Starting phenix.real_space_refine on Tue Mar 3 11:43:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mdw_23782/03_2026/7mdw_23782.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mdw_23782/03_2026/7mdw_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_23782/03_2026/7mdw_23782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mdw_23782/03_2026/7mdw_23782.map" model { file = "/net/cci-nas-00/data/ceres_data/7mdw_23782/03_2026/7mdw_23782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mdw_23782/03_2026/7mdw_23782.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.98, per 1000 atoms: 0.29 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: 0.18 Conformation dependent library (CDL) restraints added in 143.3 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: 0.09 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: 0.41 Time building geometry restraints manager: 0.25 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: 4.450 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.470 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.540 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG A 19 TYR 0.015 0.001 TYR R 495 PHE 0.006 0.001 PHE A 45 TRP 0.018 0.001 TRP A 34 HIS 0.000 0.000 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 3469) covalent geometry : angle 0.54594 ( 4708) SS BOND : bond 0.00077 ( 6) SS BOND : angle 0.70305 ( 12) hydrogen bonds : bond 0.32263 ( 63) hydrogen bonds : angle 11.12819 ( 141) link_NAG-ASN : bond 0.00151 ( 1) link_NAG-ASN : angle 0.75320 ( 3) *********************** 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 : 0.067 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: 0.0671 time to fit residues: 1.6992 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 : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4802 r_free = 0.4802 target = 0.231711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.216774 restraints weight = 5365.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.220170 restraints weight = 3605.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.222660 restraints weight = 2576.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.224027 restraints weight = 1920.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.225418 restraints weight = 1550.553| |-----------------------------------------------------------------------------| r_work (final): 0.4737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4738 r_free = 0.4738 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4737 r_free = 0.4737 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4649 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 : 0.005 0.041 3476 Z= 0.206 Angle : 0.665 8.122 4723 Z= 0.359 Chirality : 0.047 0.177 506 Planarity : 0.005 0.044 614 Dihedral : 7.384 89.260 511 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.38), residues: 429 helix: -2.34 (0.66), residues: 45 sheet: -1.06 (0.51), residues: 96 loop : -1.44 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 97 TYR 0.016 0.002 TYR A 78 PHE 0.020 0.002 PHE R 400 TRP 0.019 0.003 TRP A 34 HIS 0.001 0.000 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 3469) covalent geometry : angle 0.66110 ( 4708) SS BOND : bond 0.00326 ( 6) SS BOND : angle 1.21913 ( 12) hydrogen bonds : bond 0.05405 ( 63) hydrogen bonds : angle 8.26796 ( 141) link_NAG-ASN : bond 0.00045 ( 1) link_NAG-ASN : angle 2.20567 ( 3) *********************** 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 20 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.122 Fit side-chains REVERT: R 493 GLN cc_start: 0.5801 (mp10) cc_final: 0.5362 (mp10) REVERT: B 80 TYR cc_start: 0.4570 (m-80) cc_final: 0.4248 (m-10) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0390 time to fit residues: 1.1436 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 : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4792 r_free = 0.4792 target = 0.231228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.222724 restraints weight = 5656.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.224132 restraints weight = 4363.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.225312 restraints weight = 3488.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.225916 restraints weight = 2847.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.226809 restraints weight = 2454.151| |-----------------------------------------------------------------------------| r_work (final): 0.4743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4705 r_free = 0.4705 target_work(ls_wunit_k1) = 0.223 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4704 r_free = 0.4704 target_work(ls_wunit_k1) = 0.223 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4706 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3476 Z= 0.218 Angle : 0.685 7.570 4723 Z= 0.370 Chirality : 0.047 0.172 506 Planarity : 0.005 0.037 614 Dihedral : 7.746 86.902 511 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.37), residues: 429 helix: -3.13 (0.61), residues: 40 sheet: -1.58 (0.49), residues: 98 loop : -1.68 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 97 TYR 0.019 0.002 TYR R 495 PHE 0.018 0.002 PHE B 47 TRP 0.021 0.003 TRP R 