms: 0.74 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: 1.08 Conformation dependent library (CDL) restraints added in 467.3 milliseconds 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: 0.45 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: 1.20 Time building geometry restraints manager: 1.29 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.710 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.500 ------------------------------------------------------------------------------- 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 : 31.49 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 (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: -2.70 (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 TRP 0.026 0.001 TRP A 253 HIS 0.003 0.001 HIS A 613 PHE 0.014 0.001 PHE A 408 TYR 0.016 0.001 TYR A 205 ARG 0.001 0.000 ARG A 301 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 1) link_NAG-ASN : angle 2.37876 ( 3) hydrogen bonds : bond 0.12003 ( 267) hydrogen bonds : angle 6.43827 ( 786) SS BOND : bond 0.00013 ( 1) SS BOND : angle 1.80166 ( 2) covalent geometry : bond 0.00493 ( 4465) covalent geometry : angle 0.57087 ( 6097) *********************** 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 : 0.476 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: 0.1998 time to fit residues: 23.3319 Evaluate side-chains 69 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.0570 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.130010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.116275 restraints weight = 5585.301| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.23 r_work: 0.3153 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4467 Z= 0.153 Angle : 0.584 6.279 6102 Z= 0.294 Chirality : 0.044 0.287 683 Planarity : 0.005 0.042 737 Dihedral : 9.502 79.255 622 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.99 % Allowed : 12.17 % Favored : 85.84 % 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: -0.41 (0.35), residues: 530 helix: 0.33 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -1.57 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 253 HIS 0.003 0.001 HIS A 613 PHE 0.013 0.002 PHE A 110 TYR 0.017 0.002 TYR A 84 ARG 0.011 0.001 ARG A 607 Details of bonding type rmsd link_NAG-ASN : bond 0.01184 ( 1) link_NAG-ASN : angle 2.26177 ( 3) hydrogen bonds : bond 0.04165 ( 267) hydrogen bonds : angle 4.72796 ( 786) SS BOND : bond 0.00154 ( 1) SS BOND : angle 2.04755 ( 2) covalent geometry : bond 0.00358 ( 4465) covalent geometry : angle 0.58049 ( 6097) *********************** 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: 9 poor density : 83 time to evaluate : 0.486 Fit side-chains REVERT: A 232 LEU cc_start: 0.8388 (mt) cc_final: 0.8168 (mp) REVERT: A 282 VAL cc_start: 0.8893 (t) cc_final: 0.8534 (m) REVERT: A 329 PHE cc_start: 0.8523 (t80) cc_final: 0.7414 (m-10) REVERT: A 421 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7526 (mtp) REVERT: A 556 TRP cc_start: 0.6953 (m100) cc_final: 0.6524 (m-10) REVERT: A 607 ARG cc_start: 0.7411 (mtm110) cc_final: 0.6815 (ptm-80) outliers start: 9 outliers final: 5 residues processed: 86 average time/residue: 0.1442 time to fit residues: 16.2832 Evaluate side-chains 75 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU 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 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 14 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 42 optimal weight: 0.0870 chunk 51 optimal weight: 0.0050 overall best weight: 0.3772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.132573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.118219 restraints weight = 5574.377| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.35 r_work: 0.3172 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2352 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= 0.122 Angle : 0.534 7.183 6102 Z= 0.265 Chirality : 0.041 0.258 683 Planarity : 0.004 0.040 737 Dihedral : 8.336 68.423 622 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.99 % Allowed : 14.60 % Favored : 83.41 % 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: 0.56 (0.36), residues: 530 helix: 1.00 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -1.17 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.003 0.001 HIS A 613 PHE 0.018 0.001 PHE A 408 TYR 0.017 0.001 TYR A 84 ARG 0.007 0.001 ARG A 341 Details of bonding type rmsd link_NAG-ASN : bond 0.01007 ( 1) link_NAG-ASN : angle 2.09649 ( 3) hydrogen bonds : bond 0.03816 ( 267) hydrogen bonds : angle 4.43472 ( 786) SS BOND : bond 0.00049 ( 1) SS BOND : angle 1.49383 ( 2) covalent geometry : bond 0.00281 ( 4465) covalent geometry : angle 0.53174 ( 6097) *********************** 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 85 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.494 Fit side-chains REVERT: A 232 LEU cc_start: 0.8317 (mt) cc_final: 0.8099 (mp) REVERT: A 329 PHE cc_start: 0.8388 (t80) cc_final: 0.7276 (m-10) REVERT: A 421 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7539 (mtp) REVERT: A 556 TRP cc_start: 0.6969 (m100) cc_final: 0.6564 (m-10) REVERT: A 607 ARG cc_start: 0.7493 (mtm110) cc_final: 0.7000 (ptm-80) outliers start: 9 outliers final: 6 residues processed: 81 average time/residue: 0.1429 time to fit residues: 15.4240 Evaluate side-chains 76 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 276 VAL Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 455 LEU 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 12 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3404 r_free = 0.3404 target = 0.127895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.112598 restraints weight = 5656.736| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.42 r_work: 0.3189 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2377 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= 0.148 Angle : 0.547 7.311 6102 Z= 0.272 Chirality : 0.042 0.240 683 Planarity : 0.004 0.045 737 Dihedral : 7.713 61.627 622 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.32 % Allowed : 15.49 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.87 (0.36), residues: 530 helix: 1.23 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -1.05 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 128 HIS 0.004 0.001 HIS A 613 PHE 0.012 0.002 PHE A 403 TYR 0.019 0.001 TYR A 84 ARG 0.009 0.001 ARG A 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00904 ( 1) link_NAG-ASN : angle 2.19552 ( 3) hydrogen bonds : bond 0.03921 ( 267) hydrogen bonds : angle 4.43281 ( 786) SS BOND : bond 0.00037 ( 1) SS BOND : angle 1.60263 ( 2) covalent geometry : bond 0.00355 ( 4465) covalent geometry : angle 0.54443 ( 6097) *********************** 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 88 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.636 Fit side-chains REVERT: A 107 MET cc_start: 0.8639 (ttm) cc_final: 0.8424 (ttm) REVERT: A 232 LEU cc_start: 0.8344 (mt) cc_final: 0.8139 (mp) REVERT: A 329 PHE cc_start: 0.8483 (t80) cc_final: 0.7502 (m-10) REVERT: A 421 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7596 (mtp) REVERT: A 556 TRP cc_start: 0.7052 (m100) cc_final: 0.6638 (m-10) REVERT: A 607 ARG cc_start: 0.7473 (mtm110) cc_final: 0.7008 (ptm-80) outliers start: 15 outliers final: 11 residues processed: 82 average time/residue: 0.1607 time to fit residues: 17.6544 Evaluate side-chains 80 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 361 ILE 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 28 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 0.0470 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.149651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.136736 restraints weight = 5508.839| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.28 r_work: 0.3324 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2551 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= 0.137 Angle : 0.535 7.135 6102 Z= 0.266 Chirality : 0.042 0.217 683 Planarity : 0.004 0.045 737 Dihedral : 7.047 54.575 622 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.32 % Allowed : 17.48 % Favored : 79.20 % 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: 1.10 (0.36), residues: 530 helix: 1.38 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -0.90 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.004 0.001 HIS A 613 PHE 0.017 0.001 PHE A 408 TYR 0.018 0.001 TYR A 84 ARG 0.007 0.001 ARG A 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00795 ( 1) link_NAG-ASN : angle 2.36470 ( 3) hydrogen bonds : bond 0.03803 ( 267) hydrogen bonds : angle 4.38540 ( 786) SS BOND : bond 0.00042 ( 1) SS BOND : angle 1.56085 ( 2) covalent geometry : bond 0.00326 ( 4465) covalent geometry : angle 0.53180 ( 6097) *********************** 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 87 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.423 Fit side-chains