Starting phenix.real_space_refine on Wed Jun 4 16:17:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mdw_23782/06_2025/7mdw_23782.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mdw_23782/06_2025/7mdw_23782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mdw_23782/06_2025/7mdw_23782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mdw_23782/06_2025/7mdw_23782.map" model { file = "/net/cci-nas-00/data/ceres_data/7mdw_23782/06_2025/7mdw_23782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mdw_23782/06_2025/7mdw_23782.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2138 2.51 5 N 587 2.21 5 O 652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3392 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 871 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 971 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 3.81, per 1000 atoms: 1.12 Number of scatterers: 3392 At special positions: 0 Unit cell: (57.5916, 79.4066, 107.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 652 8.00 N 587 7.00 C 2138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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 R 601 " - " ASN R 343 " Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 387.4 milliseconds 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 784 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 9 sheets defined 8.5% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'R' and resid 337 through 343 Processing helix chain 'R' and resid 365 through 370 removed outlier: 3.685A pdb=" N ASN R 370 " --> pdb=" O SER R 366 " (cutoff:3.500A) Processing helix chain 'R' and resid 385 through 390 Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'B' and resid 27 through 32 removed outlier: 4.388A pdb=" N SER B 30 " --> pdb=" O ARG B 27 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AA4, first strand: chain 'R' and resid 354 through 358 removed outlier: 4.199A pdb=" N ASN R 354 " --> pdb=" O SER R 399 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER R 399 " --> pdb=" O ASN R 354 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL R 395 " --> pdb=" O ILE R 358 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN R 394 " --> pdb=" O GLU R 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 361 through 362 removed outlier: 7.585A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'R' and resid 448 through 454 removed outlier: 4.340A pdb=" N ASN R 450 " --> pdb=" O TYR R 495 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR R 495 " --> pdb=" O ASN R 450 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU R 452 " --> pdb=" O GLN R 493 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN R 493 " --> pdb=" O LEU R 452 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 473 through 474 Processing sheet with id=AA8, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.977A pdb=" N VAL B 5 " --> pdb=" O ALA B 23 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B 7 " --> pdb=" O SER B 21 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 21 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.510A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET B 34 " --> pdb=" O THR B 50 " (cutoff:3.500A) 63 hydrogen bonds defined for protein. 141 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: 1.21 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1112 1.34 - 1.46: 899 1.46 - 1.58: 1440 1.58 - 1.70: 0 1.70 - 1.81: 18 Bond restraints: 3469 Sorted by residual: bond pdb=" C1 NAG R 601 " pdb=" O5 NAG R 601 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.66e+00 bond pdb=" C5 NAG R 601 " pdb=" O5 NAG R 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C3 NAG R 601 " pdb=" O3 NAG R 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" CA ILE R 410 " pdb=" CB ILE R 410 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 9.96e-01 bond pdb=" C2 NAG R 601 " pdb=" N2 NAG R 601 " ideal model delta sigma weight residual 1.439 1.455 -0.016 2.00e-02 2.50e+03 6.29e-01 ... (remaining 3464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 4561 1.32 - 2.64: 117 2.64 - 3.96: 22 3.96 - 5.28: 6 5.28 - 6.60: 2 Bond angle restraints: 4708 Sorted by residual: angle pdb=" N GLY R 496 " pdb=" CA GLY R 496 " pdb=" C GLY R 496 " ideal model delta sigma weight residual 111.19 117.79 -6.60 1.75e+00 3.27e-01 1.42e+01 angle pdb=" C ASN A 82 " pdb=" N SER A 83 " pdb=" CA SER A 83 " ideal model delta sigma weight residual 121.54 125.96 -4.42 1.91e+00 2.74e-01 5.36e+00 angle pdb=" CA THR A 105 " pdb=" CB THR A 105 " pdb=" CG2 THR A 105 " ideal model delta sigma weight residual 110.50 114.38 -3.88 1.70e+00 3.46e-01 5.22e+00 angle pdb=" N VAL A 2 " pdb=" CA VAL A 2 " pdb=" C VAL A 2 " ideal model delta sigma weight residual 111.48 109.38 2.10 9.40e-01 1.13e+00 5.00e+00 angle pdb=" C PHE A 66 " pdb=" CA PHE A 66 " pdb=" CB PHE A 66 " ideal model delta sigma weight residual 110.42 114.77 -4.35 1.99e+00 2.53e-01 4.79e+00 ... (remaining 4703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 1872 17.94 - 35.88: 141 35.88 - 53.82: 22 53.82 - 71.77: 3 71.77 - 89.71: 2 Dihedral angle restraints: 2040 sinusoidal: 795 harmonic: 1245 Sorted by residual: dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 94 " pdb=" CB CYS A 94 " ideal model delta sinusoidal sigma weight residual -86.00 -140.97 54.97 1 1.00e+01 1.00e-02 4.09e+01 dihedral pdb=" CA THR A 105 " pdb=" C THR A 105 " pdb=" N TYR A 106 " pdb=" CA TYR A 106 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA ASP B 46 " pdb=" CB ASP B 46 " pdb=" CG ASP B 46 " pdb=" OD1 ASP B 46 " ideal model delta sinusoidal sigma weight residual -30.00 -88.19 58.19 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 2037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 372 0.039 - 0.079: 90 0.079 - 0.118: 43 0.118 - 0.157: 0 0.157 - 0.196: 1 Chirality restraints: 506 Sorted by residual: chirality pdb=" CB THR A 105 " pdb=" CA THR A 105 " pdb=" OG1 THR A 105 " pdb=" CG2 THR A 105 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" CA ILE A 68 " pdb=" N ILE A 68 " pdb=" C ILE A 68 " pdb=" CB ILE A 68 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA ILE R 468 " pdb=" N ILE R 468 " pdb=" C ILE R 468 " pdb=" CB ILE R 468 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.25e-01 ... (remaining 503 not shown) Planarity restraints: 615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 490 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO R 491 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO R 491 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 491 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 104 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C TYR A 104 " -0.023 2.00e-02 2.50e+03 pdb=" O TYR A 104 " 0.009 2.00e-02 2.50e+03 pdb=" N THR A 105 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 34 " -0.002 2.00e-02 2.50e+03 7.83e-03 1.53e+00 pdb=" CG TRP A 34 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 34 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 34 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 34 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 34 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 34 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 34 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 34 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 34 " 0.000 2.00e-02 2.50e+03 ... (remaining 612 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1006 2.81 - 3.34: 2901 3.34 - 3.86: 5326 3.86 - 4.38: 6065 4.38 - 4.90: 10459 Nonbonded interactions: 25757 Sorted by model distance: nonbonded pdb=" ND2 ASN A 52 " pdb=" O TYR R 449 " model vdw 2.293 3.120 nonbonded pdb=" OD2 ASP R 398 " pdb=" OH TYR R 423 " model vdw 2.359 3.040 nonbonded pdb=" OG SER R 477 " pdb=" OD1 ASN R 487 " model vdw 2.367 3.040 nonbonded pdb=" OH TYR R 365 " pdb=" O PRO R 384 " model vdw 2.372 3.040 nonbonded pdb=" NH2 ARG R 357 " pdb=" OD1 ASN R 394 " model vdw 2.380 3.120 ... (remaining 25752 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.470 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: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 17.010 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:3.