353 HIS 0.001 0.000 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 3469) covalent geometry : angle 0.68118 ( 4708) SS BOND : bond 0.00319 ( 6) SS BOND : angle 1.20846 ( 12) hydrogen bonds : bond 0.05533 ( 63) hydrogen bonds : angle 7.98250 ( 141) link_NAG-ASN : bond 0.00076 ( 1) link_NAG-ASN : angle 2.29461 ( 3) *********************** 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 26 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.110 Fit side-chains REVERT: A 93 TYR cc_start: 0.4699 (OUTLIER) cc_final: 0.3478 (p90) REVERT: R 493 GLN cc_start: 0.5806 (mp10) cc_final: 0.5376 (mp10) REVERT: B 80 TYR cc_start: 0.4783 (m-80) cc_final: 0.4517 (m-10) outliers start: 6 outliers final: 3 residues processed: 24 average time/residue: 0.0586 time to fit residues: 1.8618 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 : 0.081 ------------------------------------------------------------------------------- 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 350 VAL Chi-restraints excluded: chain R residue 400 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 0.4980 chunk 27 optimal weight: 0.2980 chunk 37 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 0.0470 chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 overall best weight: 0.2878 ------------------------------------------------------------------------------- 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 = 0.4776 r_free = 0.4776 target = 0.229966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.215810 restraints weight = 5272.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.218982 restraints weight = 3547.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.221270 restraints weight = 2540.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.222865 restraints weight = 1918.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.224172 restraints weight = 1499.370| |-----------------------------------------------------------------------------| r_work (final): 0.4716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4671 moved from start: 0.2712 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= 0.121 Angle : 0.562 8.102 4723 Z= 0.299 Chirality : 0.044 0.149 506 Planarity : 0.003 0.034 614 Dihedral : 7.087 88.392 511 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 1.13 % Allowed : 14.65 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.37), residues: 429 helix: -2.93 (0.64), residues: 40 sheet: -1.63 (0.46), residues: 110 loop : -1.61 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 97 TYR 0.019 0.002 TYR R 495 PHE 0.013 0.001 PHE B 47 TRP 0.011 0.002 TRP R 353 HIS 0.000 0.000 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 3469) covalent geometry : angle 0.55988 ( 4708) SS BOND : bond 0.00209 ( 6) SS BOND : angle 0.80107 ( 12) hydrogen bonds : bond 0.03932 ( 63) hydrogen bonds : angle 7.22676 ( 141) link_NAG-ASN : bond 0.00091 ( 1) link_NAG-ASN : angle 1.42785 ( 3) *********************** 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: 4 poor density : 20 time to evaluate : 0.112 Fit side-chains REVERT: A 93 TYR cc_start: 0.4454 (OUTLIER) cc_final: 0.3175 (p90) REVERT: R 493 GLN cc_start: 0.5472 (mp10) cc_final: 0.4958 (mp10) REVERT: B 80 TYR cc_start: 0.4536 (m-80) cc_final: 0.4187 (m-10) outliers start: 4 outliers final: 2 residues processed: 22 average time/residue: 0.0512 time to fit residues: 1.5773 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 : 0.145 ------------------------------------------------------------------------------- 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 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 0.0670 chunk 16 optimal weight: 0.0030 chunk 23 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.4728 ------------------------------------------------------------------------------- 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 = 0.4784 r_free = 0.4784 target = 0.230880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.223790 restraints weight = 5643.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.224861 restraints weight = 4404.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.225815 restraints weight = 3582.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.226378 restraints weight = 3002.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.226696 restraints weight = 2597.495| |-----------------------------------------------------------------------------| r_work (final): 0.4701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4740 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3476 Z= 0.167 Angle : 0.618 7.006 4723 Z= 0.331 Chirality : 0.045 0.183 506 Planarity : 0.004 0.036 614 Dihedral : 7.491 86.924 511 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.37), residues: 429 helix: -3.09 (0.61), residues: 40 sheet: -1.89 (0.48), residues: 98 loop : -1.70 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 36 TYR 0.019 0.002 TYR R 453 PHE 0.014 0.002 PHE B 47 TRP 0.015 0.002 TRP R 353 HIS 0.001 0.000 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 3469) covalent geometry : angle 0.61477 ( 4708) SS BOND : bond 0.00258 ( 6) SS BOND : angle 1.01408 ( 12) hydrogen bonds : bond 0.04340 ( 63) hydrogen bonds : angle 7.36008 ( 141) link_NAG-ASN : bond 0.00029 ( 1) link_NAG-ASN : angle 1.80052 ( 3) *********************** 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 28 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.105 Fit side-chains REVERT: A 93 TYR cc_start: 0.4666 (OUTLIER) cc_final: 0.3340 (p90) REVERT: A 114 THR cc_start: 0.5778 (OUTLIER) cc_final: 0.5434 (m) REVERT: B 80 TYR cc_start: 0.4655 (m-80) cc_final: 0.4335 (m-10) outliers start: 7 outliers final: 5 residues processed: 25 average time/residue: 0.0657 time to fit residues: 2.1686 Evaluate side-chains 28 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.113 ------------------------------------------------------------------------------- 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 350 VAL Chi-restraints excluded: chain R residue 400 PHE Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 67 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.1980 chunk 13 optimal weight: 0.0670 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.0010 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 chunk 7 optimal weight: 0.0770 chunk 34 optimal weight: 0.0470 chunk 19 optimal weight: 0.6980 overall best weight: 0.0780 ------------------------------------------------------------------------------- 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 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.232519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.219091 restraints weight = 5374.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.222016 restraints weight = 3690.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.224190 restraints weight = 2681.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.225429 restraints weight = 2031.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.226865 restraints weight = 1660.221| |-----------------------------------------------------------------------------| r_work (final): 0.4745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4587 moved from start: 0.2886 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= 0.087 Angle : 0.513 4.933 4723 Z= 0.272 Chirality : 0.043 0.183 506 Planarity : 0.003 0.035 614 Dihedral : 6.480 89.886 511 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.69 % Allowed : 15.77 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.37), residues: 429 helix: -2.71 (0.61), residues: 46 sheet: -1.73 (0.48), residues: 99 loop : -1.59 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 457 TYR 0.013 0.001 TYR R 453 PHE 0.010 0.001 PHE R 392 TRP 0.010 0.001 TRP B 104 HIS 0.001 0.000 HIS R 519 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 3469) covalent geometry : angle 0.51227 ( 4708) SS BOND : bond 0.00138 ( 6) SS BOND : angle 0.51666 ( 12) hydrogen bonds : bond 0.03003 ( 63) hydrogen bonds : angle 6.58886 ( 141) link_NAG-ASN : bond 0.00346 ( 1) link_NAG-ASN : angle 1.20935 ( 3) *********************** 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 29 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.121 Fit side-chains REVERT: A 93 TYR cc_start: 0.4271 (OUTLIER) cc_final: 0.3177 (p90) REVERT: A 114 THR cc_start: 0.5633 (OUTLIER) cc_final: 0.5328 (m) REVERT: B 51 ILE cc_start: 0.5892 (OUTLIER) cc_final: 0.5566 (mt) outliers start: 6 outliers final: 1 residues processed: 29 average time/residue: 0.0395 time to fit residues: 1.6704 Evaluate side-chains 27 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain B residue 51 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 0.0030 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.231041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.224136 restraints weight = 5680.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.225264 restraints weight = 4414.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.226309 restraints weight = 3524.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.227084 restraints weight = 2901.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.227485 restraints weight = 2439.528| |-----------------------------------------------------------------------------| r_work (final): 0.4744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4696 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3476 Z= 0.165 Angle : 0.597 5.933 4723 Z= 0.320 Chirality : 0.045 0.205 506 Planarity : 0.004 0.031 614 Dihedral : 7.318 87.326 511 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 2.25 % Allowed : 16.06 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.37), residues: 429 helix: -2.99 (0.63), residues: 40 sheet: -1.90 (0.47), residues: 99 loop : -1.72 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 38 TYR 0.016 0.002 TYR R 453 PHE 0.012 0.002 PHE B 47 TRP 0.014 0.002 TRP R 353 HIS 0.001 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 3469) covalent geometry : angle 0.59396 ( 4708) SS BOND : bond 0.00253 ( 6) SS BOND : angle 0.97021 ( 12) hydrogen bonds : bond 0.03933 ( 63) hydrogen bonds : angle 7.07592 ( 141) link_NAG-ASN : bond 0.00040 ( 1) link_NAG-ASN : angle 1.66885 ( 3) *********************** 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 29 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.118 