REVERT: A 107 MET cc_start: 0.8590 (ttm) cc_final: 0.8350 (ttm) REVERT: A 329 PHE cc_start: 0.8503 (t80) cc_final: 0.7549 (m-10) REVERT: A 382 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: A 421 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7613 (mtp) REVERT: A 556 TRP cc_start: 0.7022 (m100) cc_final: 0.6668 (m-10) REVERT: A 607 ARG cc_start: 0.7235 (mtm110) cc_final: 0.6906 (ptm-80) outliers start: 15 outliers final: 11 residues processed: 80 average time/residue: 0.1354 time to fit residues: 14.2842 Evaluate side-chains 86 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 282 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 361 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS A 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.148099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.135160 restraints weight = 5443.237| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.27 r_work: 0.3298 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4467 Z= 0.160 Angle : 0.554 6.898 6102 Z= 0.277 Chirality : 0.043 0.203 683 Planarity : 0.004 0.048 737 Dihedral : 6.706 49.847 622 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.65 % Allowed : 18.14 % 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 (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: 1.05 (0.36), residues: 530 helix: 1.34 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -0.89 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 128 HIS 0.004 0.001 HIS A 613 PHE 0.017 0.001 PHE A 408 TYR 0.020 0.002 TYR A 84 ARG 0.007 0.001 ARG A 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00685 ( 1) link_NAG-ASN : angle 2.48035 ( 3) hydrogen bonds : bond 0.03974 ( 267) hydrogen bonds : angle 4.47108 ( 786) SS BOND : bond 0.00010 ( 1) SS BOND : angle 1.80372 ( 2) covalent geometry : bond 0.00388 ( 4465) covalent geometry : angle 0.55049 ( 6097) *********************** 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 92 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.468 Fit side-chains REVERT: A 107 MET cc_start: 0.8624 (ttm) cc_final: 0.8374 (ttm) REVERT: A 317 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.9022 (t80) REVERT: A 329 PHE cc_start: 0.8471 (t80) cc_final: 0.7522 (m-10) REVERT: A 377 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7726 (pm20) REVERT: A 382 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: A 421 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7574 (mtp) REVERT: A 556 TRP cc_start: 0.7022 (m100) cc_final: 0.6598 (m-10) REVERT: A 607 ARG cc_start: 0.7304 (mtm110) cc_final: 0.7030 (ptm-80) outliers start: 21 outliers final: 12 residues processed: 85 average time/residue: 0.1385 time to fit residues: 15.6868 Evaluate side-chains 84 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU 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 282 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.144992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131677 restraints weight = 5490.233| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.34 r_work: 0.3224 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4467 Z= 0.146 Angle : 0.550 6.569 6102 Z= 0.275 Chirality : 0.042 0.186 683 Planarity : 0.004 0.048 737 Dihedral : 6.328 44.922 622 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.32 % Allowed : 19.91 % Favored : 76.77 % 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 (0.36), residues: 530 helix: 1.27 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.91 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.005 0.001 HIS A 613 PHE 0.017 0.001 PHE A 408 TYR 0.021 0.001 TYR A 590 ARG 0.007 0.001 ARG A 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00664 ( 1) link_NAG-ASN : angle 2.57123 ( 3) hydrogen bonds : bond 0.03866 ( 267) hydrogen bonds : angle 4.44154 ( 786) SS BOND : bond 0.00075 ( 1) SS BOND : angle 1.66983 ( 2) covalent geometry : bond 0.00349 ( 4465) covalent geometry : angle 0.54605 ( 6097) *********************** 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 85 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.393 Fit side-chains REVERT: A 107 MET cc_start: 0.8608 (ttm) cc_final: 0.8354 (ttm) REVERT: A 317 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.9013 (t80) REVERT: A 329 PHE cc_start: 0.8448 (t80) cc_final: 0.7426 (m-10) REVERT: A 382 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8148 (mt-10) REVERT: A 421 MET cc_start: 0.8064 (ttm) cc_final: 0.7569 (mtp) REVERT: A 556 TRP cc_start: 0.7010 (m100) cc_final: 0.6569 (m-10) REVERT: A 607 ARG cc_start: 0.7311 (mtm110) cc_final: 0.6906 (ptm-80) outliers start: 15 outliers final: 12 residues processed: 80 average time/residue: 0.1384 time to fit residues: 14.6223 Evaluate side-chains 84 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU 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 282 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 382 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 28 optimal weight: 0.5980 chunk 14 optimal weight: 0.0030 chunk 35 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.145669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.132460 restraints weight = 5384.722| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.32 r_work: 0.3272 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2760 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= 0.134 Angle : 0.536 7.062 6102 Z= 0.268 Chirality : 0.041 0.171 683 Planarity : 0.004 0.048 737 Dihedral : 5.934 39.334 622 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.98 % Allowed : 20.13 % 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 (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: 1.14 (0.36), residues: 530 helix: 1.36 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -0.76 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.005 0.001 HIS A 613 PHE 0.015 0.001 PHE A 408 TYR 0.016 0.001 TYR A 84 ARG 0.006 0.001 ARG A 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 1) link_NAG-ASN : angle 2.57432 ( 3) hydrogen bonds : bond 0.03758 ( 267) hydrogen bonds : angle 4.39730 ( 786) SS BOND : bond 0.00035 ( 1) SS BOND : angle 1.55361 ( 2) covalent geometry : bond 0.00318 ( 4465) covalent geometry : angle 0.53235 ( 6097) *********************** 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 96 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.487 Fit side-chains REVERT: A 107 MET cc_start: 0.8594 (ttm) cc_final: 0.8337 (ttm) REVERT: A 317 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.9017 (t80) REVERT: A 329 PHE cc_start: 0.8444 (t80) cc_final: 0.7444 (m-10) REVERT: A 377 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7714 (pm20) REVERT: A 382 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8160 (mt-10) REVERT: A 421 MET cc_start: 0.8158 (ttm) cc_final: 0.7558 (mtp) REVERT: A 556 TRP cc_start: 0.6988 (m100) cc_final: 0.6565 (m-10) REVERT: A 607 ARG cc_start: 0.7251 (mtm110) cc_final: 0.6893 (ptm-80) outliers start: 18 outliers final: 12 residues processed: 91 average time/residue: 0.1394 time to fit residues: 16.8634 Evaluate side-chains 86 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 282 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 453 THR Chi-restraints excluded: chain A residue 455 LEU 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 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.148194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135253 restraints weight = 5538.209| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.27 r_work: 0.3263 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2700 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= 0.155 Angle : 0.558 7.441 6102 Z= 0.280 Chirality : 0.042 0.167 683 Planarity : 0.004 0.049 737 Dihedral : 5.780 37.295 622 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.98 % Allowed : 20.80 % Favored : 75.22 % 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: 1.09 (0.36), residues: 530 helix: 1.30 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -0.76 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.005 0.001 HIS A 613 PHE 0.017 0.001 PHE A 408 TYR 0.029 0.002 TYR A 300 ARG 0.006 0.001 ARG A 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00623 ( 1) link_NAG-ASN : angle 2.46643 ( 3) hydrogen bonds : bond 0.03921 ( 267) hydrogen bonds : angle 4.46303 ( 786) SS BOND : bond 0.00039 ( 1) SS BOND : angle 1.76279 ( 2) covalent geometry : bond 0.00372 ( 4465) covalent geometry : angle 0.55447 ( 6097) *********************** 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 90 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.440 Fit side-chains REVERT: A 107 MET cc_start: 0.8628 (ttm) cc_final: 0.8368 (ttm) REVERT: A 317 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.9004 (t80) REVERT: A 329 PHE cc_start: 0.8440 (t80) cc_final: 0.7489 (m-10) REVERT: A 377 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7689 (pm20) REVERT: A 382 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: A 421 MET cc_start: 0.8057 (ttm) cc_final: 0.7519 (mtp) REVERT: A 556 TRP cc_start: 0.7036 (m100) cc_final: 0.6598 (m-10) REVERT: A 590 TYR cc_start: 0.8482 (m-80) cc_final: 0.8282 (m-80) REVERT: A 606 ILE cc_start: 0.7196 (mp) cc_final: 0.6874 (mp) outliers start: 18 outliers final: 13 residues processed: 83 average time/residue: 0.1353 time to fit residues: 14.9091 Evaluate side-chains 88 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 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 453 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 537 ILE 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 8 optimal weight: 0.9990 chunk 48 optimal weight: 0.0570 chunk 38 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 40 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 overall best weight: 0.4098 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.147426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134148 restraints weight = 5372.304| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.32 r_work: 0.3227 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4467 Z= 0.121 Angle : 0.524 7.224 6102 Z= 0.262 Chirality : 0.040 0.153 683 Planarity : 0.004 0.048 737 Dihedral : 5.323 34.686 622 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.88 % Allowed : 21.90 % Favored : 75.22 % 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: 1.30 (0.36), residues: 530 helix: 1.44 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -0.57 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.005 0.001 HIS A 613 PHE 0.015 0.001 PHE A 408 TYR 0.015 0.001 TYR A 84 ARG 0.008 0.001 ARG A 607 Details of bonding type rmsd link_NAG-ASN : bond 0.00633 ( 1) link_NAG-ASN : angle 2.33536 ( 3) hydrogen bonds : bond 0.03624 ( 267) hydrogen bonds : angle 4.35527 ( 786) SS BOND : bond 0.00029 ( 1) SS BOND : angle 1.36239 ( 2) covalent geometry : bond 0.00283 ( 4465) covalent geometry : angle 0.52116 ( 6097) ********************** 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 92 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.476 Fit side-chains REVERT: A 107 MET cc_start: 0.8585 (ttm) cc_final: 0.8326 (ttm) REVERT: A 298 ASP cc_start: 0.7423 (p0) cc_final: 0.6544 (t0) REVERT: A 329 PHE cc_start: 0.8371 (t80) cc_final: 0.7313 (m-10) REVERT: A 377 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7699 (pm20) REVERT: A 382 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8151 (mt-10) REVERT: A 421 MET cc_start: 0.8073 (ttm) cc_final: 0.7439 (mtp) REVERT: A 556 TRP cc_start: 0.6983 (m100) cc_final: 0.6592 (m-10) REVERT: A 590 TYR cc_start: 0.8419 (m-80) cc_final: 0.8191 (m-80) outliers start: 13 outliers final: 9 residues processed: 87 average time/residue: 0.1436 time to fit residues: 16.4807 Evaluate side-chains 88 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 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 453 THR Chi-restraints excluded: chain A residue 455 LEU 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 9 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.0970 chunk 52 optimal weight: 0.0070 chunk 30 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.151205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.138199 restraints weight = 5449.796| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.27 r_work: 0.3298 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4467 Z= 0.121 Angle : 0.521 7.234 6102 Z= 0.262 Chirality : 0.040 0.150 683 Planarity : 0.005 0.097 737 Dihedral : 5.075 30.621 622 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.43 % Allowed : 22.12 % 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 (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: 1.29 (0.36), residues: 530 helix: 1.42 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -0.59 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 553 HIS 0.002 0.001 HIS A 178 PHE 0.016 0.001 PHE A 408 TYR 0.015 0.001 TYR A 84 ARG 0.012 0.001 ARG A 607 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 1) link_NAG-ASN : angle 2.11044 ( 3) hydrogen bonds : bond 0.03621 ( 267) hydrogen bonds : angle 4.34896 ( 786) SS BOND : bond 0.00035 ( 1) SS BOND : angle 1.32881 ( 2) covalent geometry : bond 0.00284 ( 4465) covalent geometry : angle 0.51851 ( 6097) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2526.66 seconds wall clock time: 44 minutes 50.85 seconds (2690.85 seconds total)