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4325 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 : 0.002 0.031 3476 Z= 0.117 Angle : 0.547 6.596 4723 Z= 0.311 Chirality : 0.041 0.196 506 Planarity : 0.003 0.043 614 Dihedral : 12.676 89.707 1238 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.38), residues: 429 helix: -1.98 (0.79), residues: 39 sheet: -0.34 (0.53), residues: 98 loop : -1.21 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 34 HIS 0.000 0.000 HIS A 30 PHE 0.006 0.001 PHE A 45 TYR 0.015 0.001 TYR R 495 ARG 0.002 0.000 ARG A 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 1) link_NAG-ASN : angle 0.75320 ( 3) hydrogen bonds : bond 0.32263 ( 63) hydrogen bonds : angle 11.12819 ( 141) SS BOND : bond 0.00077 ( 6) SS BOND : angle 0.70305 ( 12) covalent geometry : bond 0.00215 ( 3469) covalent geometry : angle 0.54594 ( 4708) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.323 Fit side-chains REVERT: B 80 TYR cc_start: 0.4771 (m-80) cc_final: 0.4339 (m-80) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1841 time to fit residues: 4.9007 Evaluate side-chains 20 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 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 = 0.4786 r_free = 0.4786 target = 0.230104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.215298 restraints weight = 5315.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.218592 restraints weight = 3560.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.221046 restraints weight = 2554.598| |-----------------------------------------------------------------------------| r_work (final): 0.4692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4691 r_free = 0.4691 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4691 r_free = 0.4691 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4752 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3476 Z= 0.245 Angle : 0.720 8.592 4723 Z= 0.390 Chirality : 0.048 0.185 506 Planarity : 0.005 0.048 614 Dihedral : 7.716 88.597 511 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 0.85 % Allowed : 9.01 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.30 (0.37), residues: 429 helix: -2.83 (0.65), residues: 40 sheet: -1.21 (0.51), residues: 94 loop : -1.50 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 34 HIS 0.001 0.000 HIS A 30 PHE 0.020 0.003 PHE R 400 TYR 0.019 0.002 TYR A 78 ARG 0.006 0.001 ARG A 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00002 ( 1) link_NAG-ASN : angle 2.49994 ( 3) hydrogen bonds : bond 0.05740 ( 63) hydrogen bonds : angle 8.50366 ( 141) SS BOND : bond 0.00355 ( 6) SS BOND : angle 1.34762 ( 12) covalent geometry : bond 0.00538 ( 3469) covalent geometry : angle 0.71497 ( 4708) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.360 Fit side-chains REVERT: R 493 GLN cc_start: 0.5889 (mp10) cc_final: 0.5670 (mp10) REVERT: B 80 TYR cc_start: 0.4562 (m-80) cc_final: 0.4296 (m-10) outliers start: 3 outliers final: 1 residues processed: 22 average time/residue: 0.1412 time to fit residues: 4.4146 Evaluate side-chains 21 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.4980 chunk 23 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.0980 chunk 34 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 overall best weight: 0.2378 ------------------------------------------------------------------------------- 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 = 0.4807 r_free = 0.4807 target = 0.232767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.218270 restraints weight = 5234.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.221436 restraints weight = 3568.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.223746 restraints weight = 2579.361| |-----------------------------------------------------------------------------| r_work (final): 0.4715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4715 r_free = 0.4715 target_work(ls_wunit_k1) = 0.224 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4713 r_free = 0.4713 target_work(ls_wunit_k1) = 0.223 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4654 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3476 Z= 0.116 Angle : 0.551 6.713 4723 Z= 0.294 Chirality : 0.043 0.146 506 Planarity : 0.003 0.033 614 Dihedral : 6.871 89.546 511 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.56 % Allowed : 12.39 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.29 (0.38), residues: 429 helix: -2.58 (0.62), residues: 46 sheet: -1.28 (0.50), residues: 96 loop : -1.47 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 104 HIS 0.000 0.000 HIS R 519 PHE 0.012 0.001 PHE B 47 TYR 0.016 0.001 TYR R 495 ARG 0.003 0.000 ARG A 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 1) link_NAG-ASN : angle 1.39867 ( 3) hydrogen bonds : bond 0.04370 ( 63) hydrogen bonds : angle 7.49770 ( 141) SS BOND : bond 0.00176 ( 6) SS BOND : angle 0.79588 ( 12) covalent geometry : bond 0.00259 ( 3469) covalent geometry : angle 0.54935 ( 4708) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.390 Fit side-chains REVERT: A 93 TYR cc_start: 0.4328 (OUTLIER) cc_final: 0.3197 (p90) REVERT: R 493 GLN cc_start: 0.5970 (mp10) cc_final: 0.5383 (mp10) REVERT: B 80 TYR cc_start: 0.4559 (m-80) cc_final: 0.4165 (m-10) outliers start: 2 outliers final: 1 residues processed: 21 average time/residue: 0.1428 time to fit residues: 4.5127 Evaluate side-chains 22 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 31 optimal weight: 0.0030 chunk 40 optimal weight: 0.1980 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 overall best weight: 0.2390 ------------------------------------------------------------------------------- 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 = 0.4838 r_free = 0.4838 target = 0.235937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.228648 restraints weight = 5645.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.229805 restraints weight = 4524.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.230707 restraints weight = 3695.740| |-----------------------------------------------------------------------------| r_work (final): 0.4745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4745 r_free = 0.4745 target_work(ls_wunit_k1) = 0.227 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4745 r_free = 0.4745 target_work(ls_wunit_k1) = 0.227 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4602 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3476 Z= 0.110 Angle : 0.526 6.164 4723 Z= 0.278 Chirality : 0.043 0.146 506 Planarity : 0.003 0.030 614 Dihedral : 6.750 89.948 511 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 1.41 % Allowed : 12.39 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.32 (0.38), residues: 429 helix: -2.63 (0.61), residues: 46 sheet: -1.45 (0.49), residues: 98 loop : -1.41 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 353 HIS 0.000 0.000 HIS A 30 PHE 0.011 0.001 PHE B 47 TYR 0.017 0.001 TYR R 495 ARG 0.002 0.000 ARG B 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 1) link_NAG-ASN : angle 1.23045 ( 3) hydrogen bonds : bond 0.03750 ( 63) hydrogen bonds : angle 7.00879 ( 141) SS BOND : bond 0.00179 ( 6) SS BOND : angle 0.69514 ( 12) covalent geometry : bond 0.00247 ( 3469) covalent geometry : angle 0.52481 ( 4708) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.348 Fit side-chains REVERT: A 93 TYR cc_start: 0.4286 (OUTLIER) cc_final: 0.3183 (p90) REVERT: R 493 GLN cc_start: 0.6082 (mp10) cc_final: 0.5458 (mp10) REVERT: B 80 TYR cc_start: 0.4476 (m-80) cc_final: 0.4037 (m-80) outliers start: 5 outliers final: 3 residues processed: 23 average time/residue: 0.1307 time to fit residues: 4.2952 Evaluate side-chains 23 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain R residue 400 PHE Chi-restraints excluded: chain B residue 98 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 0.0030 chunk 1 optimal weight: 0.0570 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 overall best weight: 0.1708 ------------------------------------------------------------------------------- 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 = 0.4811 r_free = 0.4811 target = 0.233274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.218608 restraints weight = 5343.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.221940 restraints weight = 3604.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.224371 restraints weight = 2579.261| |-----------------------------------------------------------------------------| r_work (final): 0.4715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4629 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3476 Z= 0.093 Angle : 0.506 6.098 4723 Z= 0.268 Chirality : 0.043 0.195 506 Planarity : 0.003 0.030 614 Dihedral : 6.447 88.948 511 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.13 % Allowed : 13.24 % Favored : 85.63 % 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: -2.34 (0.38), residues: 429 helix: -2.60 (0.62), residues: 46 sheet: -1.44 (0.49), residues: 99 loop : -1.44 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 104 HIS 0.000 0.000 HIS A 30 PHE 0.010 0.001 PHE B 47 TYR 0.016 0.001 TYR R 495 ARG 0.002 0.000 ARG B 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 