Fit side-chains REVERT: A 93 TYR cc_start: 0.4839 (OUTLIER) cc_final: 0.3710 (p90) REVERT: A 114 THR cc_start: 0.5554 (OUTLIER) cc_final: 0.5215 (m) REVERT: B 51 ILE cc_start: 0.6019 (OUTLIER) cc_final: 0.5646 (mt) REVERT: B 80 TYR cc_start: 0.4770 (m-80) cc_final: 0.4384 (m-10) outliers start: 8 outliers final: 4 residues processed: 28 average time/residue: 0.0609 time to fit residues: 2.2491 Evaluate side-chains 28 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 400 PHE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 67 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.0010 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 0.0980 chunk 35 optimal weight: 0.5980 chunk 8 optimal weight: 0.0970 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.0470 overall best weight: 0.1682 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.234399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.227442 restraints weight = 5695.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.228361 restraints weight = 4425.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.229542 restraints weight = 3643.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.230039 restraints weight = 3015.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.230870 restraints weight = 2598.616| |-----------------------------------------------------------------------------| r_work (final): 0.4775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4584 moved from start: 0.3180 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= 0.094 Angle : 0.527 5.647 4723 Z= 0.278 Chirality : 0.043 0.194 506 Planarity : 0.003 0.034 614 Dihedral : 6.692 89.228 511 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 2.54 % Allowed : 15.77 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.37), residues: 429 helix: -2.92 (0.65), residues: 40 sheet: -1.79 (0.48), residues: 99 loop : -1.66 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 457 TYR 0.013 0.001 TYR R 453 PHE 0.009 0.001 PHE B 47 TRP 0.008 0.001 TRP B 104 HIS 0.001 0.000 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 3469) covalent geometry : angle 0.52568 ( 4708) SS BOND : bond 0.00150 ( 6) SS BOND : angle 0.63357 ( 12) hydrogen bonds : bond 0.03147 ( 63) hydrogen bonds : angle 6.65016 ( 141) link_NAG-ASN : bond 0.00209 ( 1) link_NAG-ASN : angle 1.21056 ( 3) *********************** 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 28 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.070 Fit side-chains REVERT: A 93 TYR cc_start: 0.4552 (OUTLIER) cc_final: 0.3576 (p90) REVERT: A 114 THR cc_start: 0.5352 (OUTLIER) cc_final: 0.5025 (m) REVERT: B 51 ILE cc_start: 0.6008 (OUTLIER) cc_final: 0.5673 (mt) outliers start: 9 outliers final: 5 residues processed: 27 average time/residue: 0.0526 time to fit residues: 1.9135 Evaluate side-chains 27 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.104 ------------------------------------------------------------------------------- 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 362 VAL Chi-restraints excluded: chain R residue 400 PHE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 67 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 11 optimal weight: 0.0060 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.4767 r_free = 0.4767 target = 0.229648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.221555 restraints weight = 5602.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.222980 restraints weight = 4290.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.224190 restraints weight = 3394.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.224821 restraints weight = 2750.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.225501 restraints weight = 2351.225| |-----------------------------------------------------------------------------| r_work (final): 0.4687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4771 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3476 Z= 0.185 Angle : 0.635 7.041 4723 Z= 0.341 Chirality : 0.046 0.204 506 Planarity : 0.004 0.031 614 Dihedral : 7.529 87.103 511 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 2.82 % Allowed : 15.77 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.37), residues: 429 helix: -3.10 (0.62), residues: 40 sheet: -1.92 (0.44), residues: 111 loop : -1.86 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 38 TYR 0.014 0.002 TYR B 32 PHE 0.014 0.002 PHE B 47 TRP 0.015 0.002 TRP R 353 HIS 0.001 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 3469) covalent geometry : angle 0.63210 ( 4708) SS BOND : bond 0.00329 ( 6) SS BOND : angle 1.13688 ( 12) hydrogen bonds : bond 0.04136 ( 63) hydrogen bonds : angle 7.18259 ( 141) link_NAG-ASN : bond 0.00088 ( 1) link_NAG-ASN : angle 1.80641 ( 3) *********************** 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 31 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 21 time to evaluate : 0.094 Fit side-chains REVERT: A 93 TYR cc_start: 0.4697 (OUTLIER) cc_final: 0.3380 (p90) REVERT: A 114 THR cc_start: 0.5916 (OUTLIER) cc_final: 0.5583 (m) REVERT: B 80 TYR cc_start: 0.4656 (m-80) cc_final: 0.4304 (m-10) outliers start: 10 outliers final: 8 residues