1) link_NAG-ASN : angle 1.07850 ( 3) hydrogen bonds : bond 0.03317 ( 63) hydrogen bonds : angle 6.71459 ( 141) SS BOND : bond 0.00140 ( 6) SS BOND : angle 0.58757 ( 12) covalent geometry : bond 0.00208 ( 3469) covalent geometry : angle 0.50561 ( 4708) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.340 Fit side-chains REVERT: A 93 TYR cc_start: 0.4302 (OUTLIER) cc_final: 0.3211 (p90) REVERT: R 493 GLN cc_start: 0.6171 (mp10) cc_final: 0.5536 (mp10) REVERT: B 80 TYR cc_start: 0.4443 (m-80) cc_final: 0.3987 (m-80) outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.1292 time to fit residues: 4.5458 Evaluate side-chains 24 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain R residue 400 PHE Chi-restraints excluded: chain B residue 98 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.0370 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 0.0000 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.0870 chunk 8 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 overall best weight: 0.2040 ------------------------------------------------------------------------------- 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 = 0.4836 r_free = 0.4836 target = 0.235901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.228697 restraints weight = 5724.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.229901 restraints weight = 4497.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.230546 restraints weight = 3657.173| |-----------------------------------------------------------------------------| r_work (final): 0.4737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4604 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3476 Z= 0.097 Angle : 0.501 6.302 4723 Z= 0.266 Chirality : 0.042 0.182 506 Planarity : 0.003 0.029 614 Dihedral : 6.534 89.792 511 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 1.69 % Allowed : 12.96 % Favored : 85.35 % 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: -2.36 (0.38), residues: 429 helix: -2.70 (0.61), residues: 46 sheet: -1.40 (0.52), residues: 92 loop : -1.47 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 353 HIS 0.000 0.000 HIS A 30 PHE 0.009 0.001 PHE R 400 TYR 0.013 0.001 TYR R 453 ARG 0.002 0.000 ARG A 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00161 ( 1) link_NAG-ASN : angle 1.09223 ( 3) hydrogen bonds : bond 0.03279 ( 63) hydrogen bonds : angle 6.62146 ( 141) SS BOND : bond 0.00164 ( 6) SS BOND : angle 0.62278 ( 12) covalent geometry : bond 0.00218 ( 3469) covalent geometry : angle 0.50040 ( 4708) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.368 Fit side-chains REVERT: A 93 TYR cc_start: 0.4343 (OUTLIER) cc_final: 0.3254 (p90) REVERT: A 114 THR cc_start: 0.5809 (OUTLIER) cc_final: 0.5494 (m) REVERT: R 493 GLN cc_start: 0.6196 (mp10) cc_final: 0.5528 (mp10) REVERT: B 80 TYR cc_start: 0.4401 (m-80) cc_final: 0.3948 (m-80) outliers start: 6 outliers final: 4 residues processed: 25 average time/residue: 0.1276 time to fit residues: 4.5305 Evaluate side-chains 27 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain R residue 400 PHE Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 98 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.0870 chunk 27 optimal weight: 0.0870 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.0020 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 overall best weight: 0.1944 ------------------------------------------------------------------------------- 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 = 0.4835 r_free = 0.4835 target = 0.235851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.228758 restraints weight = 5629.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.229735 restraints weight = 4427.