processed: 29 average time/residue: 0.0436 time to fit residues: 1.6614 Evaluate side-chains 31 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 21 time to evaluate : 0.083 ------------------------------------------------------------------------------- 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 362 VAL Chi-restraints excluded: chain R residue 400 PHE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 67 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.0670 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 6 optimal weight: 0.0770 chunk 11 optimal weight: 0.0770 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 0.0980 chunk 32 optimal weight: 0.0000 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 overall best weight: 0.0638 ------------------------------------------------------------------------------- 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 = 0.4823 r_free = 0.4823 target = 0.235844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.229001 restraints weight = 5684.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.230167 restraints weight = 4412.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.230795 restraints weight = 3553.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.231831 restraints weight = 3018.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.232266 restraints weight = 2530.844| |-----------------------------------------------------------------------------| r_work (final): 0.4787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4525 moved from start: 0.3349 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= 0.086 Angle : 0.522 7.011 4723 Z= 0.274 Chirality : 0.043 0.187 506 Planarity : 0.003 0.035 614 Dihedral : 6.366 89.905 511 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.69 % Allowed : 16.90 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.37), residues: 429 helix: -2.90 (0.66), residues: 40 sheet: -1.64 (0.50), residues: 92 loop : -1.70 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 457 TYR 0.012 0.001 TYR R 453 PHE 0.013 0.001 PHE R 515 TRP 0.010 0.001 TRP B 104 HIS 0.000 0.000 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 3469) covalent geometry : angle 0.52118 ( 4708) SS BOND : bond 0.00124 ( 6) SS BOND : angle 0.54394 ( 12) hydrogen bonds : bond 0.02836 ( 63) hydrogen bonds : angle 6.44720 ( 141) link_NAG-ASN : bond 0.00313 ( 1) link_NAG-ASN : angle 1.27417 ( 3) ********************** 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 28 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.089 Fit side-chains REVERT: A 93 TYR cc_start: 0.4485 (OUTLIER) cc_final: 0.3613 (p90) REVERT: B 51 ILE cc_start: 0.5972 (OUTLIER) cc_final: 0.5584 (mt) outliers start: 6 outliers final: 3 residues processed: 27 average time/residue: 0.0626 time to fit residues: 2.2440 Evaluate side-chains 27 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.069 ------------------------------------------------------------------------------- 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 B residue 51 ILE Chi-restraints excluded: chain B residue 67 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 chunk 34 optimal weight: 0.3980 chunk 28 optimal weight: 0.0370 chunk 21 optimal weight: 0.5980 chunk 25 optimal weight: 0.0980 chunk 9 optimal weight: 0.0770 chunk 11 optimal weight: 0.0570 chunk 13 optimal weight: 0.8980 overall best weight: 0.1134 ------------------------------------------------------------------------------- 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 = 0.4821 r_free = 0.4821 target = 0.235480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.228419 restraints weight = 5678.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.229635 restraints weight = 4451.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.230405 restraints weight = 3583.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.231337 restraints weight = 3016.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.231727 restraints weight = 2553.829| |-----------------------------------------------------------------------------| r_work (final): 0.4781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4545 moved from start: 0.3310 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= 0.087 Angle : 0.506 7.620 4723 Z= 0.266 Chirality : 0.043 0.200 506 Planarity : 0.003 0.034 614 Dihedral : 6.332 88.748 511 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 1.69 % Allowed : 16.90 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.38), residues: 429 helix: -2.90 (0.60), residues: 46 sheet: -1.54 (0.49), residues: 92 loop : -1.67 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 97 TYR 0.012 0.001 TYR R 453 PHE 0.012 0.001 PHE R 515 TRP 0.007 0.001 TRP R 436 HIS 0.000 0.000 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 3469) covalent geometry : angle 0.50519 ( 4708) SS BOND : bond 0.00153 ( 6) SS BOND : angle 0.53821 ( 12) hydrogen bonds : bond 0.02749 ( 63) hydrogen bonds : angle 6.27170 ( 141) link_NAG-ASN : bond 0.00178 ( 1) link_NAG-ASN : angle 0.98756 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 815.39 seconds wall clock time: 14 minutes 44.29 seconds (884.29 seconds total)