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.230746 restraints weight = 3648.846| |-----------------------------------------------------------------------------| r_work (final): 0.4780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4562 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 : 0.002 0.029 3476 Z= 0.093 Angle : 0.496 6.586 4723 Z= 0.263 Chirality : 0.042 0.199 506 Planarity : 0.003 0.029 614 Dihedral : 6.436 89.485 511 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.25 % Allowed : 12.96 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.38), residues: 429 helix: -2.71 (0.60), residues: 46 sheet: -1.36 (0.51), residues: 92 loop : -1.45 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 353 HIS 0.000 0.000 HIS A 30 PHE 0.009 0.001 PHE R 400 TYR 0.014 0.001 TYR R 453 ARG 0.001 0.000 ARG B 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00124 ( 1) link_NAG-ASN : angle 1.04845 ( 3) hydrogen bonds : bond 0.03142 ( 63) hydrogen bonds : angle 6.48954 ( 141) SS BOND : bond 0.00152 ( 6) SS BOND : angle 0.55823 ( 12) covalent geometry : bond 0.00209 ( 3469) covalent geometry : angle 0.49524 ( 4708) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.341 Fit side-chains REVERT: A 93 TYR cc_start: 0.4534 (OUTLIER) cc_final: 0.3626 (p90) outliers start: 8 outliers final: 6 residues processed: 27 average time/residue: 0.1470 time to fit residues: 5.3151 Evaluate side-chains 27 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain R residue 400 PHE Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 98 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.0060 chunk 27 optimal weight: 0.0980 chunk 41 optimal weight: 0.0270 chunk 16 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 chunk 24 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 0.0980 overall best weight: 0.0630 ------------------------------------------------------------------------------- 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 = 0.4856 r_free = 0.4856 target = 0.238261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.231314 restraints weight = 5646.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.232254 restraints weight = 4411.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.232793 restraints weight = 3643.568| |-----------------------------------------------------------------------------| r_work (final): 0.4798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4487 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3476 Z= 0.080 Angle : 0.488 6.259 4723 Z= 0.259 Chirality : 0.042 0.193 506 Planarity : 0.003 0.029 614 Dihedral : 6.020 87.188 511 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.69 % Allowed : 13.80 % Favored : 84.51 % 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: -2.26 (0.38), residues: 429 helix: -2.65 (0.62), residues: 46 sheet: -1.25 (0.50), residues: 92 loop : -1.43 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.000 0.000 HIS A 30 PHE 0.010 0.001 PHE B 47 TYR 0.011 0.001 TYR R 453 ARG 0.005 0.000 ARG B 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 1) link_NAG-ASN : angle 0.92128 ( 3) hydrogen bonds : bond 0.02945 ( 63) hydrogen bonds : angle 6.26954 ( 141) SS BOND : bond 0.00120 ( 6) SS BOND : angle 0.44366 ( 12) covalent geometry : bond 0.00179 ( 3469) covalent geometry : angle 0.48815 ( 4708) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.358 Fit side-chains REVERT: A 93 TYR cc_start: 0.4516 (OUTLIER) cc_final: 0.3654 (p90) outliers start: 6 outliers final: 3 residues processed: 25 average time/residue: 0.1188 time to fit residues: 4.2551 Evaluate side-chains 23 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain R residue 400 PHE Chi-restraints excluded: chain B residue 98 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 18 optimal weight: 0.0870 chunk 14 optimal weight: 0.0980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.229637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.215975 restraints weight = 5324.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.219016 restraints weight = 3569.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.220909 restraints weight = 2571.093| |-----------------------------------------------------------------------------| r_work (final): 0.4681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4739 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3476 Z= 0.133 Angle : 0.564 7.942 4723 Z= 0.301 Chirality : 0.044 0.198 506 Planarity : 0.003 0.027 614 Dihedral : 6.927 88.566 511 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 1.69 % Allowed : 13.52 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.39 (0.38), residues: 429 helix: -2.99 (0.64), residues: 40 sheet: -1.44 (0.48), residues: 99 loop : -1.48 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 353 HIS 0.001 0.000 HIS A 30 PHE 0.011 0.001 PHE R 400 TYR 0.015 0.002 TYR R 453 ARG 0.006 0.000 ARG A 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00069 ( 1) link_NAG-ASN : angle 1.35634 ( 3) hydrogen bonds : bond 0.03577 ( 63) hydrogen bonds : angle 6.78281 ( 141) SS BOND : bond 0.00217 ( 6) SS BOND : angle 0.79703 ( 12) covalent geometry : bond 0.00300 ( 3469) covalent geometry : angle 0.56210 ( 4708) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.376 Fit side-chains REVERT: A 93 TYR cc_start: 0.4334 (OUTLIER) cc_final: 0.3072 (p90) REVERT: A 114 THR cc_start: 0.5802 (OUTLIER) cc_final: 0.5482 (m) outliers start: 6 outliers final: 4 residues processed: 22 average time/residue: 0.1230 time to fit residues: 3.9730 Evaluate side-chains 23 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain R residue 400 PHE Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 98 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 0.1980 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 34 optimal weight: 0.0030 chunk 14 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.233110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.226140 restraints weight = 5610.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.227291 restraints weight = 4393.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.228303 restraints weight = 3569.798| |-----------------------------------------------------------------------------| r_work (final): 0.4718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4688 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3476 Z= 0.130 Angle : 0.564 8.396 4723 Z= 0.301 Chirality : 0.044 0.192 506 Planarity : 0.003 0.027 614 Dihedral : 6.901 89.322 511 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.41 % Allowed : 13.80 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.48 (0.38), residues: 429 helix: -2.96 (0.64), residues: 40 sheet: -1.59 (0.48), residues: 99 loop : -1.51 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 353 HIS 0.001 0.000 HIS A 30 PHE 0.011 0.001 PHE B 47 TYR 0.014 0.002 TYR R 453 ARG 0.004 0.000 ARG A 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00033 ( 1) link_NAG-ASN : angle 1.28065 ( 3) hydrogen bonds : bond 0.03550 ( 63) hydrogen bonds : angle 6.87846 ( 141) SS BOND : bond 0.00197 ( 6) SS BOND : angle 0.76936 ( 12) covalent geometry : bond 0.00294 ( 3469) covalent geometry : angle 0.56280 ( 4708) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.340 Fit side-chains REVERT: A 93 TYR cc_start: 0.4566 (OUTLIER) cc_final: 0.3282 (p90) REVERT: A 114 THR cc_start: 0.5675 (OUTLIER) cc_final: 0.5348 (m) outliers start: 5 outliers final: 2 residues processed: 22 average time/residue: 0.1220 time to fit residues: 3.9063 Evaluate side-chains 22 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain R residue 400 PHE Chi-restraints excluded: chain B residue 57 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 0.0770 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 0.0670 chunk 20 optimal weight: 0.6980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.231497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.223490 restraints weight = 5616.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.224886 restraints weight = 4291.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.225690 restraints weight = 3420.882| |-----------------------------------------------------------------------------| r_work (final): 0.4691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4748 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3476 Z= 0.153 Angle : 0.601 8.462 4723 Z= 0.322 Chirality : 0.045 0.196 506 Planarity : 0.004 0.029 614 Dihedral : 7.171 88.201 511 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 1.97 % Allowed : 13.24 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.67 (0.37), residues: 429 helix: -3.06 (0.62), residues: 40 sheet: -1.71 (0.48), residues: 99 loop : -1.66 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 353 HIS 0.001 0.000 HIS A 30 PHE 0.012 0.002 PHE B 47 TYR 0.014 0.002 TYR R 453 ARG 0.007 0.000 ARG A 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00046 ( 1) link_NAG-ASN : angle 1.45367 ( 3) hydrogen bonds : bond 0.03805 ( 63) hydrogen bonds : angle 7.06233 ( 141) SS BOND : bond 0.00224 ( 6) SS BOND : angle 0.90589 ( 12) covalent geometry : bond 0.00343 ( 3469) covalent geometry : angle 0.59888 ( 4708) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1747.07 seconds wall clock time: 31 minutes 4.88 seconds (1864.88 seconds total)